Contacts of the helix formed by residues 105 - 121 (chain T) in PDB entry 5A0Q
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 VAL 105 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69T HIS* 4.6 2.0 - - + +
70T ILE* 3.8 35.4 - - + -
103T LEU* 4.1 0.4 - - - -
104T PRO* 1.3 70.5 - - + +
106T SER* 1.3 65.4 + - - +
108T LEU* 3.1 14.6 + - - +
109T VAL* 3.1 16.1 + - + +
134T ILE* 4.1 21.3 - - + +
136T GLY* 4.0 13.9 - - - +
137T TYR 3.1 30.5 - - - +
138T ASP* 3.5 17.4 + - + +
143T HIS* 4.9 2.7 - - + +
145T PHE* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104T PRO* 4.4 8.7 - - - +
105T VAL* 1.3 79.2 + - - +
107T ARG* 1.3 65.7 + - - +
109T VAL* 3.4 4.4 + - - +
110T SER* 3.0 26.8 + - - -
138T ASP* 4.6 8.8 + - - -
143T HIS* 5.7 1.6 - - - -
145T PHE* 4.0 29.2 - - - -
153T TYR* 6.0 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101T ARG* 4.7 10.7 - - - +
103T LEU* 4.8 4.3 - - + -
104T PRO* 3.6 33.7 + - + +
105T VAL 3.2 0.4 - - - -
106T SER* 1.3 83.4 + - - +
108T LEU* 1.3 55.7 + - - +
110T SER* 3.2 11.7 + - - -
111T LEU* 3.1 31.4 + - + +
74b GLU* 3.0 41.6 + - - +
77b LEU* 3.7 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66T VAL* 3.8 17.5 - - + -
70T ILE* 4.1 17.3 - - + -
88T MET* 3.6 32.3 - - + +
91T GLU* 3.5 33.0 - - + -
92T CYS* 3.7 24.2 - - - -
103T LEU* 3.4 17.6 - - + +
104T PRO 3.9 1.2 + - - -
105T VAL 3.1 10.3 + - - +
107T ARG* 1.3 75.4 - - - +
109T VAL* 1.4 60.4 + - - +
111T LEU* 3.2 13.2 + - + +
112T ILE* 3.1 24.7 + - + +
134T ILE* 4.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105T VAL 3.1 14.1 + - - +
106T SER* 3.6 9.2 - - - +
107T ARG 3.3 0.2 - - - -
108T LEU* 1.4 73.1 - - - +
110T SER* 1.4 58.3 + - - +
112T ILE* 3.1 22.2 + - + +
113T GLY* 3.1 9.9 + - - -
134T ILE* 4.0 24.7 - - + -
145T PHE* 3.8 39.7 - - + -
147T THR* 3.9 8.0 - - + +
153T TYR* 3.7 39.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106T SER 3.0 15.9 + - - -
107T ARG* 3.2 14.6 + - - -
109T VAL* 1.4 76.9 - - - +
111T LEU* 1.3 60.8 + - - +
113T GLY* 3.5 2.3 + - - -
114T SER* 3.3 23.5 + - - -
153T TYR* 4.2 24.3 + - - -
77b LEU* 5.6 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87T PHE* 4.1 19.3 - - + -
88T MET* 5.3 0.2 - - + -
91T GLU* 3.3 42.2 - - + +
103T LEU* 5.3 3.4 - - + -
107T ARG* 3.1 15.7 + - + +
108T LEU* 3.2 15.9 + - + +
110T SER* 1.3 76.0 - - - +
112T ILE* 1.3 62.1 + - - +
114T SER* 3.2 12.1 + - - +
115T LYS* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84T LEU* 4.5 18.2 - - + -
88T MET* 3.4 39.5 - - + -
108T LEU* 3.1 6.7 + - + +
109T VAL* 3.1 18.3 + - + +
111T LEU* 1.3 75.2 - - - +
113T GLY* 1.3 62.3 + - - +
115T LYS* 3.3 3.8 + - - +
116T THR* 2.9 41.3 + - - +
132T LEU* 4.5 6.3 - - + -
134T ILE* 3.4 37.9 - - + -
147T THR* 4.1 23.1 - - + +
151T ALA 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109T VAL 3.1 11.8 + - - -
110T SER 3.5 4.4 + - - -
111T LEU 3.2 0.6 - - - -
112T ILE* 1.3 76.3 - - - +
114T SER* 1.3 54.2 + - - +
116T THR* 4.6 0.2 - - - -
117T GLN* 3.0 24.4 + - - +
151T ALA* 3.1 41.9 + - - +
153T TYR* 4.8 6.3 - - - -
85U ARG* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110T SER 3.3 13.3 + - - -
111T LEU* 3.2 18.5 + - - +
113T GLY* 1.3 77.3 - - - +
115T LYS* 1.3 55.9 + - - +
117T GLN* 3.5 12.8 - - - +
118T ILE* 3.1 19.4 - - - +
89U ASP* 4.6 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83T LEU* 3.9 20.0 + - - +
84T LEU* 4.0 12.4 - - + +
87T PHE* 3.6 45.8 - - + -
111T LEU 3.0 14.8 + - - +
112T ILE* 3.3 3.3 + - - +
114T SER* 1.3 72.6 - - - +
116T THR* 1.3 62.9 - - - +
117T GLN 3.2 2.1 + - - -
118T ILE* 3.4 21.2 + - + +
119T PRO* 3.8 1.7 - - - +
125T ARG* 5.4 3.3 + - - +
128T TYR* 3.2 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84T LEU* 4.0 13.3 - - - +
112T ILE* 2.9 28.3 + - - +
113T GLY 4.0 3.4 - - - -
115T LYS* 1.3 77.4 - - - +
117T GLN* 1.4 60.5 + - - +
118T ILE 3.4 0.2 - - - -
119T PRO* 3.5 11.9 - - - +
120T THR* 3.9 11.5 - - + +
128T TYR* 3.7 24.5 + - + +
148T CYS 4.8 2.0 - - - +
149T PRO 3.2 27.8 - - - +
150T SER* 3.8 18.4 - - - +
151T ALA* 3.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113T GLY 3.0 16.0 + - - +
114T SER* 3.5 14.1 - - - +
115T LYS 3.2 1.2 - - - -
116T THR* 1.4 74.7 - - - +
118T ILE* 1.3 66.5 + - + +
120T THR* 2.8 34.0 + - - -
121T GLN* 3.5 11.6 + - + +
151T ALA* 3.5 10.6 - - - +
82U ALA* 2.9 36.7 + - - +
83U ASP* 3.5 16.2 - - - +
86U SER* 4.0 21.7 + - - +
129U ARG* 3.6 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114T SER 3.1 26.5 - - - +
115T LYS* 3.4 18.8 - - + +
117T GLN* 1.3 77.3 - - + +
119T PRO* 1.3 68.3 - - + +
121T GLN* 3.2 14.7 + - + +
122T ARG* 3.4 52.3 + - - +
125T ARG* 3.7 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 119 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T VAL* 3.0 13.2 - - - +
115T LYS 3.8 7.9 - - - +
116T THR 3.5 10.3 - - - +
118T ILE* 1.3 95.7 - - + +
120T THR* 1.3 56.0 + - - +
122T ARG 3.0 22.7 - - - +
125T ARG* 3.2 31.1 - - + +
126T ARG 3.3 35.7 - - - +
127T PRO* 3.7 5.8 - - + -
128T TYR* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T VAL* 3.7 18.8 - - - +
19T ILE* 4.9 0.9 - - - +
22T ILE* 3.7 31.4 - - + -
116T THR 3.9 14.6 - - - +
117T GLN* 2.8 25.6 + - - +
119T PRO* 1.3 77.2 - - - +
121T GLN* 1.4 52.8 + - - +
122T ARG 3.6 1.0 + - - +
127T PRO* 4.6 12.6 - - + -
149T PRO 5.0 0.9 - - - +
150T SER* 4.9 14.1 - - - -
151T ALA 5.4 1.3 - - - +
82U ALA* 5.8 2.3 - - + +
129U ARG* 2.8 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117T GLN* 3.9 15.3 - - + +
118T ILE* 3.2 10.3 + - - +
120T THR* 1.4 76.8 + - - +
122T ARG* 1.4 57.9 + - + +
83U ASP* 3.0 15.0 - - - +
86U SER* 6.1 0.4 - - - +
122U TYR* 2.7 48.5 - - + +
128U VAL* 3.4 7.9 - - + +
129U ARG* 2.9 66.2 + - - -
131U PHE* 3.5 23.9 - - + +
----------------------------------------------------------
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