Contacts of the strand formed by residues 26 - 33 (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 VAL 26 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G GLN* 4.0 0.2 - - - +
24G GLU 4.0 7.0 - - - +
25G LYS* 1.3 81.8 - - - +
27G GLN* 1.3 73.6 + - - +
46G THR* 3.3 6.3 - - - +
47G LEU* 2.7 35.7 + - + +
49G SER* 3.4 11.0 - - - +
50G GLU* 3.4 33.2 - - + +
51G PRO* 4.1 17.5 - - + -
93G PRO* 3.4 34.8 - - + +
94G ASN* 3.9 4.5 - - - -
95G LYS* 4.7 2.2 - - + -
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Residues in contact with GLN 27 (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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22G GLN* 4.1 2.8 + - - +
26G VAL* 1.3 78.6 - - - +
28G ALA* 1.3 60.4 + - - +
29G MET 4.1 0.7 - - - -
44G THR* 3.8 9.0 - - + -
45G ARG 3.5 4.3 - - - -
46G THR* 5.4 0.7 - - + +
90G ARG* 3.7 36.1 - - - +
94G ASN* 2.9 30.7 + - + +
95G LYS* 2.9 24.9 + - - +
177H GLU* 4.7 2.4 + - - -
180H TYR* 3.3 58.1 - - + +
181H ARG* 4.1 14.9 + - - +
184H LEU* 4.3 11.0 - - + +
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Residues in contact with ALA 28 (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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27G GLN* 1.3 73.5 - - - +
29G MET* 1.3 62.3 + - - +
30G TYR* 3.5 26.2 - - + -
44G THR* 3.4 4.3 - - - -
45G ARG* 2.9 33.6 + - + +
47G LEU* 3.9 26.2 - - + -
57G LEU* 4.5 8.3 - - + -
95G LYS* 3.7 9.0 - - + -
97G VAL* 4.6 4.5 - - + -
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Residues in contact with MET 29 (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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27G GLN 4.1 0.6 - - - -
28G ALA* 1.3 70.9 - - - +
30G TYR* 1.3 62.6 + - - +
31G ILE* 3.9 3.0 + - + +
42G CYS* 3.6 34.3 - - + -
43G LYS 3.5 7.0 - - - +
44G THR* 3.6 7.4 - - - +
87G ASP* 5.2 0.2 - - - +
89G PHE* 6.0 2.0 - - - -
90G ARG* 3.6 32.1 - - - +
95G LYS 2.9 13.3 + - - +
96G LEU* 3.6 13.7 - - + -
97G VAL 3.0 24.3 + - - -
223G PHE* 3.7 20.6 - - + -
227G ARG* 5.5 7.0 - - - +
708G CL 3.6 26.2 - - + -
173H ARG* 4.1 12.6 - - - +
177H GLU* 4.6 3.8 - - - +
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Residues in contact with TYR 30 (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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28G ALA* 3.5 27.1 - - + -
29G MET* 1.3 73.2 - - - +
31G ILE* 1.3 59.6 + - - +
32G TRP* 3.4 11.9 - - + -
42G CYS* 2.9 26.2 - - - +
43G LYS 2.8 15.5 + - - +
45G ARG* 3.8 21.6 + - - -
47G LEU* 5.2 0.2 - - - +
57G LEU* 3.9 8.3 - - + +
58G PRO* 2.6 48.3 + - - +
60G TRP* 3.6 38.8 - + + -
79G LEU* 4.3 5.4 - - + -
81G PRO* 4.3 14.1 - - + -
97G VAL* 3.6 15.0 - - + -
99G CYS* 3.5 22.0 - - - -
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Residues in contact with ILE 31 (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* 4.2 5.6 - - + +
30G TYR* 1.3 77.3 - - - +
32G TRP* 1.3 67.3 - - - +
40G LEU* 3.5 28.9 - - + -
41G ARG 3.3 8.5 - - - +
42G CYS* 4.3 1.3 - - + -
96G LEU* 4.2 24.9 - - + -
97G VAL 2.8 18.9 + - - +
98G LEU* 3.6 12.7 - - + +
99G CYS* 2.8 31.2 + - - +
220G VAL* 4.9 11.0 - - + -
223G PHE* 3.6 49.1 - - + -
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Residues in contact with TRP 32 (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* 3.4 23.1 - - + -
31G ILE* 1.3 78.4 - - - +
33G ILE* 1.3 77.9 + - - +
40G LEU* 3.4 7.7 - - - +
41G ARG* 2.8 58.3 + - + +
42G CYS* 3.6 9.6 - - - -
43G LYS* 3.9 14.4 - - + -
62G PHE* 3.3 57.6 - + + -
67G THR* 4.3 0.8 - - + +
69G GLN* 4.2 3.4 - - - +
79G LEU* 3.6 37.2 - - + -
98G LEU* 4.9 2.2 - - - -
99G CYS 4.2 9.0 - - - +
101G VAL* 3.9 10.5 - - + -
162H TYR* 4.6 2.0 - + - -
163H CYS* 3.9 26.7 - - + -
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Residues in contact with ILE 33 (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* 1.3 89.0 - - - +
34G ASP* 1.3 70.3 + - - +
37G GLY* 3.9 28.0 - - - +
38G GLU 4.4 0.2 - - - +
39G GLY 3.4 6.5 - - - +
40G LEU* 4.2 14.6 - - + -
69G GLN* 3.3 11.6 - - - +
98G LEU* 5.3 7.0 - - + -
99G CYS 5.0 3.6 + - - +
101G VAL* 3.7 9.6 - - + +
111G THR* 3.9 19.7 + - - +
219G TRP* 3.3 46.0 - - + +
347G ASP* 4.6 5.6 - - - +
349G PHE* 4.6 10.1 - - + -
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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