Contacts of the helix formed by residues 96 - 112 (chain A) in PDB entry 3D77
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 ASP 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLY 3.4 1.6 + - - -
95A SER* 1.3 94.0 + - - +
97A ASN* 1.3 59.3 - - - +
98A CYS* 2.9 13.5 + - - +
99A ASN* 2.8 20.5 + - - +
100A LYS* 2.9 34.4 + - - +
122A EDO 3.6 30.8 + - - +
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Residues in contact with ASN 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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50A TYR* 3.6 42.3 + - + -
61A ASP 2.9 22.1 + - - +
62A GLU* 3.1 29.3 - - - +
63A ALA* 4.0 5.5 - - - +
96A ASP* 1.3 76.3 - - - +
98A CYS* 1.3 66.1 + - - +
100A LYS* 3.5 4.5 + - - +
101A ILE* 3.2 28.1 + - - +
122A EDO 5.2 1.7 + - - +
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Residues in contact with CYS 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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24A HIS* 5.8 0.2 - - - -
43A PRO* 5.1 0.9 - - + -
46A THR* 3.4 30.4 - - - +
47A CYS* 2.1 53.4 - - - +
50A TYR* 4.5 7.9 - - - -
96A ASP* 2.9 7.0 + - - +
97A ASN* 1.3 78.8 - - - +
99A ASN* 1.3 58.1 + - - +
101A ILE* 3.1 4.9 + - - +
102A TYR 2.9 23.6 + - - -
122A EDO 4.1 17.7 - - - +
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Residues in contact with ASN 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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41A ASN* 3.3 34.7 + - - +
94A GLY* 3.3 8.8 - - - -
95A SER* 3.0 41.8 + - - +
96A ASP* 2.8 13.5 + - - +
98A CYS* 1.3 73.7 - - - +
100A LYS* 1.3 59.6 + - - +
102A TYR* 3.3 13.1 + - - -
103A ASN* 2.9 38.7 + - - +
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Residues in contact with LYS 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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62A GLU* 3.0 48.0 + - - +
63A ALA* 3.8 12.8 - - + -
64A ASN* 5.2 2.8 + - - -
92A THR* 4.2 18.2 - - - +
93A SER* 3.5 18.3 + - - +
94A GLY* 3.5 32.8 - - - +
96A ASP* 2.9 23.2 + - - +
97A ASN* 3.6 9.7 + - - +
98A CYS 3.2 0.2 - - - -
99A ASN* 1.3 75.9 + - - +
101A ILE* 1.3 59.4 + - - +
103A ASN* 3.3 3.3 + - - +
104A LEU* 3.0 27.0 + - - +
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Residues in contact with ILE 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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46A THR 4.5 1.1 - - - +
49A MET* 3.6 32.1 - - + -
50A TYR* 3.8 24.0 - - + +
53A LEU* 3.8 26.0 - - + -
59A VAL* 4.2 10.5 - - + -
63A ALA* 4.1 21.1 - - + +
92A THR* 4.6 1.3 - - + -
97A ASN 3.2 13.0 + - - +
98A CYS 3.1 7.6 + - - +
100A LYS* 1.3 75.4 - - - +
102A TYR* 1.3 60.3 + - - +
104A LEU* 3.3 15.6 + - + +
105A ALA* 2.8 29.5 + - - +
116A TRP* 4.1 11.7 - - + -
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Residues in contact with TYR 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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39A LEU* 3.9 16.2 + - + -
40A VAL* 3.4 14.3 - - - -
41A ASN* 3.4 54.0 + - + +
46A THR* 3.6 19.8 - - + -
49A MET* 4.6 5.4 - - - -
98A CYS 2.9 9.2 + - - +
99A ASN* 3.5 11.9 - - - +
101A ILE* 1.3 75.4 - - - +
103A ASN* 1.3 76.2 + - - +
105A ALA* 3.2 2.5 + - - +
106A LYS* 2.9 64.4 + - + +
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Residues in contact with ASN 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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93A SER* 2.9 26.2 + - - +
94A GLY* 3.8 3.6 - - - -
99A ASN* 2.9 33.7 + - - +
100A LYS 3.7 4.5 - - - +
101A ILE 3.2 0.2 - - - -
102A TYR* 1.3 95.9 - - - +
104A LEU* 1.3 57.7 + - - +
106A LYS* 3.5 6.0 + - - +
107A CYS* 3.0 29.9 + - - +
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Residues in contact with LEU 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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53A LEU* 5.3 0.7 - - + -
65A VAL* 3.8 28.9 - - + -
70A MET* 5.0 2.7 - - + -
86A MET* 4.1 14.6 - - + -
89A CYS* 3.8 34.8 - - + +
90A LEU* 4.1 6.1 - - + -
92A THR* 4.1 10.3 - - + +
100A LYS 3.0 14.7 + - - +
101A ILE* 3.6 15.3 - - + +
103A ASN* 1.3 74.0 - - - +
105A ALA* 1.3 60.3 + - - +
107A CYS* 3.2 3.6 + - - +
108A VAL* 2.9 42.5 + - + +
116A TRP* 3.8 27.4 - - + -
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Residues in contact with ALA 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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39A LEU* 3.5 26.5 - - + -
49A MET* 4.2 3.1 - - + -
101A ILE 2.8 20.7 + - - +
102A TYR 3.7 0.2 - - - +
104A LEU* 1.3 72.9 - - - +
106A LYS* 1.3 57.9 + - - +
108A VAL* 3.3 0.9 + - - +
109A GLN* 2.8 37.3 + - - +
116A TRP* 3.5 40.6 - - + +
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Residues in contact with LYS 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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37A GLY 5.0 5.1 + - - -
39A LEU* 3.0 41.9 + - + +
102A TYR* 2.9 50.9 + - + +
103A ASN* 3.6 7.6 - - - +
105A ALA* 1.3 77.3 - - - +
107A CYS* 1.3 62.4 + - - +
109A GLN* 3.9 8.0 + - + +
110A GLU* 3.0 50.3 + - + +
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Residues in contact with CYS 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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88A LYS* 4.4 17.3 - - - -
89A CYS* 2.0 53.2 - - + +
103A ASN 3.0 18.0 + - - +
104A LEU* 3.2 4.5 + - - +
106A LYS* 1.3 76.4 - - - +
108A VAL* 1.3 59.5 + - - +
110A GLU* 3.4 8.6 + - - +
111A SER* 2.7 31.2 + - - -
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Residues in contact with VAL 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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85A VAL* 3.9 16.2 - - + -
86A MET* 3.8 25.1 - - + -
89A CYS* 4.2 7.2 - - + -
104A LEU* 2.9 30.2 + - + +
105A ALA 3.8 3.1 - - - +
107A CYS* 1.3 77.4 - - - +
109A GLN* 1.3 59.8 + - - +
111A SER 3.1 0.9 + - - -
112A ALA* 2.9 43.9 + - - +
115A VAL* 3.9 19.5 - - + -
116A TRP* 3.7 29.8 - - + -
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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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34A VAL* 2.9 27.6 + - - +
35A ASN* 5.0 1.2 + - - +
37A GLY* 3.9 26.6 - - - +
39A LEU* 4.3 16.8 - - - +
105A ALA* 2.8 25.6 + - - +
106A LYS* 4.1 8.3 + - + +
108A VAL* 1.3 71.0 - - - +
110A GLU* 1.3 62.1 + - + +
111A SER 3.4 0.3 + - - -
112A ALA 4.5 4.5 - - - -
113A PRO* 3.4 30.2 - - + +
116A TRP* 3.6 41.3 + - + +
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Residues in contact with GLU 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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88A LYS* 5.5 0.9 - - - +
106A LYS* 3.0 43.4 + - + +
107A CYS* 3.8 8.0 - - - +
108A VAL 3.2 0.2 - - - -
109A GLN* 1.3 77.8 - - + +
111A SER* 1.3 60.5 + - - +
113A PRO* 5.2 1.2 - - - +
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Residues in contact with SER 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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85A VAL* 3.6 17.9 - - - +
88A LYS* 2.6 38.4 + - - +
107A CYS 2.7 21.3 + - - -
108A VAL 3.1 1.8 + - - -
110A GLU* 1.3 82.7 - - - +
112A ALA* 1.3 58.9 + - - +
113A PRO* 4.0 4.2 - - - +
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Residues in contact with ALA 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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81A ARG* 4.1 22.0 - - + +
85A VAL* 4.0 19.5 - - + -
108A VAL* 2.9 16.1 + - - +
111A SER* 1.3 75.2 - - - +
113A PRO* 1.3 62.8 - - - +
114A ASP 3.2 7.8 + - - -
115A VAL* 3.4 34.1 + - + +
116A TRP 4.4 0.3 + - - -
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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