Contacts of the helix formed by residues 82 - 96 (chain A) in PDB entry 1GEY
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 ARG 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A SER* 1.3 71.4 - - - +
83A GLY* 1.3 64.5 + - - +
85A ASP* 4.6 1.2 - - - +
86A GLU* 2.9 43.0 + - - +
222A ARG* 3.1 42.2 + - + +
244A PRO 4.3 13.4 + - - +
245A LEU* 4.2 3.4 - - + +
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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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81A SER* 2.9 27.7 + - - -
82A ARG* 1.3 75.0 - - - +
84A ALA* 1.3 62.1 + - - -
85A ASP 3.0 5.8 - - - -
86A GLU 3.4 2.9 + - - -
87A GLY 3.6 0.2 + - - -
222A ARG* 3.2 9.9 + - - -
223A CYS 3.8 6.1 - - - -
224A GLY* 3.2 18.4 - - - +
413A PPE 3.4 17.3 - - - -
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Residues in contact with ALA 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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83A GLY* 1.3 71.4 - - - -
85A ASP* 1.3 59.4 + - - +
86A GLU 3.3 0.4 - - - -
87A GLY* 3.1 5.7 + - - +
88A ILE* 3.0 31.9 + - - +
184A ASP* 5.0 1.1 - - - +
186A ALA* 5.3 0.4 - - + -
209A LEU* 4.2 21.6 - - + +
210A ARG 3.7 19.1 - - - +
211A THR* 4.4 4.5 - - + -
224A GLY* 4.0 2.9 - - - -
225A PHE 5.2 2.2 - - - +
413A PPE 2.9 38.2 + - + +
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Residues in contact with ASP 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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82A ARG 4.6 2.0 - - - +
83A GLY 3.0 0.4 - - - -
84A ALA* 1.3 75.7 - - - +
86A GLU* 1.3 65.2 + - - +
88A ILE* 3.3 15.7 + - - +
89A GLU* 3.3 16.2 + - - +
110A TYR* 3.0 37.6 + - - -
112A MET* 3.6 24.4 - - + +
116A SER* 4.8 1.9 + - - -
222A ARG* 4.0 12.4 + - - +
413A PPE 3.2 22.6 + - - +
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Residues in contact with GLU 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 SER* 3.5 12.9 - - - +
82A ARG* 2.9 66.9 + - + +
83A GLY 3.4 4.3 + - - +
84A ALA 3.3 0.4 - - - -
85A ASP* 1.3 78.2 - - - +
87A GLY* 1.3 57.6 + - - +
89A GLU* 3.2 10.6 + - + +
90A LEU* 2.9 45.5 + - + +
93A ARG* 5.2 5.9 + - - +
240A ILE* 4.8 9.2 - - - +
241A ALA* 5.1 7.6 + - - +
244A PRO* 4.0 13.0 - - - +
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Residues in contact with GLY 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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81A SER* 3.9 7.3 + - - -
83A GLY 3.6 3.2 + - - -
84A ALA* 3.1 12.0 + - - -
86A GLU* 1.3 79.9 - - - +
88A ILE* 1.3 60.1 + - - +
90A LEU* 3.6 8.1 + - - +
91A LEU* 3.3 29.8 + - - +
209A LEU* 3.9 9.6 - - - -
225A PHE 6.3 0.2 - - - -
226A THR* 4.0 18.5 + - - -
236A LEU* 5.7 0.2 - - - +
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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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84A ALA 3.0 19.2 + - - +
85A ASP* 3.5 25.6 - - - +
86A GLU 3.2 0.4 - - - -
87A GLY* 1.3 77.5 - - - +
89A GLU* 1.3 62.6 + - - +
91A LEU* 3.7 1.1 + - - -
92A ILE* 3.5 10.5 + - + +
110A TYR* 4.0 11.4 - - + -
112A MET* 4.3 9.4 - - + +
113A TYR* 3.6 35.2 - - + -
116A SER* 4.1 17.7 - - - +
151A TYR* 2.6 46.2 + - + +
184A ASP* 4.5 2.5 - - - +
209A LEU* 3.5 19.3 - - + -
413A PPE 4.6 1.1 - - + -
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Residues in contact with GLU 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 ASP 3.3 9.2 + - - +
86A GLU* 3.2 13.3 + - - +
88A ILE* 1.3 78.3 - - - +
90A LEU* 1.3 65.6 + - - +
92A ILE* 3.1 6.7 + - - +
93A ARG* 2.9 51.4 + - + +
112A MET* 6.0 1.5 - - + +
116A SER* 3.4 32.6 + - - +
119A THR* 5.3 7.8 - - - +
120A ILE* 4.7 13.4 - - + +
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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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79A LEU* 3.9 31.4 - - + -
81A SER* 4.7 1.1 - - - -
86A GLU* 2.9 36.0 + - + +
87A GLY* 3.7 10.3 - - - +
89A GLU* 1.3 75.3 - - - +
91A LEU* 1.3 57.2 + - - +
93A ARG* 3.2 32.6 + - - +
94A ALA* 2.9 32.7 + - - +
236A LEU* 3.7 16.0 - - + +
239A VAL* 3.9 14.1 - - + +
240A ILE* 3.9 31.6 - - + -
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLY 3.3 18.3 + - - +
88A ILE 3.9 0.2 - - - +
89A GLU 3.2 0.6 - - - -
90A LEU* 1.3 76.3 - - - +
92A ILE* 1.3 57.8 + - - +
95A PHE* 3.1 49.1 + - + +
149A VAL* 4.0 10.9 - - + +
151A TYR* 3.8 16.8 - - + +
180A ILE* 4.5 6.7 - - + -
182A VAL* 3.6 37.5 - - + -
207A ALA* 4.4 18.2 - - + -
209A LEU* 4.2 9.2 - - + -
226A THR* 5.1 2.7 - - + -
232A VAL* 4.8 2.5 - - + -
236A LEU* 4.1 28.5 - - + -
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Residues in contact with ILE 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 ILE* 3.5 7.9 - - + +
89A GLU 3.1 6.2 + - - +
91A LEU* 1.3 74.7 - - - +
93A ARG* 1.3 62.4 + - - +
96A CYS* 3.0 41.6 + - + +
103A ILE* 3.8 15.0 - - + -
113A TYR 4.3 5.6 - - - +
116A SER* 3.9 25.8 - - - -
117A ALA* 3.9 16.2 - - + +
120A ILE* 3.8 19.6 - - + +
122A VAL* 3.9 29.4 - - + -
149A VAL* 5.4 0.2 - - + -
151A TYR* 3.2 25.1 - - + +
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Residues in contact with ARG 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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86A GLU* 5.2 5.7 + - - +
89A GLU* 2.9 45.6 + - - +
90A LEU* 3.7 25.2 - - - +
92A ILE* 1.3 75.9 - - - +
94A ALA* 1.3 60.6 + - - +
96A CYS 4.7 5.0 - - - +
120A ILE* 3.8 24.7 - - + -
239A VAL* 2.7 45.0 + - + +
240A ILE* 4.4 3.6 - - - +
241A ALA* 4.8 3.2 - - - +
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Residues in contact with ALA 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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90A LEU 2.9 16.7 + - - +
93A ARG* 1.3 79.3 - - - +
95A PHE* 1.3 73.9 + - + +
96A CYS 3.9 0.2 - - - -
235A LEU* 4.4 12.7 - - + +
236A LEU* 3.8 20.4 - - + -
239A VAL* 4.0 20.2 - - + +
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Residues in contact with PHE 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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91A LEU* 3.1 43.9 + - + +
94A ALA* 1.3 93.5 - - + +
96A CYS* 1.3 59.7 + - - +
101A ASP* 3.3 1.7 - - - +
148A LYS* 3.1 41.0 + - + +
149A VAL* 4.1 14.6 - - + -
180A ILE* 4.0 36.3 - - + -
232A VAL* 4.3 15.5 - - + -
235A LEU* 3.8 32.5 - - + -
236A LEU* 4.4 6.3 - - + -
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Residues in contact with CYS 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 ILE* 3.0 24.8 + - + +
93A ARG* 4.7 4.7 - - - +
94A ALA 3.9 0.6 - - - -
95A PHE* 1.3 76.9 - - - +
97A GLU* 1.3 61.8 + - - +
98A PRO* 3.4 10.0 - - - +
101A ASP* 3.6 9.2 - - + -
102A ALA 4.1 4.0 - - - -
103A ILE* 3.0 36.8 - - - -
120A ILE* 5.6 0.9 - - - +
122A VAL* 3.6 21.4 - - + +
148A LYS* 3.8 20.9 - - - -
149A VAL* 3.9 9.2 - - - -
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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