Contacts of the helix formed by residues 96 - 112 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A PHE* 3.9 20.5 - - - -
77A TYR 5.8 3.4 - - - -
95A SER* 1.3 71.4 - - - +
97A GLN* 1.3 64.7 + - - -
98A GLU 3.2 0.2 - - - -
99A VAL* 3.4 12.0 + - - +
100A ASN* 3.0 32.9 + - - -
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER 3.1 7.3 + - - +
96A GLY* 1.3 71.5 - - - -
98A GLU* 1.3 69.6 + - + +
100A ASN* 3.7 7.8 - - - +
101A GLU* 2.8 51.5 + - - +
143A GLN* 6.2 2.2 - - - +
147A VAL* 4.6 15.8 - - + +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 3.9 9.4 - - + +
95A SER* 2.5 42.2 + - - +
96A GLY 3.2 0.2 - - - -
97A GLN* 1.3 89.9 - - + +
99A VAL* 1.3 64.3 + - - +
101A GLU* 3.9 14.0 - - - +
102A ALA* 3.1 24.8 + - - +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO* 3.4 33.2 - - + +
47A GLU* 4.1 17.0 - - + -
49A ALA* 3.8 4.8 - - + +
50A VAL* 3.8 24.5 - - + -
74A PHE 4.7 1.6 - - - +
76A PHE* 3.9 22.9 - - + -
95A SER* 4.5 9.9 - - - +
96A GLY 3.4 20.5 + - - +
97A GLN 3.3 0.6 - - - -
98A GLU* 1.3 77.9 - - - +
100A ASN* 1.3 60.4 + - - +
102A ALA* 3.3 2.4 + - - +
103A ALA* 3.0 27.0 + - - +
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Residues in contact with ASN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A THR* 3.3 22.1 - - + +
76A PHE* 2.9 49.3 + - - +
77A TYR* 5.1 1.8 - - - +
96A GLY 3.0 21.9 + - - +
97A GLN* 3.8 7.8 - - - +
99A VAL* 1.3 76.0 - - - +
101A GLU* 1.3 64.2 + - - +
103A ALA* 3.6 1.2 + - - +
104A CYS* 3.1 29.1 + - - -
144A GLN* 5.1 8.1 - - - +
147A VAL* 4.2 17.2 - - + +
148A PHE* 5.7 2.0 - - + -
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLN* 2.8 44.6 + - - +
98A GLU* 3.9 12.8 - - - +
99A VAL 3.3 0.2 - - - -
100A ASN* 1.3 74.5 - - - +
102A ALA* 1.3 64.9 + - - +
104A CYS* 3.4 3.3 + - - +
105A ASP* 3.1 27.9 + - - -
147A VAL* 3.8 20.9 - - + +
150A LYS* 3.1 29.4 + - - +
151A LYS* 3.7 22.0 - - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 3.7 20.4 - - - +
50A VAL* 3.9 11.4 - - + -
98A GLU 3.1 17.0 + - - +
99A VAL 3.7 3.8 - - - +
101A GLU* 1.3 76.2 - - - +
103A ALA* 1.3 62.9 + - - +
105A ASP* 3.2 9.5 + - - +
106A ILE* 3.0 29.5 + - + +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA* 3.9 13.6 - - + +
56A VAL* 5.8 1.1 - - - -
60A HIS* 4.8 2.9 + - - -
73A THR* 4.9 0.4 - - - -
74A PHE* 3.3 43.0 + - + +
75A THR* 3.8 10.3 - - + -
99A VAL 3.0 16.1 + - - +
100A ASN 3.9 0.2 - - - +
101A GLU 3.3 0.2 - - - -
102A ALA* 1.3 76.0 - - - +
104A CYS* 1.3 62.1 + - - +
106A ILE* 3.3 7.5 + - - +
107A ALA* 3.0 25.2 + - - +
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Residues in contact with CYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A THR* 4.1 17.9 - - + +
75A THR* 4.6 0.2 - - - -
100A ASN 3.1 24.1 + - - +
101A GLU 3.6 4.9 - - - +
102A ALA 3.3 0.2 - - - -
103A ALA* 1.3 76.0 - - - +
105A ASP* 1.3 57.2 + - - +
107A ALA* 3.4 2.3 + - - +
108A ARG* 3.0 30.7 + - - +
118A VAL* 5.0 2.9 - - + +
147A VAL* 4.1 4.3 - - - -
148A PHE* 3.6 36.8 - - - -
151A LYS* 3.7 33.4 - - + -
153A VAL* 4.7 3.6 - - + -
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLU 3.1 13.0 + - - +
102A ALA* 3.2 11.2 + - - +
104A CYS* 1.3 76.0 - - - +
106A ILE* 1.3 57.9 + - + +
108A ARG* 3.6 5.8 + - - +
109A GLN* 3.0 27.3 + - - +
151A LYS* 2.9 38.3 + - - +
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Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA* 3.8 28.9 - - - +
53A PRO* 3.9 21.3 - - + +
56A VAL* 4.4 7.9 - - + -
57A ARG* 3.5 54.3 - - + +
60A HIS* 3.9 11.4 - - + -
102A ALA* 3.0 18.1 + - + +
103A ALA* 3.7 6.1 - - - +
105A ASP* 1.3 73.6 - - + +
107A ALA* 1.3 66.5 + - - +
109A GLN* 3.2 8.9 + - - +
110A VAL* 3.1 23.1 + - + +
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A HIS* 4.1 27.7 + - + +
71A MET* 3.9 12.4 - - + +
73A THR* 4.2 12.6 - - + -
103A ALA 3.0 17.0 + - - +
104A CYS 3.7 3.8 - - - +
106A ILE* 1.3 76.4 - - - +
108A ARG* 1.3 57.1 + - - +
110A VAL* 3.3 1.4 + - - -
111A ALA* 2.8 29.6 + - - +
118A VAL* 3.9 20.5 - - + +
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 5.2 5.1 - - - +
104A CYS 3.0 16.9 + - - +
105A ASP* 3.8 6.3 - - - +
107A ALA* 1.3 72.7 - - - +
109A GLN* 1.3 69.8 + - - +
111A ALA* 4.4 5.9 - - - +
112A ASP* 2.9 58.4 + - - +
116A ALA 4.9 2.6 + - - -
118A VAL* 3.5 30.5 - - + +
151A LYS 5.0 5.4 + - - +
152A ASN 3.2 25.1 + - - -
153A VAL* 4.0 1.2 - - - +
154A ASP* 3.1 35.6 + - - +
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 2.8 38.4 + - - +
61A ARG* 3.6 17.7 - - - +
105A ASP 3.0 14.7 + - - +
106A ILE* 3.2 11.7 + - - +
108A ARG* 1.3 78.2 - - - +
110A VAL* 1.3 61.6 + - + +
112A ASP* 3.4 15.9 + - - +
113A GLU* 3.4 22.5 + - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 3.8 27.8 - - + +
60A HIS* 3.7 28.9 - - + +
61A ARG* 3.7 37.7 - - + +
64A LEU* 3.3 21.2 - - + +
71A MET* 3.8 9.6 - - - -
106A ILE 3.1 15.7 + - - +
107A ALA 4.0 2.0 - - - +
109A GLN* 1.3 73.8 - - + +
111A ALA* 1.3 65.3 + - - +
112A ASP 3.1 1.6 - - - -
113A GLU* 2.9 18.7 + - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 3.1 8.3 + - - -
71A MET* 3.9 15.4 - - + +
107A ALA 2.8 21.5 + - - +
108A ARG* 3.2 9.6 + - - +
110A VAL* 1.3 72.7 - - - +
112A ASP* 1.3 57.9 + - - +
113A GLU 3.1 1.1 + - - -
114A GLY 3.0 26.0 + - - +
116A ALA* 3.6 25.9 + - - +
117A LEU 4.3 0.4 - - - -
118A VAL* 3.6 22.4 - - + -
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 4.2 9.4 + - - +
108A ARG* 2.9 45.6 + - - +
109A GLN* 3.5 13.0 - - - +
110A VAL 3.1 0.4 - - - -
111A ALA* 1.3 76.4 - - - +
113A GLU* 1.3 60.5 + - + +
114A GLY 3.3 2.8 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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