Contacts of the helix formed by residues 97 - 116 (chain A) in PDB entry 3W8I
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 GLU 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ARG* 2.5 49.6 + - - +
96A PRO* 1.3 95.2 - - - +
98A PRO* 1.3 74.6 - - + +
99A GLU* 3.3 12.5 + - - +
100A PHE* 3.3 15.9 + - + -
101A GLN* 3.3 23.7 + - - +
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Residues in contact with PRO 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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96A PRO 3.7 4.2 - - - +
97A GLU* 1.3 87.2 - - + +
99A GLU* 1.3 69.4 + - - +
101A GLN* 3.4 14.8 + - - +
102A ASP* 2.9 32.0 + - - +
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Residues in contact with GLU 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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97A GLU* 3.7 10.4 - - - +
98A PRO* 1.3 94.9 - - + +
100A PHE* 1.3 64.1 + - + +
102A ASP* 3.5 7.1 - - - +
103A LEU* 2.9 24.9 + - - +
144A THR* 3.7 7.0 - - - +
147A ASN* 3.6 33.9 - - + +
148A VAL* 3.9 22.7 - - + +
150A LYS 6.1 0.6 - - - -
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Residues in contact with PHE 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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93A ILE* 4.0 31.6 - - + -
95A ARG* 3.3 37.9 - - + +
97A GLU* 3.3 36.1 + - + +
98A PRO 3.3 0.2 - - - -
99A GLU* 1.3 79.3 - - + +
101A GLN* 1.3 61.4 + - - +
102A ASP 3.2 0.4 - - - -
103A LEU* 3.2 11.6 + - + +
104A ASN* 2.9 35.5 + - - +
148A VAL* 4.0 26.0 - - + -
208A PHE* 3.9 22.4 - + + -
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Residues in contact with GLN 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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95A ARG 3.4 15.0 + - - +
96A PRO* 3.7 18.9 + - - +
97A GLU 3.3 12.5 + - - +
98A PRO* 3.6 20.6 - - - +
100A PHE* 1.3 76.4 - - - +
102A ASP* 1.3 59.1 + - - +
104A ASN* 3.3 10.1 + - - +
105A GLU* 3.0 29.8 + - - +
108A ARG* 5.5 0.3 + - - -
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Residues in contact with ASP 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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98A PRO 2.9 18.5 + - - +
99A GLU* 3.5 7.4 - - - +
101A GLN* 1.3 75.3 - - - +
103A LEU* 1.3 59.6 + - - +
105A GLU* 3.3 10.5 + - - +
106A LYS* 2.9 62.4 + - - +
144A THR* 3.4 21.6 + - + +
147A ASN* 4.5 12.4 + - + +
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Residues in contact with LEU 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 ILE* 3.9 14.1 - - + -
99A GLU 2.9 13.3 + - - +
100A PHE* 3.3 13.7 - - + +
102A ASP* 1.3 75.9 - - - +
104A ASN* 1.3 59.5 - - - +
106A LYS* 3.9 0.3 - - - -
107A ALA* 2.9 33.2 + - - +
141A LEU* 3.8 21.3 - - + -
144A THR* 3.3 14.8 - - + +
145A VAL* 4.5 6.7 - - + -
148A VAL* 4.2 10.5 - - + -
204A ILE* 4.2 17.9 - - + -
205A LEU* 4.2 9.4 - - + -
208A PHE* 3.7 42.4 - - + -
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Residues in contact with ASN 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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92A MET* 3.6 18.5 - - + +
93A ILE* 2.4 55.4 + - - +
94A GLU* 4.7 1.0 - - - +
95A ARG 5.1 1.6 + - - +
100A PHE 2.9 23.4 + - - +
101A GLN* 3.7 8.0 - - - +
103A LEU* 1.3 75.9 - - - +
105A GLU* 1.3 57.3 + - - +
107A ALA* 3.9 4.2 - - - +
108A ARG* 2.9 58.2 + - - +
205A LEU* 4.1 3.3 - - - +
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Residues in contact with GLU 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 GLN 3.0 16.6 + - - +
102A ASP* 3.8 16.4 - - - +
103A LEU 3.3 0.2 - - - -
104A ASN* 1.3 77.5 - - - +
106A LYS* 1.3 73.4 + - + +
108A ARG* 3.3 11.3 + - - +
109A ALA* 2.9 29.8 + - + +
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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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102A ASP* 2.9 42.8 + - - +
105A GLU* 1.3 89.8 + - + +
107A ALA* 1.3 61.2 + - - +
109A ALA* 3.2 6.8 + - - +
110A LEU* 2.9 30.0 + - - +
137A ALA 5.0 3.1 - - - +
140A GLU* 3.4 48.6 + - + +
141A LEU* 3.6 23.7 - - + +
144A THR* 3.5 16.8 - - - +
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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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103A LEU* 2.9 19.1 + - + +
104A ASN* 3.9 2.5 - - - +
106A LYS* 1.3 75.5 - - - +
108A ARG* 1.3 63.6 + - - +
110A LEU* 3.3 4.3 + - - +
111A LYS* 2.9 31.1 + - - +
141A LEU* 3.6 11.3 - - + +
201A THR* 3.6 24.9 - - + -
204A ILE* 6.4 0.2 - - + -
205A LEU* 3.8 27.1 - - + -
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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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85A ALA 5.1 3.9 - - - +
87A ASP* 2.7 49.8 + - - +
92A MET* 3.4 19.1 - - - +
93A ILE 5.7 0.2 + - - -
101A GLN 5.5 0.4 + - - -
104A ASN* 2.9 39.5 + - - +
105A GLU* 3.4 9.9 - - - +
107A ALA* 1.3 75.6 - - - +
109A ALA* 1.3 62.4 + - - +
111A LYS* 3.3 12.1 + - - +
112A GLN* 2.9 46.3 + - + +
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Residues in contact with ALA 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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105A GLU* 2.9 16.9 + - + +
106A LYS* 3.5 11.2 - - - +
108A ARG* 1.3 76.3 - - - +
110A LEU* 1.3 63.1 + - - +
112A GLN* 3.2 13.7 + - - +
113A ILE* 2.9 38.2 + - + +
137A ALA* 5.2 4.7 - - + -
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Residues in contact with LEU 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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106A LYS 2.9 16.3 + - - +
107A ALA* 3.6 6.3 - - - +
109A ALA* 1.3 76.4 - - - +
111A LYS* 1.3 58.4 + - - +
113A ILE* 3.3 2.2 + - + +
114A LEU* 2.9 53.6 + - + +
134A ILE* 4.6 6.3 - - + -
137A ALA* 4.1 27.7 - - + +
138A ILE* 4.0 22.9 - - + -
141A LEU* 4.6 6.7 - - + -
167A PHE* 3.7 26.2 - - + -
197A LEU* 4.6 2.0 - - + -
201A THR* 3.4 24.7 - - - +
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Residues in contact with LYS 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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84A ALA 4.3 3.5 + - - +
85A ALA* 3.6 24.1 - - - +
86A ASP 3.1 24.0 + - - -
87A ASP* 4.3 9.3 - - - +
88A VAL* 4.6 3.2 - - - +
92A MET* 5.6 2.4 - - - -
107A ALA 2.9 21.6 + - - +
108A ARG* 3.7 10.3 - - - +
110A LEU* 1.3 75.3 - - + +
112A GLN* 1.3 56.7 + - - +
114A LEU* 3.5 2.5 + - + +
115A SER* 2.9 29.6 + - - -
198A ILE* 3.7 35.7 - - + +
201A THR* 3.9 18.4 - - + -
202A ASN* 2.8 33.8 + - - +
205A LEU* 5.0 7.9 - - - +
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Residues in contact with GLN 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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85A ALA* 3.8 22.1 + - + +
108A ARG* 2.9 37.0 + - - +
109A ALA* 3.6 13.9 - - - +
111A LYS* 1.3 75.7 - - - +
113A ILE* 1.3 65.2 + - + +
115A SER* 3.0 12.4 + - - -
116A LYS* 3.0 26.7 + - + +
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Residues in contact with ILE 113 (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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109A ALA* 2.9 20.9 + - + +
110A LEU* 3.8 4.3 - - + +
112A GLN* 1.3 75.7 - - + +
114A LEU* 1.3 63.1 + - - +
116A LYS* 3.0 23.2 + - + +
117A ILE* 3.7 7.1 + - - +
130A THR* 4.3 9.3 - - + +
133A ASP* 3.8 28.5 - - + +
134A ILE* 3.6 26.9 - - + -
137A ALA* 3.7 27.8 - - + -
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Residues in contact with LEU 114 (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 LEU* 3.3 15.4 - - - +
110A LEU* 2.9 38.7 + - + +
111A LYS* 3.8 4.0 - - + +
113A ILE* 1.3 77.7 - - - +
115A SER* 1.3 60.4 + - - +
117A ILE* 3.3 30.7 + - + +
134A ILE* 3.9 34.3 - - + -
174A PHE* 4.3 8.7 - - + -
194A ALA* 3.9 17.0 - - + +
197A LEU* 3.9 22.7 - - + -
198A ILE* 3.6 30.5 - - + +
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Residues in contact with SER 115 (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 LEU* 2.5 30.6 + - - +
82A ARG* 3.3 19.5 + - - +
84A ALA* 3.9 1.6 - - - +
85A ALA* 3.3 26.5 + - - -
111A LYS 2.9 14.2 + - - -
112A GLN 3.3 10.5 - - - -
114A LEU* 1.3 77.4 - - - +
116A LYS* 1.3 69.2 + - - +
117A ILE 3.2 0.9 - - - -
118A PRO* 3.3 13.9 - - - +
119A ASP* 5.0 2.1 - - - +
198A ILE* 4.5 0.8 - - - +
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Residues in contact with LYS 116 (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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82A ARG 5.3 3.8 + - - -
112A GLN* 3.0 32.3 + - + +
113A ILE* 3.0 13.8 + - + +
115A SER* 1.3 86.8 + - - +
117A ILE* 1.3 62.9 + - - +
118A PRO* 3.5 1.3 - - - -
119A ASP* 3.2 29.9 + - + +
120A GLU* 3.3 38.1 - - + +
130A THR* 5.3 1.1 - - + -
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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