Contacts of the helix formed by residues 82 - 94 (chain A) in PDB entry 1DWQ
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 ALA 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.4 26.9 - - + +
10A HIS 3.7 6.7 - - - +
11A THR* 4.4 2.2 + - - +
78A GLY* 3.5 13.5 - - - -
79A GLU 2.8 23.8 + - - +
81A CSA 1.3 68.7 + - - +
83A GLY* 1.3 62.5 + - - +
84A LEU 3.1 0.7 - - - -
85A ASN* 2.9 34.4 + - - +
86A ILE* 3.1 13.5 + - - +
105A SER* 4.1 0.2 - - - -
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Residues in contact with GLY 83 (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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80A SER 3.9 0.2 + - - -
81A CSA 3.0 2.2 + - - -
82A ALA* 1.3 76.0 - - - +
84A LEU* 1.4 54.8 + - - +
86A ILE* 3.4 7.2 + - - +
87A ALA* 3.0 26.7 + - - +
102A PHE* 3.7 13.9 - - - -
105A SER* 3.0 24.5 + - - -
106A LEU 3.4 12.6 - - - -
108A PRO* 3.7 11.7 - - - +
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Residues in contact with LEU 84 (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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54A PHE* 3.5 24.9 - - + -
81A CSA 3.2 11.8 + - + +
82A ALA 3.1 0.6 - - - -
83A GLY* 1.4 74.2 - - - +
85A ASN* 1.3 59.5 + - - +
87A ALA* 3.5 2.5 + - - +
88A ILE* 2.9 37.4 + - + +
106A LEU* 3.5 31.6 - - + +
108A PRO* 3.9 17.5 - - + -
114A PRO 3.5 24.7 - - - +
117A THR* 5.1 0.9 - - - +
118A VAL* 3.9 7.0 - - + -
179A LEU* 5.4 1.8 - - + +
184A LEU* 3.7 28.5 - - + -
190A PHE* 4.1 13.5 - - + -
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Residues in contact with ASN 85 (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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9A ILE* 3.7 18.4 - - + +
10A HIS 4.2 3.0 + - - -
11A THR* 5.7 0.4 - - - +
38A MET* 4.1 3.1 - - - +
54A PHE* 3.5 17.3 - - - -
57A TYR* 3.7 18.9 - - - -
58A SER* 2.8 35.8 + - - -
61A LEU* 3.7 18.4 - - + +
82A ALA* 2.9 33.8 + - - +
84A LEU* 1.3 75.5 - - - +
86A ILE* 1.3 58.8 + - - +
88A ILE* 3.8 1.6 - - - +
89A ALA* 2.9 29.8 + - - +
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Residues in contact with ILE 86 (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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9A ILE* 5.6 0.7 - - + -
76A ILE* 3.7 42.6 - - + +
78A GLY* 3.8 14.8 - - - +
82A ALA 3.1 13.1 + - - +
83A GLY* 3.6 6.5 - - - +
85A ASN* 1.3 74.5 - - + +
87A ALA* 1.3 63.4 + - - +
89A ALA* 3.2 5.8 + - - +
90A ALA* 2.9 24.7 + - + +
97A ILE* 5.6 1.6 - - + -
100A GLY* 4.2 16.4 - - - -
101A VAL 3.6 27.6 - - - +
102A PHE* 4.1 27.1 - - + -
195A TYR* 4.6 6.1 - - + -
198A ILE* 4.7 7.2 - - + -
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Residues in contact with ALA 87 (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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83A GLY 3.0 14.2 + - - +
84A LEU 3.7 4.0 - - - +
85A ASN 3.4 0.2 - - - -
86A ILE* 1.3 78.3 - - - +
88A ILE* 1.3 61.5 + - - +
90A ALA* 3.5 0.9 + - - +
91A ASP* 3.3 20.1 + - - +
108A PRO* 4.1 2.5 - - + -
190A PHE* 3.5 48.6 - - + -
195A TYR* 3.6 26.5 - - + +
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Residues in contact with ILE 88 (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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54A PHE* 3.5 41.1 - - + +
55A ASP* 3.2 33.0 - - - +
58A SER* 3.5 16.2 - - - +
62A LEU* 4.2 13.0 - - + +
84A LEU* 2.9 28.1 + - + +
85A ASN 3.8 4.0 - - - +
87A ALA* 1.3 71.9 - - - +
89A ALA* 1.3 62.7 + - - +
91A ASP* 3.7 8.7 + - - +
92A ARG* 3.5 27.5 + - - +
184A LEU* 5.1 2.0 - - + -
187A ARG* 3.9 7.3 + - - +
190A PHE* 3.8 20.0 - - + -
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Residues in contact with ALA 89 (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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58A SER* 6.0 0.2 - - - -
61A LEU* 3.9 13.7 - - + -
62A LEU* 3.7 13.4 - - + +
65A LEU* 3.6 25.8 - - + -
76A ILE* 4.2 8.3 - - + -
85A ASN 2.9 17.9 + - - +
86A ILE 3.6 3.6 - - - +
88A ILE* 1.3 77.0 - - - +
90A ALA* 1.3 49.2 + - - +
92A ARG* 3.0 6.6 + - - +
93A TYR* 2.8 35.3 + - - +
97A ILE* 4.0 1.8 - - - -
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Residues in contact with ALA 90 (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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86A ILE* 2.9 20.7 + - + +
87A ALA 4.0 1.3 - - - +
88A ILE 3.5 0.2 - - - -
89A ALA* 1.3 67.2 - - - +
91A ASP* 1.3 57.5 + - - +
92A ARG 2.9 10.7 + - - -
94A VAL* 3.0 26.9 + - - +
97A ILE* 3.5 15.7 - - + +
194A GLY* 3.5 1.7 - - - -
195A TYR* 3.7 23.6 - - + -
198A ILE* 3.4 30.1 - - + -
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Residues in contact with ASP 91 (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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87A ALA 3.3 12.8 + - - +
88A ILE* 4.0 6.1 - - - +
89A ALA 3.4 0.6 - - - -
90A ALA* 1.3 73.6 - - - +
92A ARG* 1.3 66.3 + - - +
94A VAL* 6.1 0.4 - - - -
187A ARG* 4.7 7.2 + - - +
189A LYS 4.3 0.9 - - - +
190A PHE* 3.3 17.7 - - - -
191A THR* 3.0 44.5 + - + +
194A GLY* 4.2 5.4 - - - -
195A TYR* 2.9 26.8 + - - +
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Residues in contact with ARG 92 (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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55A ASP* 3.2 29.3 + - - +
62A LEU* 3.7 22.0 - - + +
88A ILE* 3.5 23.7 + - - +
89A ALA 3.0 7.8 + - - +
91A ASP* 1.3 83.6 + - - +
93A TYR* 1.3 94.1 + - + +
94A VAL* 3.7 2.7 - - - -
95A ASP* 3.4 10.6 - - - +
187A ARG* 4.7 4.0 - - - +
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Residues in contact with TYR 93 (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 LEU* 3.5 40.8 + - + +
65A LEU* 3.6 27.6 - - + -
66A GLU* 2.9 42.9 + - - +
89A ALA 2.8 13.2 + - - +
90A ALA 3.9 0.7 - - - -
92A ARG* 1.3 102.1 - - + +
94A VAL* 1.3 64.4 + - - +
95A ASP* 3.0 20.0 - - - +
96A LYS* 2.8 34.0 + - + -
97A ILE* 3.4 12.4 - - + +
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Residues in contact with VAL 94 (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 LYS* 5.1 1.6 - - - -
90A ALA 3.0 18.9 + - - +
91A ASP 6.1 0.2 - - - -
92A ARG 3.7 1.1 - - - +
93A TYR* 1.3 73.4 - - - +
95A ASP* 1.3 77.5 + - + +
97A ILE* 3.1 23.1 + - - +
193A LYS* 3.7 10.3 - - + +
194A GLY* 3.5 6.7 - - - +
197A SER* 3.4 22.7 - - - +
198A ILE* 3.4 27.8 - - + -
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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