Contacts of the helix formed by residues 99 - 113 (chain F) in PDB entry 6D84
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 ASN 99 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU* 3.5 30.7 - - - +
97F ASP* 2.9 15.4 + - - +
98F PRO* 1.3 77.0 - - - +
100F PRO* 1.3 70.3 - - - +
101F LEU* 3.2 19.4 + - - +
102F ILE* 3.3 23.8 - - + +
103F ARG* 3.4 13.0 - - - +
146P ALA 4.0 8.1 + - - -
147P PRO 4.3 0.6 + - - -
148P ARG* 3.6 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F PRO 3.3 10.0 - - - +
99F ASN* 1.3 90.0 - - - +
101F LEU* 1.3 57.6 + - - +
103F ARG* 3.4 29.1 - - - +
104F ALA* 2.9 32.4 + - - +
134F ASP* 3.2 29.8 - - + +
136F TYR* 4.0 5.4 - - + -
137F VAL* 4.4 6.0 - - + +
148P ARG* 3.4 27.4 - - + +
149P PRO* 3.8 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU* 3.7 23.8 - - + -
67F LYS* 4.1 22.9 - - - +
99F ASN* 3.2 16.0 + - - +
100F PRO* 1.3 80.7 - - - +
102F ILE* 1.3 57.2 + - - +
104F ALA* 3.9 0.5 - - - +
105F LEU* 2.9 29.9 + - - +
108F ARG* 4.9 2.0 - - - +
136F TYR* 3.3 31.6 - - + +
116P GLU* 4.5 4.7 - - - +
134P TYR* 4.8 19.7 - - + +
135P ILE* 5.4 2.7 - - + -
146P ALA* 4.7 6.7 - - + -
147P PRO 3.9 12.8 - - - +
148P ARG 5.4 0.2 - - - -
149P PRO* 3.7 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F GLN* 5.8 0.2 - - - +
60F THR 5.0 3.1 - - - +
61F ASP 6.1 0.9 - - - +
62F ASN 5.3 1.3 - - - +
63F LEU* 3.8 24.2 - - + -
66F LYS* 3.8 37.0 - - + -
70F TYR* 4.9 1.6 - - - +
94F ASP* 4.1 16.3 - - + +
97F ASP* 3.3 37.0 - - + +
99F ASN* 3.3 15.7 - - + +
101F LEU* 1.3 76.2 - - - +
103F ARG* 1.3 63.5 + - - +
105F LEU* 3.5 10.4 - - + +
106F ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F ASP 3.4 21.1 - - - +
95F CYS* 3.7 18.6 + - - +
96F GLU* 6.0 0.2 - - - +
97F ASP* 3.2 33.7 + - + +
98F PRO* 4.5 3.0 + - - -
99F ASN 3.4 7.6 + - - +
100F PRO* 3.4 37.2 + - - +
101F LEU 3.3 0.6 - - - -
102F ILE* 1.3 77.7 - - - +
104F ALA* 1.3 57.8 + - - +
106F ALA* 3.2 4.7 + - - +
107F VAL* 2.9 31.0 + - - +
128F LYS* 5.2 4.9 - - - +
129F CYS* 5.1 3.4 - - - -
132F ASP* 2.5 43.7 + - - -
134F ASP* 4.5 4.0 - - - +
137F VAL* 4.2 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F PRO 2.9 17.4 + - - +
103F ARG* 1.3 76.1 - - - +
105F LEU* 1.3 56.8 + - - +
107F VAL* 4.2 3.8 - - - -
108F ARG* 2.9 34.1 + - - +
136F TYR* 3.6 23.1 - - + -
137F VAL* 3.7 18.5 - - - +
140F THR* 3.3 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU* 4.1 17.5 - - + +
66F LYS* 4.9 1.8 - - + -
67F LYS* 3.5 51.8 - - + +
70F TYR* 3.6 28.3 - - + -
101F LEU 2.9 18.8 + - - +
102F ILE* 3.5 8.1 - - + +
104F ALA* 1.3 77.2 - - - +
106F ALA* 1.3 52.5 + - - +
108F ARG* 3.3 15.5 - - + +
109F THR* 2.5 38.1 + - - +
115P ASP* 3.7 24.5 - - - +
116P GLU* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F TYR* 4.0 18.8 - - - +
91F PHE* 3.9 12.5 - - + -
94F ASP* 4.1 15.5 - - + -
95F CYS* 4.1 11.0 - - - -
102F ILE 2.9 18.1 + - - +
103F ARG 3.2 4.5 + - - +
105F LEU* 1.3 73.8 - - - +
107F VAL* 1.3 61.4 + - - +
109F THR* 3.5 8.0 - - - -
110F MET* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F CYS* 3.9 8.7 - - - -
103F ARG 2.9 21.2 + - - +
104F ALA* 3.7 7.6 - - - +
105F LEU 3.3 0.2 - - - -
106F ALA* 1.3 77.2 - - - +
108F ARG* 1.3 62.6 + - - +
110F MET* 3.1 18.6 + - + +
111F GLY 3.1 10.2 + - - -
125F PRO 5.3 0.9 - - - +
126F LEU* 3.9 8.5 - - + -
129F CYS* 3.7 33.4 - - + -
137F VAL* 4.5 2.0 - - + +
140F THR* 4.1 2.5 - - + -
141F ALA* 3.8 21.8 - - + +
144F CYS* 3.3 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F MET* 4.6 2.8 - - - +
101F LEU* 4.4 2.4 + - - +
104F ALA* 2.9 22.3 + - - +
105F LEU* 3.3 42.9 - - + +
107F VAL* 1.3 77.5 - - - +
109F THR* 1.3 59.9 + - - +
111F GLY 4.0 0.9 - - - +
112F CYS* 3.6 15.9 + - - -
136F TYR* 3.3 35.1 + - - -
140F THR* 2.7 37.2 + - + +
144F CYS* 5.1 1.1 - - - -
147F LYS* 3.2 33.3 + - - +
115P ASP* 3.4 27.5 + - - +
116P GLU* 4.2 7.5 + - - -
119P ASP* 2.9 31.6 + - - +
124P GLN* 4.2 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F TYR* 3.2 47.4 - - + +
73F LEU* 4.9 1.3 - - + -
74F MET* 5.2 9.8 - - + +
91F PHE* 3.6 27.1 - - + -
105F LEU* 2.5 24.8 + - - +
106F ALA 3.5 6.3 - - - -
108F ARG* 1.3 77.0 - - - +
110F MET* 1.3 64.3 + - - +
111F GLY 3.3 0.2 + - - -
112F CYS* 3.4 3.1 + - - +
113F ILE* 3.3 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F PHE* 3.6 40.4 - - + -
92F VAL* 5.6 0.9 - - + -
95F CYS* 3.8 19.1 - - - -
106F ALA 2.9 22.6 + - - +
107F VAL* 3.1 10.3 + - + +
109F THR* 1.3 75.4 - - - +
111F GLY* 1.3 62.2 + - - +
112F CYS 3.8 0.2 + - - -
113F ILE* 3.8 18.7 + - - +
119F THR* 4.9 0.7 - - - +
122F LEU* 3.6 52.0 - - + +
125F PRO* 3.9 29.2 - - + -
126F LEU* 4.7 8.5 - - + +
144F CYS* 4.6 3.8 - - - -
148F LEU* 6.0 0.7 - - - +
151F ILE* 4.9 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F VAL 3.1 10.1 + - - -
108F ARG 3.9 0.4 + - - -
109F THR 3.2 0.4 - - - -
110F MET* 1.3 77.6 - - - +
112F CYS* 1.3 60.6 + - - +
144F CYS* 3.6 21.3 - - - -
147F LYS* 3.7 27.5 - - - +
148F LEU* 5.2 2.5 - - - -
151F ILE* 3.3 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F MET* 3.7 42.8 - - + +
77F ALA* 5.3 1.0 - - - +
108F ARG 3.6 7.7 + - - +
109F THR 3.4 4.2 + - - +
111F GLY* 1.3 73.6 - - - +
113F ILE* 1.3 61.5 + - - +
114F ARG* 3.1 13.1 + - - +
147F LYS* 3.4 30.3 - - - -
19P ARG* 5.4 0.9 - - - -
21P TYR* 3.5 33.1 - - - +
22P ARG 6.0 1.4 - - - -
119P ASP* 5.6 1.1 - - - -
120P PHE 5.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F LEU* 4.3 27.8 - - + +
74F MET* 4.9 3.8 - - - +
77F ALA* 3.7 18.8 - - + -
84F ALA* 5.8 3.6 - - + -
87F ALA* 6.2 0.2 - - + -
91F PHE* 3.7 32.5 - - + -
109F THR* 3.3 25.1 + - + +
110F MET* 3.8 11.1 - - - +
111F GLY 3.3 1.2 - - - -
112F CYS* 1.3 73.4 - - - +
114F ARG* 1.3 59.7 + - - +
115F VAL* 3.4 18.8 + - + +
118F ILE* 4.8 17.9 - - + -
119F THR* 3.9 5.9 - - - +
122F LEU* 5.6 1.5 - - + +
151F ILE* 3.3 15.6 - - - +
----------------------------------------------------------
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