Contacts of the helix formed by residues 70 - 81 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.6 30.3 - - + -
34A PRO* 3.8 17.2 - - + +
37A MET* 5.8 0.9 - - - -
65A LEU* 3.6 16.5 - - + +
67A ASN* 3.0 17.3 + - - +
68A GLY 2.9 1.2 - - - -
69A HIS* 1.3 79.3 - - + +
71A VAL* 1.3 56.7 + - - +
72A ALA 3.1 3.1 - - - -
73A LEU* 2.9 30.8 + - + +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 3.6 9.4 - - - -
68A GLY 2.9 14.4 + - - +
69A HIS 3.0 4.6 - - - +
70A ALA* 1.3 76.2 - - - +
72A ALA* 1.3 65.8 + - - +
74A LEU* 2.9 6.0 + - + -
75A TYR* 2.9 57.2 + - + +
93A PHE* 3.6 23.1 - - + -
102A GLY 3.4 26.5 - - - +
104A PRO* 3.4 24.2 - - + -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.9 18.7 - - + +
22A THR* 4.6 11.8 + - + -
23A VAL* 3.8 29.6 - - + -
30A HIS 4.6 1.6 - - - +
34A PRO* 4.4 8.3 - - + -
69A HIS 4.7 0.8 + - - +
70A ALA 3.0 1.4 + - - -
71A VAL* 1.3 83.5 - - - +
73A LEU* 1.3 57.0 + - - +
75A TYR* 4.0 9.9 - - - +
76A SER* 2.8 32.8 + - - -
93A PHE* 4.7 5.6 - - + -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.5 29.6 - - + -
19A ALA* 4.5 2.2 - - + -
33A ALA 5.2 0.4 - - - -
34A PRO* 3.9 29.7 - - + +
37A MET* 3.8 35.9 - - + +
38A ALA* 4.1 2.0 - - - -
41A ALA* 3.9 21.5 - - + -
63A PHE* 6.1 1.1 - - + -
65A LEU* 5.1 7.0 - - + -
70A ALA* 2.9 14.5 + - + +
72A ALA* 1.3 78.0 - - - +
74A LEU* 1.3 59.7 + - - +
76A SER* 3.3 4.2 + - - -
77A MET* 3.0 35.4 + - + +
154A PHE* 4.3 11.7 - - + -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 3.7 30.7 - - + -
63A PHE* 4.1 15.3 - - + -
65A LEU* 4.1 25.5 - - + +
70A ALA 3.8 0.8 + - - -
71A VAL* 2.9 12.0 + - + +
73A LEU* 1.3 80.9 - - - +
75A TYR* 1.3 58.1 + - + +
77A MET* 3.2 4.4 + - - +
78A LEU* 2.8 49.4 + - + +
104A PRO* 4.1 29.4 - - + -
110A GLY 4.6 5.6 - - - +
111A VAL* 4.1 18.8 - - + -
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 5.4 3.6 - - + -
71A VAL* 2.9 41.6 + - + +
72A ALA* 4.0 5.8 - - - +
74A LEU* 1.3 77.6 - - + +
76A SER* 1.3 62.1 + - - +
78A LEU* 3.4 3.3 + - + -
79A HIS* 3.0 24.9 + - - +
85A LEU* 3.6 21.0 - - + +
90A LEU* 3.6 20.1 - - + +
93A PHE* 3.7 18.4 - + - -
100A THR* 3.6 29.4 - - + -
101A PRO* 2.8 43.7 + - - +
103A HIS 3.8 5.5 + - - -
104A PRO* 4.3 2.9 - - + +
105A GLU 4.8 0.7 + - - -
108A LEU* 3.6 25.3 - - + +
111A VAL* 4.9 6.3 - - + -
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.4 17.9 - - - -
18A LEU* 3.6 25.6 - - - +
19A ALA* 3.4 21.7 + - - -
22A THR* 4.7 0.7 + - - -
72A ALA 2.8 22.4 + - - -
73A LEU* 3.5 7.6 - - - -
75A TYR* 1.3 77.8 - - - +
77A MET* 1.3 57.1 + - - +
79A HIS* 3.4 1.6 + - - +
80A LEU* 2.9 38.3 + - - +
90A LEU* 4.4 4.0 - - - +
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Residues in contact with MET 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.4 40.2 - - + -
41A ALA* 3.7 43.7 - - + +
42A HIS* 4.2 1.3 - - - +
45A TRP* 3.7 42.8 - - + -
73A LEU* 3.0 23.0 + - + +
74A LEU* 3.2 5.1 + - - +
76A SER* 1.3 72.7 - - - +
78A LEU* 1.3 60.1 + - - +
80A LEU* 4.6 2.5 - - - -
81A THR* 2.7 45.8 + - + +
297A TYR* 4.2 10.5 - - + +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 3.6 20.0 - - + -
74A LEU* 2.8 37.6 + - + +
75A TYR* 3.7 6.1 - - + +
77A MET* 1.3 79.0 - - - +
79A HIS* 1.3 60.3 + - - +
82A GLY 3.5 1.4 + - - -
83A TYR* 3.0 65.6 + - + +
85A LEU* 3.9 14.1 - - + -
108A LEU* 4.1 26.0 - - + -
109A PRO 4.1 8.5 - - - +
110A GLY* 4.0 15.3 - - - +
111A VAL* 4.2 5.4 - - + -
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Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.4 3.8 - - + -
75A TYR 3.0 17.4 + - - +
76A SER 3.8 2.2 - - - +
78A LEU* 1.3 79.2 - - - +
80A LEU* 1.3 79.7 + - + +
81A THR 3.3 0.3 + - - -
82A GLY* 3.4 9.9 + - - -
83A TYR 4.5 1.3 + - - +
85A LEU* 2.7 34.8 + - + +
86A SER* 3.7 7.5 - - - -
87A ILE* 3.4 42.0 - - + +
90A LEU* 4.5 10.5 - - + -
289A VAL* 4.5 0.2 - - + -
294A TYR* 2.7 36.7 + + - -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 4.1 11.7 - - + -
15A ILE* 3.6 40.6 - - + -
18A LEU* 4.0 13.5 - - + -
76A SER 2.9 27.2 + - - +
77A MET* 4.1 4.0 - - - +
79A HIS* 1.3 77.8 - - + +
81A THR* 1.3 62.2 + - + +
82A GLY 3.6 0.5 + - - -
289A VAL* 3.5 44.0 - - + -
293A VAL* 4.3 6.1 - - + -
294A TYR* 4.2 15.2 - - + -
297A TYR* 3.4 33.4 - - + +
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 3.5 15.9 - - + -
52A PRO* 3.3 16.9 - - - +
77A MET* 2.7 34.4 + - + +
80A LEU* 1.3 78.3 - - + +
82A GLY* 1.3 57.0 + - - +
83A TYR* 3.4 23.1 - - - -
297A TYR* 4.1 18.9 - - + +
301A ILE* 3.6 38.5 - - + +
302A LEU* 4.1 11.9 + - - +
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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