Contacts of the helix formed by residues 84 - 98 (chain G) in PDB entry 2W8B
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 PHE 84 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277D SER* 4.2 6.3 - - - -
279D GLN* 3.4 37.7 - - + -
70G ILE 3.4 26.0 - - - -
71G VAL* 3.8 30.7 - - + -
72G TYR* 3.5 43.1 - + + -
80G ILE* 4.6 4.0 - - + -
81G ARG* 3.1 24.9 + - + +
82G SER 3.0 1.2 - - - -
83G ASP* 1.3 81.9 - - + +
85G ALA* 1.3 58.6 + - - +
86G GLN 3.5 1.6 - - - -
87G MET* 3.5 14.3 + - + +
88G LEU* 2.9 33.9 + - - +
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Residues in contact with ALA 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G ILE* 5.2 0.9 - - + -
81G ARG 3.9 2.5 + - - +
82G SER* 2.9 22.8 + - - +
83G ASP 3.4 0.2 - - - -
84G PHE* 1.3 73.3 - - - +
86G GLN* 1.3 62.9 + - - +
88G LEU* 3.2 2.4 + - - +
89G ASP* 2.8 37.4 + - - +
132G TYR* 3.4 27.8 + - + +
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Residues in contact with GLN 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G SER 4.4 1.2 + - - -
83G ASP 4.7 7.1 + - - +
85G ALA* 1.3 79.3 - - - +
87G MET* 1.3 74.3 + - + +
89G ASP* 2.8 22.6 + - - +
90G ALA* 3.0 12.0 + - - +
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Residues in contact with MET 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G GLN 5.4 2.7 - - - +
68G ASN* 2.8 41.5 - - + +
69G ASN* 3.6 4.0 - - - -
70G ILE 3.3 41.1 - - - +
71G VAL* 3.7 18.4 - - + -
83G ASP 5.5 1.1 - - - +
84G PHE* 3.5 20.4 + - + +
85G ALA 3.4 0.6 - - - -
86G GLN* 1.3 88.1 - - + +
88G LEU* 1.3 73.0 - - + +
90G ALA* 3.2 15.1 - - - +
91G HIS* 3.1 29.6 - - - -
171G LEU* 4.1 3.6 - - + -
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Residues in contact with LEU 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G VAL* 4.0 15.5 - - + -
80G ILE* 3.7 38.6 - - + -
84G PHE 2.9 21.7 + - - +
85G ALA 3.5 4.0 - - - +
86G GLN 3.1 0.2 - - - -
87G MET* 1.3 95.7 + - + +
89G ASP* 1.3 58.8 + - - +
91G HIS* 3.0 5.8 + - - +
92G ALA* 2.9 23.7 + - - +
129G VAL* 4.2 11.0 - - + -
132G TYR* 3.6 30.1 - - + -
133G LEU* 3.6 10.7 - - + +
171G LEU* 4.0 25.8 - - + -
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Residues in contact with ASP 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ALA* 2.8 26.3 + - - +
86G GLN* 2.8 13.0 + - - +
88G LEU* 1.3 71.9 - - - +
90G ALA* 1.3 66.7 + - - +
92G ALA* 3.1 7.0 + - - +
93G ASN* 2.8 28.0 + - - +
96G ARG* 5.2 0.3 + - - -
132G TYR* 3.0 24.5 + - - -
136G LYS* 3.1 24.9 + - - +
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Residues in contact with ALA 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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86G GLN 3.0 9.6 + - - +
87G MET* 3.2 14.4 - - - +
89G ASP* 1.3 76.7 - - - +
91G HIS* 1.3 64.6 + - + +
93G ASN* 2.8 20.9 - - - +
94G PHE* 2.9 15.3 + - - +
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Residues in contact with HIS 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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68G ASN* 2.7 33.3 + - - -
69G ASN* 3.8 17.2 - - + +
87G MET* 3.1 33.2 - - - -
88G LEU* 3.0 8.7 + - - +
90G ALA* 1.3 86.0 - - + +
92G ALA* 1.3 56.7 + - - +
94G PHE* 3.3 5.4 + - - +
95G LEU* 2.9 36.2 + - + +
133G LEU* 4.6 3.4 - - + -
171G LEU* 3.7 25.6 - - + +
173G TYR* 2.6 41.3 + + - +
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Residues in contact with ALA 92 (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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88G LEU 2.9 9.6 + - - +
89G ASP* 3.1 7.4 + - - +
91G HIS* 1.3 77.0 - - - +
93G ASN* 1.3 63.7 + - - +
95G LEU* 3.0 2.4 + - - +
96G ARG* 3.0 32.5 + - - +
133G LEU* 3.7 18.1 - - + +
136G LYS* 3.6 33.9 - - + -
138G VAL* 3.7 15.2 - - + +
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Residues in contact with ASN 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ASP 2.8 25.4 + - - +
90G ALA* 2.8 28.8 - - - +
92G ALA* 1.3 71.9 - - - +
94G PHE* 1.3 64.3 + - - +
96G ARG* 2.8 30.8 - - - +
97G SER* 2.9 34.7 + - - +
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Residues in contact with PHE 94 (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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90G ALA 2.9 18.3 + - - +
91G HIS* 3.5 6.5 - - - +
92G ALA 3.2 0.2 - - - -
93G ASN* 1.3 81.0 + - - +
95G LEU* 1.3 61.2 + - + +
97G SER* 4.6 1.6 - - - -
98G ASN* 2.8 56.9 + - - +
101G TYR* 3.7 46.7 - + + -
173G TYR* 4.2 26.9 - + - +
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Residues in contact with LEU 95 (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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91G HIS* 2.9 24.0 + - + +
92G ALA 3.0 4.0 + - - +
94G PHE* 1.3 76.5 - - + +
96G ARG* 1.3 65.5 + - - +
98G ASN 3.2 12.1 - - - -
99G PRO* 3.5 2.6 - - - +
101G TYR* 3.3 36.1 - - + +
103G VAL* 3.8 29.4 - - + +
133G LEU* 4.2 14.8 - - + -
138G VAL* 3.9 20.2 - - + -
142G GLN* 3.0 30.6 + - + +
173G TYR* 4.0 26.9 - - + +
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Residues in contact with ARG 96 (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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89G ASP 5.2 0.4 + - - -
92G ALA* 3.0 17.9 + - - +
93G ASN* 2.8 43.7 - - - +
95G LEU* 1.3 78.6 - - - +
97G SER* 1.3 63.7 + - - +
98G ASN 3.1 1.2 + - - -
99G PRO* 3.5 17.1 - - - +
136G LYS* 2.7 42.0 + - - +
137G GLY* 3.5 25.8 - - - +
138G VAL* 4.4 3.8 - - + -
142G GLN* 5.2 2.9 - - - +
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Residues in contact with SER 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G ASN* 2.9 26.9 + - - +
94G PHE* 3.9 1.6 - - - -
96G ARG* 1.3 76.7 - - - +
98G ASN* 1.3 74.4 + - - +
99G PRO* 3.7 6.5 - - - +
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Residues in contact with ASN 98 (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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94G PHE* 2.8 47.9 + - + +
95G LEU 3.2 8.0 - - - +
97G SER* 1.3 91.9 + - - +
99G PRO* 1.3 56.1 - - - +
100G SER* 3.1 3.8 - - - -
101G TYR* 2.9 55.6 + - + +
142G GLN* 3.4 0.2 - - - +
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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