Contacts of the helix formed by residues 96 - 112 (chain B) in PDB entry 4M3P
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 GLY 96 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 3.9 19.6 - - - -
77B TYR 6.0 1.6 - - - -
95B SER* 1.3 70.4 - - - +
97B GLN* 1.3 62.1 + - - -
98B GLU 3.2 0.4 - - - -
99B VAL* 3.3 23.3 + - - +
100B ASN* 3.5 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER 2.8 8.2 + - - +
96B GLY* 1.3 71.5 - - - -
98B GLU* 1.3 63.7 + - + +
100B ASN* 3.4 9.6 + - - +
101B GLU* 2.9 54.0 + - - +
143B GLN* 6.0 2.4 - - - +
146B GLU* 5.4 7.4 - - - +
147B VAL* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 3.9 7.9 - - + +
95B SER* 3.1 31.2 + - - +
96B GLY 3.2 0.6 - - - -
97B GLN* 1.3 77.8 - - + +
99B VAL* 1.3 59.8 + - - +
101B GLU* 3.9 15.5 - - - +
102B ALA* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 3.3 43.3 - - + +
47B GLU* 4.0 10.8 - - + -
49B ALA* 3.7 5.1 - - + +
50B VAL* 3.9 27.8 - - + -
74B PHE 5.0 0.9 - - - +
76B PHE* 4.1 11.9 - - + -
95B SER* 4.7 6.3 - - - -
96B GLY* 3.3 25.7 + - - +
97B GLN 3.2 0.4 - - - -
98B GLU* 1.3 78.2 - - - +
100B ASN* 1.3 56.0 + - - +
102B ALA* 3.4 2.9 + - - +
103B ALA* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B THR* 3.3 21.1 - - + +
76B PHE* 2.9 51.8 + - - -
77B TYR 4.6 3.8 - - - -
96B GLY 3.5 16.7 + - - -
97B GLN* 3.4 10.8 + - - +
98B GLU 3.3 0.4 - - - -
99B VAL* 1.3 76.0 - - - +
101B GLU* 1.3 64.5 + - - +
103B ALA* 3.7 1.4 - - - +
104B CYS* 3.0 31.5 + - - -
144B GLN* 3.9 10.2 + - - +
147B VAL* 4.4 15.9 - - + +
148B PHE* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN* 2.9 50.2 + - - +
98B GLU* 3.9 15.0 - - - +
100B ASN* 1.3 75.7 - - - +
102B ALA* 1.3 64.4 + - - +
104B CYS* 3.4 3.0 + - - +
105B ASP* 3.0 29.5 + - - +
147B VAL* 3.9 20.1 - - + +
150B LYS* 3.3 32.0 + - - +
151B LYS* 3.9 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 3.8 19.5 - - - +
50B VAL* 3.8 12.1 - - + -
98B GLU 3.0 18.7 + - - +
99B VAL 3.7 4.0 - - - +
101B GLU* 1.3 77.2 - - - +
103B ALA* 1.3 62.5 + - - +
105B ASP* 3.1 11.4 + - - +
106B ILE* 3.0 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.9 13.1 - - + +
56B VAL* 5.8 0.9 - - - -
60B HIS* 4.8 2.9 + - - -
73B THR* 4.9 2.0 - - - -
74B PHE* 3.3 42.7 + - + +
75B THR* 3.9 4.5 - - + -
99B VAL 2.9 16.7 + - - +
100B ASN 3.7 4.7 - - - +
101B GLU 3.3 0.2 - - - -
102B ALA* 1.3 77.0 - - - +
104B CYS* 1.3 61.8 + - - +
106B ILE* 3.2 7.8 + - - +
107B ALA* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR* 3.9 16.4 - - + -
75B THR* 4.4 1.8 - - - -
100B ASN 3.0 26.1 + - - +
101B GLU 3.6 4.9 - - - +
103B ALA* 1.3 73.9 - - - +
105B ASP* 1.3 64.1 + - - +
107B ALA* 3.3 1.9 + - - +
108B ARG* 2.9 25.4 + - - +
118B VAL* 5.0 2.6 - - + +
147B VAL* 4.1 12.8 - - - -
148B PHE* 3.8 35.2 - - - -
151B LYS* 3.7 26.5 - - + -
153B VAL* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU 3.0 15.1 + - - +
102B ALA* 3.1 10.9 + - - +
104B CYS* 1.3 74.3 - - - +
106B ILE* 1.3 59.1 + - + +
108B ARG* 3.5 7.2 + - - +
109B GLN* 2.9 28.1 + - - +
151B LYS* 2.7 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.7 27.1 - - + +
53B PRO* 3.9 24.7 - - + +
56B VAL* 4.2 13.2 - - + -
57B ARG* 3.6 51.1 - - + +
60B HIS* 3.9 12.3 - - + -
102B ALA* 3.0 14.2 + - + +
103B ALA* 3.2 5.6 + - - +
105B ASP* 1.3 76.7 - - + +
107B ALA* 1.3 64.8 + - - +
109B GLN* 3.2 7.7 + - - +
110B VAL* 3.0 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B HIS* 4.1 22.4 + - + +
71B MET* 4.0 16.1 - - + +
73B THR* 4.3 11.7 - - + -
103B ALA 3.0 15.9 + - - +
104B CYS 3.7 3.4 - - - +
106B ILE* 1.3 76.5 - - - +
108B ARG* 1.3 52.3 + - - +
110B VAL* 3.3 2.6 + - - +
111B ALA* 2.8 36.4 + - - +
118B VAL* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 4.7 3.2 - - - +
104B CYS 2.9 18.1 + - - +
105B ASP* 3.5 8.3 - - - +
107B ALA* 1.3 73.8 - - - +
109B GLN* 1.3 66.5 + - - +
111B ALA* 3.3 9.1 + - - +
112B ASP* 3.1 62.5 + - - +
116B ALA 4.7 3.8 + - - -
117B LEU* 5.8 0.6 - - - +
118B VAL* 3.4 30.8 - - + +
151B LYS 4.9 10.5 - - - -
152B ASN 4.0 14.6 + - - -
153B VAL* 4.7 1.0 - - - +
154B ASP* 3.2 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 2.8 38.5 + - - +
61B ARG* 3.5 21.8 - - - +
105B ASP 2.9 15.0 + - - +
106B ILE* 3.2 10.2 + - - +
108B ARG* 1.3 78.0 - - - +
110B VAL* 1.3 63.2 + - + +
112B ASP* 3.5 12.1 + - - +
113B GLU* 3.4 23.2 + - - +
501B SRT 5.0 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 4.0 18.8 - - + +
60B HIS* 3.9 34.5 - - + +
61B ARG* 3.8 34.5 - - + +
64B LEU* 3.6 15.8 - - + +
71B MET* 3.9 10.8 - - - -
106B ILE* 3.0 16.9 + - + +
107B ALA 4.0 2.2 - - - +
109B GLN* 1.3 78.5 - - + +
111B ALA* 1.3 65.8 + - - +
113B GLU* 2.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 3.1 6.3 + - - -
71B MET* 4.0 16.7 - - + +
107B ALA 2.8 21.6 + - - +
108B ARG* 3.3 7.8 + - - +
110B VAL* 1.3 71.3 - - - +
112B ASP* 1.3 58.5 + - - +
114B GLY 2.9 28.6 + - - +
116B ALA* 3.6 26.6 + - - +
117B LEU 4.2 0.2 - - - -
118B VAL* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 3.9 10.7 + - - +
108B ARG* 3.1 55.9 + - - +
109B GLN* 3.6 8.6 - - - +
110B VAL 3.1 0.2 - - - -
111B ALA* 1.3 75.1 - - - +
113B GLU* 1.3 58.2 + - + +
114B GLY 3.3 3.0 + - - +
----------------------------------------------------------
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