Contacts of the strand formed by residues 95 - 102 (chain G) in PDB entry 2QC8
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 LYS 95 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G VAL* 4.7 1.1 - - + -
27G GLN 2.9 11.9 + - - +
28G ALA* 3.7 7.8 - - + -
29G MET 2.9 24.1 + - - -
50G GLU* 2.6 31.6 + - - -
51G PRO* 3.6 39.0 + - + -
84G MET* 3.9 24.1 - - + +
85G PHE 3.5 12.3 - - - +
86G ARG* 4.7 10.7 - - + +
87G ASP* 3.8 13.0 - - - +
92G ASP* 4.6 7.7 + - - -
93G PRO* 3.6 15.7 + - - +
94G ASN* 1.3 82.7 - - - +
96G LEU* 1.3 66.3 + - - +
97G VAL* 4.6 4.7 - - + -
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Residues in contact with LEU 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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29G MET* 3.6 26.0 - - + +
31G ILE* 4.2 8.5 - - + -
83G ALA 4.6 0.2 - - - -
84G MET* 3.4 3.8 - - - +
85G PHE* 2.8 42.9 + - + +
86G ARG 4.3 3.4 - - - +
87G ASP* 3.3 33.7 - - - +
88G PRO* 3.9 20.4 - - + -
89G PHE* 4.5 7.4 - - + -
95G LYS* 1.3 77.3 - - - +
97G VAL* 1.3 63.9 + - - +
98G LEU 4.2 0.2 - - - -
220G VAL* 4.4 12.3 - - + -
223G PHE* 4.4 14.1 - - + -
224G ILE* 4.1 22.4 - - + -
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Residues in contact with VAL 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ALA* 4.6 3.1 - - + -
29G MET 3.0 13.8 + - - +
30G TYR* 3.6 20.6 - - + -
31G ILE* 2.8 32.1 + - - +
57G LEU* 3.5 40.6 - - + -
81G PRO* 3.7 23.1 - - + -
83G ALA 3.4 9.9 - - - +
84G MET* 4.7 0.2 - - + -
95G LYS* 4.6 9.4 - - + -
96G LEU* 1.3 80.5 - - - +
98G LEU* 1.3 66.3 + - - +
99G CYS* 3.6 6.3 + - - -
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Residues in contact with LEU 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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31G ILE* 3.6 26.1 - - + +
32G TRP* 4.9 2.2 - - - -
33G ILE* 5.3 6.1 - - + -
40G LEU* 4.9 4.5 - - + -
81G PRO* 3.9 1.0 - - - +
82G ALA* 2.9 26.4 + - + +
83G ALA* 2.7 24.0 + - + +
96G LEU 4.2 0.4 - - - -
97G VAL* 1.3 72.3 - - - +
99G CYS* 1.3 69.7 + - - +
114G ARG* 4.9 5.6 - - - +
216G ASP* 3.8 46.9 - - + +
219G TRP* 4.3 20.9 - - + -
220G VAL* 3.8 18.9 - - + +
349G PHE* 4.5 9.4 - - + -
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Residues in contact with CYS 99 (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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30G TYR* 3.5 34.1 - - - -
31G ILE 2.8 18.7 + - - +
32G TRP* 4.2 8.9 - - - +
33G ILE* 5.0 3.8 + - - +
79G LEU* 3.6 28.9 - - + -
80G VAL 3.4 10.8 - - - +
81G PRO* 4.2 8.1 - - - -
82G ALA* 4.6 2.2 - - - -
97G VAL* 3.8 16.2 - - - -
98G LEU* 1.3 87.7 - - - +
100G GLU* 1.3 63.4 + - - +
101G VAL* 4.2 1.2 + - - +
114G ARG* 5.7 1.1 - - - -
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Residues in contact with GLU 100 (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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78G TYR 3.7 0.3 - - - +
79G LEU* 3.7 5.0 - - - -
80G VAL* 3.1 33.2 + - + +
82G ALA* 4.4 4.5 - - + +
99G CYS* 1.3 75.0 - - - +
101G VAL* 1.3 62.3 + - - +
102G PHE* 3.5 18.3 - - + -
112G ASN* 3.0 26.9 + - - +
114G ARG* 2.9 44.9 + - + +
115G HIS* 3.2 37.9 + - - +
118G LYS* 5.5 1.9 - - - +
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Residues in contact with VAL 101 (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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32G TRP* 3.9 26.2 - - + -
33G ILE* 3.7 25.4 - - + +
62G PHE* 3.9 20.6 - - + -
69G GLN* 4.4 3.1 - - - +
77G MET* 4.0 13.5 - - + -
78G TYR 3.5 9.9 - - - +
79G LEU* 4.7 1.3 - - + +
99G CYS 5.0 0.4 - - - +
100G GLU* 1.3 75.0 - - - +
102G PHE* 1.3 64.5 + - - +
109G ALA* 3.1 34.1 + - + -
111G THR* 5.8 0.7 - - - +
112G ASN* 3.0 26.6 + - + +
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Residues in contact with PHE 102 (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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77G MET* 3.6 12.3 - - - +
78G TYR* 3.0 42.6 + - + -
80G VAL* 3.7 31.6 - - + -
100G GLU* 3.5 42.2 - - + -
101G VAL* 1.3 76.3 - - - +
103G LYS* 1.3 63.4 + - - +
106G ARG* 3.6 30.3 - - - +
107G ARG 3.3 5.4 - - - +
108G PRO* 3.6 23.3 - - + -
109G ALA 4.0 0.7 - - - +
112G ASN* 4.0 1.8 - - - -
115G HIS* 3.8 23.8 - + - -
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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