Contacts of the helix formed by residues 70 - 81 (chain B) in PDB entry 1GPU
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B HIS 4.7 0.2 - - - -
33B ALA* 3.6 29.8 - - + -
34B PRO* 3.8 16.7 - - + +
37B MET* 5.8 1.1 - - - -
65B LEU* 3.6 17.1 - - + +
67B ASN* 3.0 17.4 + - - +
68B GLY 2.9 1.6 - - - -
69B HIS* 1.3 78.7 - - + +
71B VAL* 1.3 57.3 + - - +
72B ALA 3.1 3.6 - - - -
73B LEU* 2.9 31.0 + - + +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.7 9.0 - - - -
68B GLY 2.9 14.2 + - - +
69B HIS 3.0 4.4 - - - +
70B ALA* 1.3 75.7 - - - +
72B ALA* 1.3 69.3 + - - +
73B LEU 3.0 0.2 - - - -
74B LEU* 2.9 6.3 + - + +
75B TYR* 2.9 57.2 + - + +
93B PHE* 3.6 22.9 - - + -
101B PRO 4.1 0.4 - - - +
102B GLY 3.4 26.9 - - - +
104B PRO* 3.5 23.8 - - + -
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA* 3.8 19.0 - - + +
22B THR* 4.5 11.5 + - + -
23B VAL* 3.7 29.6 - - + -
30B HIS 4.7 1.3 - - - +
34B PRO* 4.4 7.6 - - + -
69B HIS 4.7 0.6 + - - -
70B ALA 3.0 2.0 + - - -
71B VAL* 1.3 81.4 - - - +
73B LEU* 1.3 57.2 + - - +
75B TYR* 3.6 10.7 + - - +
76B SER* 2.8 32.7 + - - -
93B PHE* 4.7 5.6 - - + -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.4 30.1 - - + -
19B ALA* 4.4 2.5 - - + -
33B ALA 4.7 0.4 - - - +
34B PRO* 3.8 30.5 - - + +
37B MET* 3.7 35.9 - - + +
38B ALA* 4.2 2.0 - - - -
41B ALA* 3.9 20.6 - - + -
63B PHE* 6.0 1.3 - - + -
65B LEU* 5.1 7.4 - - + -
70B ALA* 2.9 15.0 + - + +
72B ALA* 1.3 77.6 - - - +
74B LEU* 1.3 60.2 + - - +
76B SER* 3.3 4.0 + - - -
77B MET* 3.0 35.2 + - + +
154B PHE* 4.2 11.7 - - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 3.6 30.3 - - + -
63B PHE* 4.0 16.6 - - + -
65B LEU* 4.2 26.0 - - + +
70B ALA 3.8 0.8 + - - -
71B VAL* 2.9 11.0 + - + +
73B LEU* 1.3 78.3 - - - +
75B TYR* 1.3 61.1 + - + +
77B MET* 3.2 4.5 + - - +
78B LEU* 2.9 48.1 + - + +
104B PRO* 4.1 28.5 - - + -
110B GLY 4.7 5.2 - - - +
111B VAL* 4.2 19.3 - - + -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 5.3 3.1 - - + -
71B VAL* 2.9 36.7 + - + +
72B ALA* 4.0 5.6 - - - +
74B LEU* 1.3 76.7 - - + +
76B SER* 1.3 62.7 + - - +
78B LEU* 3.4 4.0 + - + -
79B HIS* 3.0 24.6 + - - +
85B LEU* 3.7 19.9 - - + +
90B LEU* 3.5 20.3 - - + +
93B PHE* 3.7 17.3 - + - -
100B THR* 3.5 31.9 - - + -
101B PRO* 2.8 46.9 + - - +
103B HIS 3.8 3.6 + - - -
104B PRO* 4.2 2.8 - - + +
105B GLU 4.8 0.9 + - - -
108B LEU* 3.8 23.5 - - + +
111B VAL* 4.9 7.2 - - + -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 4.4 18.2 - - - -
18B LEU* 3.6 23.8 + - - +
19B ALA* 3.4 22.5 + - - -
22B THR* 4.7 0.5 + - - -
72B ALA 2.8 21.7 + - - -
73B LEU* 3.4 7.9 - - - -
74B LEU 3.2 0.2 - - - -
75B TYR* 1.3 76.2 - - - +
77B MET* 1.3 57.3 + - - +
79B HIS* 3.4 2.1 + - - +
80B LEU* 2.9 37.4 + - - +
90B LEU* 4.4 3.8 - - - +
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Residues in contact with MET 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.3 43.1 - - + -
41B ALA* 3.7 41.5 - - + +
42B HIS* 4.2 1.3 - - - -
45B TRP* 3.8 41.3 - - + +
73B LEU* 3.0 22.6 + - + +
74B LEU* 3.2 4.2 + - - +
76B SER* 1.3 73.6 - - - +
78B LEU* 1.3 59.3 + - - +
80B LEU* 4.6 2.5 - - - -
81B THR* 2.7 46.9 + - + +
297B TYR* 4.1 11.0 - - + +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 3.7 15.7 - - + -
74B LEU* 2.9 36.9 + - + +
75B TYR* 3.7 6.3 - - + +
77B MET* 1.3 78.6 - - - +
79B HIS* 1.3 59.7 + - - +
82B GLY 3.5 1.2 + - - -
83B TYR* 2.9 70.5 + - + +
85B LEU* 3.9 13.5 - - + -
108B LEU* 4.1 26.5 - - + -
109B PRO 4.2 6.7 - - - +
110B GLY* 3.8 16.8 - - - +
111B VAL* 4.2 6.5 - - + -
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Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.4 3.1 - - + -
75B TYR 3.0 16.7 + - - +
76B SER 3.7 2.5 - - - +
78B LEU* 1.3 77.8 - - - +
80B LEU* 1.3 78.2 + - + +
81B THR 3.3 0.7 + - - -
82B GLY* 3.4 9.4 + - - -
83B TYR 4.5 1.7 + - - +
85B LEU* 2.7 34.7 + - + +
86B SER* 3.7 7.3 - - - -
87B ILE* 3.5 40.6 - - + +
90B LEU* 4.4 11.0 - - + -
289B VAL* 4.5 0.2 - - + -
294B TYR* 2.6 37.8 + + - -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 5.1 0.2 - - - +
14B THR* 4.1 12.6 - - + -
15B ILE* 3.6 40.6 - - + -
18B LEU* 4.0 11.2 - - + -
76B SER 2.9 26.9 + - - +
77B MET* 4.1 4.5 - - - +
79B HIS* 1.3 78.8 - - + +
81B THR* 1.3 59.2 + - + +
82B GLY 3.6 0.7 + - - -
289B VAL* 3.6 42.4 - - + -
293B VAL* 4.3 7.6 - - + -
294B TYR* 4.2 16.0 - - + -
297B TYR* 3.3 35.1 - - + +
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 3.6 16.8 - - + -
52B PRO* 3.3 17.3 - - - +
77B MET* 2.7 32.5 + - + +
80B LEU* 1.3 77.7 - - + +
82B GLY* 1.3 58.0 + - - +
83B TYR* 3.4 22.7 - - - -
297B TYR* 4.2 17.7 - - + +
301B ILE* 3.6 37.7 - - + +
302B LEU* 4.1 12.7 + - - +
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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
------------------------------------------------------------
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