Contacts of the helix formed by residues 123 - 145 (chain F) in PDB entry 2Q9Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 123 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F SER* 3.7 17.7 + - - -
48F PRO* 5.6 6.5 - - - -
122F LEU* 1.3 75.1 - - - +
124F PRO* 1.3 76.7 - - - +
125F GLU* 3.3 13.4 + - - +
126F GLU* 3.1 34.0 + - - +
127F LEU* 2.9 20.2 + - - +
124G TYR* 4.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F PRO* 6.3 2.0 - - + -
122F LEU 4.6 0.4 - - - +
123F SER* 1.3 88.9 - - - +
125F GLU* 1.3 79.5 + - - +
127F LEU* 3.4 10.8 + - + +
128F ALA* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F SER* 3.3 13.9 + - - +
124F PRO* 1.3 93.9 - - - +
126F GLU* 1.3 57.4 + - - +
128F ALA* 3.2 8.4 + - - +
129F PHE* 3.0 26.9 + - - +
124G TYR* 3.8 24.1 - - + +
127G SER* 3.2 38.1 - - - +
128G LEU* 5.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F SER* 4.3 1.1 + - - -
93F LEU* 5.0 3.1 - - - +
96F ARG* 2.8 55.1 + - - +
97F LEU* 5.3 1.3 - - + +
100F ILE* 3.7 25.1 - - + +
121F SER 4.0 0.2 - - - +
122F LEU* 3.7 8.2 - - + +
123F SER* 3.1 36.0 + - - +
125F GLU* 1.3 74.7 - - - +
127F LEU* 1.3 59.4 + - - +
129F PHE* 3.4 5.7 + - - +
130F ALA* 3.0 29.5 + - - +
124G TYR* 3.6 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F LEU* 3.7 18.2 - - + +
111F GLU* 4.2 24.7 - - + +
122F LEU* 4.1 25.3 - - + +
123F SER 2.9 15.9 + - - +
124F PRO* 3.5 9.6 - - + +
126F GLU* 1.3 78.2 - - - +
128F ALA* 1.3 61.6 + - - +
130F ALA* 3.4 2.8 + - - +
131F ARG* 3.1 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F PRO 3.1 12.7 + - - +
125F GLU* 3.6 10.3 - - - +
127F LEU* 1.3 73.8 - - - +
129F PHE* 1.3 67.4 + - - +
131F ARG* 3.4 12.0 + - - +
132F GLU* 3.1 40.1 + - - +
123G THR* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LEU* 3.4 33.9 - - + -
100F ILE* 4.2 14.1 - - + -
101F GLU* 3.8 34.5 - - + -
125F GLU 3.0 12.7 + - - +
126F GLU* 3.6 10.8 - - - +
128F ALA* 1.3 76.5 - - - +
130F ALA* 1.3 58.4 + - - +
132F GLU* 3.3 11.4 + - - +
133F PHE* 3.0 34.4 + + + +
117G TYR* 3.9 18.2 - + - -
120G SER* 3.9 26.2 - - - -
121G LEU* 4.0 24.9 - - + -
124G TYR* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F ILE* 3.6 25.6 - - + -
104F PHE* 4.5 6.1 - - + +
107F VAL* 5.0 7.4 - - + -
108F LEU* 3.8 24.0 - - + +
122F LEU* 5.1 0.7 - - + -
126F GLU 3.0 16.6 + - - +
127F LEU* 3.6 6.3 - - - +
129F PHE* 1.3 77.5 - - - +
131F ARG* 1.3 61.9 + - - +
133F PHE* 3.2 8.7 + - - +
134F MET* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F LEU* 3.7 22.1 - - + +
111F GLU* 6.0 0.8 - - - +
127F LEU* 3.1 56.1 + - - +
128F ALA* 3.7 10.1 - - - +
130F ALA* 1.3 75.8 - - - +
132F GLU* 1.3 64.9 + - + +
134F MET* 3.3 3.5 + - - +
135F ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F ALA* 3.1 28.3 + - - +
129F PHE* 3.6 6.7 - - - +
131F ARG* 1.3 75.0 - - + +
133F PHE* 1.3 61.7 + - - +
135F ALA* 3.8 6.0 - - - +
136F ASN* 2.9 32.8 + - - +
120G SER* 2.8 41.4 + - - +
123G THR* 5.2 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F ILE* 6.1 0.4 - - + -
101F GLU* 3.6 50.7 - - + -
104F PHE* 3.6 42.6 - + + -
129F PHE* 3.0 20.5 + + + +
130F ALA* 3.2 13.0 + - - +
132F GLU* 1.3 76.9 - - - +
134F MET* 1.3 60.3 + - - +
136F ASN* 3.8 5.0 - - - +
137F THR* 2.9 38.2 + - - -
81G TYR* 5.0 4.5 - + - -
85G LEU* 5.8 7.9 - - + -
88G ARG* 5.3 1.1 - - + -
113G TRP* 3.8 28.9 - + - -
117G TYR* 3.9 19.7 - + - -
120G SER* 5.1 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F PHE* 3.7 32.5 - - + -
105F PRO* 4.3 15.5 - - + +
108F LEU* 3.2 36.6 - - + -
130F ALA 3.1 12.0 + - - +
131F ARG* 3.8 6.7 - - - +
132F GLU 3.3 0.2 - - - -
133F PHE* 1.3 77.4 - - - +
135F ALA* 1.3 57.6 + - - +
137F THR* 3.3 1.2 + - - -
138F GLU* 2.9 61.4 + - + +
158F LEU* 4.6 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F ARG 3.0 17.2 + - - +
132F GLU* 3.9 6.7 - - - +
134F MET* 1.3 77.5 - - - +
136F ASN* 1.3 62.9 + - - +
138F GLU* 4.1 8.6 - - - +
139F SER* 3.1 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 136 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F GLU 2.9 19.3 + - - +
133F PHE* 3.8 5.8 - - - +
135F ALA* 1.3 78.1 - - - +
137F THR* 1.3 57.2 + - - +
139F SER* 3.8 4.3 - - - -
140F TYR* 3.0 28.4 + - - +
112G GLU* 5.2 0.9 - - - +
113G TRP* 2.9 56.1 + - - +
116G ASN* 2.9 37.4 + - + +
117G TYR* 3.8 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F PHE* 4.4 12.1 - - + -
133F PHE* 2.9 33.8 + - - -
134F MET 3.8 2.7 - - - -
136F ASN* 1.3 74.1 - - - +
138F GLU* 1.3 64.9 + - - +
140F TYR* 3.5 2.1 - - - +
141F LEU* 3.0 41.8 + - + +
158F LEU* 4.4 4.7 - - + -
81G TYR* 4.3 18.6 - - + -
84G LEU* 4.1 15.0 - - + +
113G TRP* 3.4 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F MET* 2.9 53.1 + - + +
135F ALA* 4.1 7.0 - - - +
137F THR* 1.3 73.4 - - - +
139F SER* 1.3 58.5 + - - +
141F LEU* 3.4 5.2 + - - +
142F LYS* 2.9 31.3 + - - +
146F LEU* 5.5 0.7 - - - +
158F LEU* 3.7 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F ALA 3.1 17.8 + - - -
136F ASN* 3.8 5.8 - - - -
138F GLU* 1.3 78.8 - - - +
140F TYR* 1.3 64.1 + - - +
142F LYS* 3.1 9.9 + - - +
143F ASN* 2.9 44.1 + - - +
112G GLU* 4.9 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F ASN* 3.0 19.2 + - - +
137F THR 3.5 4.0 - - - +
138F GLU 3.3 0.2 - - - -
139F SER* 1.3 77.2 - - - +
141F LEU* 1.3 81.1 + - + +
143F ASN* 3.7 3.3 - - - +
144F VAL* 2.8 62.4 + - + +
24G PHE* 4.1 10.7 - - - -
80G LEU* 4.2 15.0 + - + +
84G LEU* 3.8 26.0 - - + +
107G ALA* 5.0 0.2 - - - +
109G GLU* 3.5 34.8 - - + -
110G GLU* 3.1 32.0 + - + +
112G GLU* 6.1 0.7 - - - -
113G TRP* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F THR* 3.0 32.2 + - + +
138F GLU* 3.7 4.9 - - - +
140F TYR* 1.3 102.4 - - + +
142F LYS* 1.3 62.2 + - - +
144F VAL* 4.7 1.3 - - - +
145F ALA* 3.1 10.0 + - - +
146F LEU* 3.0 37.1 + - + +
156F VAL* 5.9 2.2 - - + -
158F LEU* 4.3 19.7 - - + -
77G VAL* 4.6 20.9 - - + -
80G LEU* 3.9 33.4 - - + -
81G TYR* 4.8 7.9 - - + +
84G LEU* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F GLU 2.9 18.6 + - - +
139F SER* 3.5 8.7 - - - +
141F LEU* 1.3 77.1 - - - +
143F ASN* 1.3 68.4 + - - +
146F LEU* 3.6 16.9 + - + +
147F LYS* 2.8 54.4 + - + +
154F GLN 5.8 1.1 - - - +
155F LYS* 5.6 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F SER* 2.9 39.0 + - - +
140F TYR* 3.9 2.9 - - - +
142F LYS* 1.3 85.0 + - - +
144F VAL* 1.3 62.8 + - - +
147F LYS* 2.8 45.9 + - - +
148F HIS* 3.5 8.0 - - - -
109G GLU* 4.6 17.4 - - + +
112G GLU* 5.3 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F TYR* 2.8 40.0 + - + +
141F LEU* 4.6 1.1 - - - +
143F ASN* 1.3 73.3 - - - +
145F ALA* 1.3 59.6 + - + +
148F HIS* 4.1 7.6 + - - -
24G PHE* 4.1 17.9 - - + -
29G LEU* 3.9 14.2 - - + +
33G LEU* 4.9 2.4 - - - +
80G LEU* 4.0 28.0 - - + -
107G ALA* 5.8 1.1 - - + -
109G GLU* 3.2 46.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F LEU 3.1 5.3 + - - +
143F ASN 3.4 1.8 + - - -
144F VAL* 1.3 82.2 - - - +
146F LEU* 1.3 60.2 + - + +
147F LYS 3.2 2.0 - - - -
148F HIS* 2.7 35.4 + - - +
149F MET* 3.4 14.6 + - + +
29G LEU* 4.5 7.0 - - + -
33G LEU* 4.3 5.8 - - + +
76G THR* 3.9 15.7 - - + -
80G LEU* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il