Contacts of the helix formed by residues 78 - 91 (chain G) in PDB entry 2PGW
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 78 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127E GLN* 3.1 26.0 + - - +
130E GLY 3.4 6.3 - - - -
131E GLY* 3.7 11.9 - - - -
132E ALA* 4.2 4.2 + - - -
352E ARG* 4.7 4.1 + - - -
74G HIS* 5.7 0.9 - - - +
75G SER* 3.1 25.6 + - - +
77G HIS* 1.3 80.9 - - - +
79G VAL* 1.3 62.6 + - - +
80G ALA 3.3 2.5 - - - -
81G PRO* 3.1 12.3 - - + +
82G LEU* 3.0 34.5 + - + +
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Residues in contact with VAL 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E GLY* 3.8 8.3 - - - +
76G PRO 4.2 0.4 - - - +
77G HIS 4.8 0.7 - - - -
78G ASP* 1.3 77.7 - - - +
80G ALA* 1.3 69.6 + - - +
82G LEU* 3.7 1.9 - - - +
83G ILE* 2.9 39.2 + - + +
110G ASP* 3.4 22.4 - - - +
113G MSE 3.7 44.9 - - + +
114G TRP* 3.9 20.0 - - + +
117G GLN* 3.6 23.1 - - - +
279G GLN* 4.4 1.8 - - - +
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Residues in contact with ALA 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E GLY* 3.0 14.5 + - - +
133E HIS* 3.7 20.3 - - + +
79G VAL* 1.3 80.3 - - - +
81G PRO* 1.3 69.5 - - + +
83G ILE* 3.3 5.2 + - - +
84G ALA* 3.0 21.8 + - - +
279G GLN* 3.3 24.9 - - - +
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Residues in contact with PRO 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLY 3.2 13.0 - - - +
131E GLY* 4.1 6.1 - - - -
132E ALA 3.3 27.4 - - - +
133E HIS* 3.7 25.1 - - + +
78G ASP* 3.1 32.5 - - + +
80G ALA* 1.3 87.8 - - + +
82G LEU* 1.3 55.2 + - + +
84G ALA* 3.3 4.5 + - + +
85G ARG* 2.9 30.3 + - - +
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Residues in contact with LEU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ILE* 5.3 0.7 - - + -
71G LEU* 4.1 21.5 - - + -
74G HIS* 3.7 41.5 - - + +
75G SER 3.6 22.7 - - - +
78G ASP* 3.0 35.4 + - + +
79G VAL* 3.7 4.3 - - - +
81G PRO* 1.3 76.0 - - + +
83G ILE* 1.3 63.0 + - - +
85G ARG* 3.2 22.6 + - - +
86G ILE* 2.9 30.1 + - + +
113G MSE 4.1 12.1 - - + -
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Residues in contact with ILE 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G LEU* 5.7 1.8 - - + -
79G VAL* 2.9 40.3 + - + +
80G ALA* 3.8 4.7 - - - +
82G LEU* 1.3 77.4 - - + +
84G ALA* 1.3 59.2 + - - +
86G ILE* 3.3 4.9 + - + +
87G PHE* 2.9 29.7 + - + +
106G PHE* 3.5 49.3 - - + +
109G ILE* 4.5 9.2 - - + -
110G ASP* 4.0 28.5 - - + +
276G GLY 5.2 1.8 - - - +
280G PRO* 6.5 0.7 - - + -
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Residues in contact with ALA 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E HIS* 4.9 9.2 - - + +
318E PRO* 6.5 0.4 - - + -
80G ALA 3.0 14.3 + - - +
81G PRO* 3.5 12.1 - - + +
82G LEU 3.2 0.2 - - - -
83G ILE* 1.3 78.8 - - - +
85G ARG* 1.3 57.0 + - - +
87G PHE* 3.3 9.1 + - - +
88G HIS* 2.9 30.4 + - - +
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Residues in contact with ARG 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.5 30.3 + - + +
70G HIS* 3.5 43.4 + - - +
74G HIS* 3.7 20.1 + - - -
81G PRO 2.9 17.4 + - - +
82G LEU* 3.2 18.1 + - - +
84G ALA* 1.3 76.6 - - - +
86G ILE* 1.3 64.9 + - - +
88G HIS* 3.2 1.8 + - - -
89G GLN* 2.8 52.2 + - - +
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Residues in contact with ILE 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G LEU* 3.6 40.8 - - + +
70G HIS* 3.7 32.8 - - + -
71G LEU* 3.9 23.1 - - + -
82G LEU* 2.9 24.2 + - + +
83G ILE* 3.7 7.4 - - + +
85G ARG* 1.3 84.6 - - - +
87G PHE* 1.3 58.1 + - - +
89G GLN* 4.5 4.7 - - - +
90G GLU* 2.8 32.1 + - + +
106G PHE* 3.7 23.1 - - + -
109G ILE* 5.7 2.5 - - + -
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Residues in contact with PHE 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A TRP* 3.9 28.5 - + - -
83G ILE* 2.9 20.1 + - + +
84G ALA* 3.6 8.5 - - - +
86G ILE* 1.3 75.6 - - - +
88G HIS* 1.3 61.6 + - + +
91G TYR* 3.0 57.1 + + + +
92G LEU* 3.2 29.2 + - + -
96G ALA 4.9 0.2 - - - -
98G ILE 4.6 2.0 - - - -
99G MSE 3.9 29.8 - - + -
102G ALA* 3.5 24.9 - - + -
106G PHE* 3.7 15.1 - + + -
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Residues in contact with HIS 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 3.9 18.2 + - - -
26A TYR* 3.3 37.8 - + - +
198A ASN* 6.4 0.2 - - - -
84G ALA 2.9 16.8 + - - +
85G ARG* 4.5 0.2 - - - -
87G PHE* 1.3 77.1 - - + +
89G GLN* 1.3 57.3 + - - +
92G LEU* 3.5 34.9 - - + +
93G GLY* 2.8 34.1 + - - -
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Residues in contact with GLN 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TRP* 3.3 19.1 - - + -
26A TYR* 3.5 43.6 - - + +
70G HIS* 3.5 27.3 - - - -
85G ARG* 2.8 41.3 + - - +
86G ILE* 3.9 3.6 - - - +
88G HIS* 1.3 78.9 - - - +
90G GLU* 1.3 65.0 + - + +
94G HIS* 3.1 24.6 + - - -
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Residues in contact with GLU 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 3.7 3.8 - - - +
55A PRO* 3.6 24.2 - - + +
66G ARG* 2.8 51.3 + - - +
67G LEU* 3.9 23.1 - - + -
70G HIS* 2.8 38.8 + - + +
86G ILE 2.8 19.2 + - - +
89G GLN* 1.3 83.5 + - + +
91G TYR* 1.3 62.7 + - + +
94G HIS* 3.6 16.6 + - - -
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Residues in contact with TYR 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PRO* 3.6 36.4 - - + +
63G ILE* 3.8 6.8 - - - +
67G LEU* 3.8 33.3 - - + +
86G ILE 4.5 0.2 - - - -
87G PHE* 3.0 39.0 + + + +
89G GLN 3.5 0.4 - - - -
90G GLU* 1.3 84.1 - - + +
92G LEU* 1.3 66.3 + - - +
93G GLY 3.3 1.6 - - - -
94G HIS* 3.0 14.0 + - - +
96G ALA* 3.1 31.0 + - + +
98G ILE* 3.6 36.3 - - + -
101G ALA* 4.4 2.1 + - + -
102G ALA* 3.8 28.8 - - + -
105G ILE* 4.0 5.2 - - - +
106G PHE* 4.2 3.6 - + - -
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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