Contacts of the helix formed by residues 83 - 102 (chain A) in PDB entry 4GCK
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLU* 2.5 20.7 + - - +
82A LYS* 1.3 72.6 - - - +
84A THR* 1.3 53.6 + - - +
85A THR* 3.4 10.5 + - - -
86A ALA* 3.0 29.4 + - + +
87A ARG* 2.8 36.0 + - - +
147A GLU* 3.9 12.9 - - - +
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Residues in contact with THR 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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82A LYS 3.3 4.4 + - - -
83A ASP* 1.3 73.4 + - - +
85A THR* 1.3 64.6 + - - +
87A ARG* 3.1 13.8 + - - +
88A LEU* 3.0 28.6 + - + +
139A VAL* 3.7 23.0 + - + +
142A GLU* 4.5 0.9 - - - +
143A LYS* 3.6 33.9 + - + +
146A ARG* 4.2 12.9 + - - +
147A GLU* 3.9 15.0 + - - -
151A TYR* 3.6 22.4 - - + +
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 3.4 10.2 + - - -
84A THR* 1.3 78.0 - - - +
86A ALA* 1.3 57.7 + - - +
88A LEU* 3.3 9.7 + - - +
89A ARG* 3.0 27.7 + - - +
143A LYS* 5.7 2.9 - - - -
147A GLU* 5.0 3.5 + - - -
151A TYR* 3.9 12.0 + - - -
190A TRP* 4.1 15.7 - - + +
194A ALA* 4.7 7.0 - - + -
197A LEU* 4.5 17.2 - - + +
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Residues in contact with ALA 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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81A GLU* 3.4 28.7 - - + +
83A ASP* 3.0 25.2 + - + +
85A THR* 1.3 76.1 - - - +
87A ARG* 1.3 57.6 + - - +
89A ARG* 3.4 8.8 + - - +
90A LEU* 2.9 38.8 + - + +
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Residues in contact with ARG 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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77A ILE* 4.0 15.2 - - + +
78A LEU* 2.8 61.8 + - + +
81A GLU* 2.7 30.3 + - + +
82A LYS* 3.9 8.0 + - - +
83A ASP 2.8 17.9 + - - -
84A THR* 3.2 13.1 + - - +
86A ALA* 1.3 77.7 - - - +
88A LEU* 1.3 57.1 + - - +
90A LEU* 3.2 2.9 + - - +
91A ILE* 2.9 36.2 + - - +
139A VAL* 3.9 22.5 + - + +
142A GLU* 2.8 36.8 + - - +
146A ARG* 3.3 22.0 - - - +
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Residues in contact with LEU 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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84A THR* 3.0 24.5 + - + +
85A THR* 3.5 7.2 - - - +
87A ARG* 1.3 76.3 - - - +
89A ARG* 1.3 62.3 + - - +
91A ILE* 3.3 5.5 + - + +
92A VAL* 3.0 28.1 + - - +
136A LEU* 4.3 25.5 - - + +
139A VAL* 3.3 31.0 - - + -
140A MET* 4.3 11.9 - - + -
151A TYR* 3.4 26.2 - - - +
162A LEU* 3.9 17.9 - - + -
190A TRP* 3.8 15.0 - - + -
197A LEU* 3.9 11.2 - - + -
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Residues in contact with ARG 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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85A THR 3.0 14.6 + - - +
86A ALA* 3.6 9.6 - - - +
88A LEU* 1.3 76.6 - - - +
90A LEU* 1.3 78.1 + - - +
92A VAL* 3.4 0.7 + - - +
93A LEU* 2.9 39.6 + - - +
186A PHE* 3.7 23.7 - - + -
187A GLU* 2.9 29.5 + - - -
190A TRP* 3.5 51.6 - - + +
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Residues in contact with LEU 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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77A ILE* 3.6 25.8 - - + +
81A GLU* 3.9 31.4 - - + +
86A ALA* 2.9 22.6 + - + +
87A ARG 3.7 2.9 - - - +
89A ARG* 1.3 93.6 - - - +
91A ILE* 1.3 60.1 + - - +
93A LEU* 3.8 15.7 - - + +
94A LEU* 2.8 31.4 + - - +
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Residues in contact with ILE 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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74A ILE* 3.3 44.4 - - + -
77A ILE* 4.0 15.0 - - + -
78A LEU* 4.5 6.3 - - + -
87A ARG 2.9 24.7 + - - +
88A LEU* 3.8 4.0 - - - +
90A LEU* 1.3 75.9 - - - +
92A VAL* 1.3 63.5 + - + +
94A LEU* 3.3 2.1 + - - +
95A ILE* 3.0 35.8 + - + +
132A ILE* 4.9 3.8 - - + -
135A GLN* 5.2 2.9 - - + +
136A LEU* 3.7 33.2 - - + -
139A VAL* 4.2 23.6 - - + -
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Residues in contact with VAL 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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88A LEU 3.0 19.6 + - - +
89A ARG 3.8 2.9 - - - +
91A ILE* 1.3 74.6 - - + +
93A LEU* 1.3 68.6 + - - +
95A ILE* 3.2 5.6 + - + +
96A LEU* 3.1 40.6 + - + +
136A LEU* 5.7 4.5 - - + -
162A LEU* 4.2 22.4 - - + +
165A PHE* 3.9 13.5 - - + -
166A CYS* 3.8 25.6 - - - -
186A PHE* 3.8 12.1 - - + -
190A TRP* 3.8 17.3 - - + -
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Residues in contact with LEU 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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89A ARG* 2.9 29.8 + - - +
90A LEU* 3.8 21.1 - - + +
92A VAL* 1.3 76.6 - - - +
94A LEU* 1.3 54.6 + - - +
96A LEU* 3.7 2.0 - - - -
97A GLY* 2.7 34.2 + - - -
183A THR* 4.1 18.6 - - + -
186A PHE* 3.6 45.3 - - + -
187A GLU* 5.7 0.7 - - - +
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Residues in contact with LEU 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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70A LEU* 3.9 22.0 - - + +
73A ARG* 3.6 59.7 - - + +
74A ILE* 3.2 33.2 - - + +
77A ILE* 4.2 7.9 - - + -
90A LEU 2.8 18.5 + - - +
91A ILE 3.5 3.4 - - - +
92A VAL 3.2 0.2 - - - -
93A LEU* 1.3 77.8 - - - +
95A ILE* 1.3 57.9 + - + +
97A GLY* 5.0 0.4 - - - -
98A PHE* 2.8 30.6 + - + +
101A ARG* 4.8 1.3 - - - +
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Residues in contact with ILE 95 (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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70A LEU* 4.3 23.3 - - + -
74A ILE* 5.3 2.0 - - + -
91A ILE* 3.0 26.1 + - + +
92A VAL* 3.2 6.5 + - + +
94A LEU* 1.3 78.6 - - + +
96A LEU* 1.3 60.1 + - + +
98A PHE* 3.7 2.8 - - - +
99A GLY* 3.0 25.3 + - - -
109A LEU* 5.6 3.7 - - + +
129A PHE* 5.9 4.9 - - + -
132A ILE* 3.8 36.8 - - + -
136A LEU* 5.8 1.6 - - + -
163A LEU* 4.6 6.3 - - + -
166A CYS* 4.2 32.1 - - + -
170A LEU* 4.2 20.4 - - + +
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Residues in contact with LEU 96 (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 VAL* 3.1 38.5 + - + +
93A LEU* 3.9 1.3 - - - +
95A ILE* 1.3 77.6 - - + +
97A GLY* 1.3 61.2 + - - +
99A GLY* 3.2 0.7 + - - -
100A GLU* 2.9 31.0 + - - +
165A PHE* 4.1 12.3 - - + -
166A CYS* 3.9 39.3 - - + +
169A MET* 4.2 8.7 - - + -
170A LEU* 4.5 4.9 - - + -
182A PRO* 3.5 36.2 - - + +
183A THR* 3.9 12.6 - - + -
186A PHE* 4.0 18.2 - - + -
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Residues in contact with GLY 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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93A LEU* 2.7 21.9 + - - -
94A LEU* 4.0 0.9 - - - -
96A LEU* 1.3 75.2 - - - +
98A PHE* 1.3 61.8 + - - +
100A GLU* 3.3 3.4 + - - +
101A ARG* 3.0 39.1 + - - +
183A THR* 3.7 13.6 - - - +
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Residues in contact with PHE 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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65A PHE* 4.0 7.9 - + - -
66A ILE* 4.0 38.6 - - + -
69A SER* 3.5 25.1 - - - -
70A LEU* 3.7 22.7 - - + -
73A ARG* 3.9 21.3 - - - -
94A LEU* 2.8 25.8 + - + +
95A ILE 3.7 3.4 - - - +
97A GLY* 1.3 71.1 - - - +
99A GLY* 1.3 67.4 + - - +
101A ARG* 3.6 12.6 - - - +
102A ASN* 2.8 44.1 + - + +
105A LEU* 3.8 30.5 - - + -
106A THR 6.0 0.2 - - - -
109A LEU* 4.5 11.7 - - + -
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Residues in contact with GLY 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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95A ILE 3.0 15.5 + - - -
96A LEU 3.7 2.5 - - - -
97A GLY 3.2 0.2 - - - -
98A PHE* 1.3 82.2 - - - +
100A GLU* 1.3 62.2 + - - +
102A ASN 3.1 15.6 - - - +
106A THR* 2.7 30.1 + - - -
109A LEU* 5.2 3.4 - - - -
170A LEU* 4.2 10.1 - - - -
173A PHE* 3.4 8.4 - - - -
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Residues in contact with GLU 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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96A LEU 2.9 15.7 + - - +
97A GLY* 3.7 5.4 - - - +
99A GLY* 1.3 77.6 - - - +
101A ARG* 1.3 61.6 + - - +
102A ASN 3.4 0.5 + - - -
103A PRO* 3.8 14.2 - - - +
173A PHE* 3.6 12.7 - - + -
181A ARG* 3.6 33.7 + - - +
182A PRO* 3.5 14.0 - - + +
183A THR* 2.6 49.4 + - - -
184A ASP* 5.1 1.4 - - - +
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Residues in contact with ARG 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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73A ARG* 2.7 41.1 - - - +
94A LEU* 4.8 2.4 - - - +
97A GLY* 3.0 18.9 + - - +
98A PHE* 3.6 20.7 - - - +
100A GLU* 1.3 76.9 - - - +
102A ASN* 1.3 77.1 + - - +
103A PRO* 3.7 6.6 - - - +
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Residues in contact with ASN 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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65A PHE* 4.4 7.6 - - - -
98A PHE* 2.8 45.4 + - + +
99A GLY* 3.1 4.1 + - - -
101A ARG* 1.3 95.7 - - - +
103A PRO* 1.4 67.1 - - - +
104A GLY 3.3 2.7 - - - +
105A LEU* 3.2 36.2 + - + +
106A THR* 3.0 21.0 + - - -
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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