Contacts of the strand formed by residues 26 - 33 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F GLN* 4.0 0.2 - - - +
24F GLU 3.6 8.3 - - - +
25F LYS* 1.3 79.8 - - - +
27F GLN* 1.3 75.4 + - - +
46F THR* 3.2 7.5 - - - +
47F LEU* 2.8 35.6 + - + +
49F SER 3.5 11.2 - - - +
50F GLU* 3.5 27.8 - - + +
51F PRO* 4.3 15.9 - - + -
93F PRO* 3.2 42.4 - - + +
94F ASN* 3.9 3.4 - - - -
95F LYS* 4.8 1.3 - - + -
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Residues in contact with GLN 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F MET* 5.6 0.2 - - - +
22F GLN* 4.2 2.3 + - - +
26F VAL* 1.3 80.5 - - - +
28F ALA* 1.3 59.5 + - - +
29F MET 4.2 0.7 - - - -
44F THR* 3.9 4.3 - - + -
45F ARG 3.6 4.5 - - - -
46F THR* 5.5 0.2 - - - +
87F ASP* 5.7 0.2 - - - +
90F ARG* 3.5 40.3 - - - +
94F ASN* 3.0 29.4 + - + +
95F LYS* 3.0 24.5 + - - +
177G GLU* 4.9 2.8 + - - -
180G TYR* 3.3 47.8 - - + +
181G ARG* 3.8 17.4 + - - +
184G LEU* 4.2 19.9 - - + +
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Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F VAL 4.1 0.2 + - - -
27F GLN* 1.3 73.4 - - - +
29F MET* 1.3 61.2 + - - +
30F TYR* 3.8 25.0 - - + -
44F THR* 3.3 5.0 - - - +
45F ARG* 3.0 35.0 + - + +
47F LEU* 3.8 26.7 - - + -
57F LEU* 4.5 6.7 - - + -
95F LYS* 3.6 8.7 - - + +
97F VAL* 4.6 4.9 - - + -
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Residues in contact with MET 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F GLN 4.2 0.6 - - - -
28F ALA* 1.3 72.2 - - - +
30F TYR* 1.3 63.1 + - - +
31F ILE* 3.9 4.3 + - + +
42F CYS* 3.7 24.9 - - + -
43F LYS 3.4 6.3 - - - +
44F THR* 3.6 8.1 - - - +
87F ASP* 5.3 0.9 - - - +
89F PHE* 6.0 1.3 - - - -
90F ARG* 3.6 39.7 - - - +
95F LYS 2.9 13.8 + - - +
96F LEU* 3.6 15.7 - - + -
97F VAL* 2.9 27.9 + - - +
223F PHE* 3.6 33.9 - - + -
227F ARG* 5.4 6.7 - - - +
173G ARG* 4.2 12.6 - - - +
177G GLU* 4.6 1.8 - - - +
707G CL 3.8 11.9 - - + -
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Residues in contact with TYR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ALA* 3.8 24.9 - - + -
29F MET* 1.3 75.2 - - - +
31F ILE* 1.3 60.0 + - - +
32F TRP* 3.4 12.5 - - + -
42F CYS* 3.0 25.8 - - - +
43F LYS 2.8 12.9 + - - +
45F ARG* 3.7 27.1 + - - -
57F LEU* 4.0 7.2 - - + +
58F PRO* 2.5 45.6 + - - +
60F TRP* 3.7 35.0 - + + -
79F LEU* 4.2 6.7 - - + -
81F PRO* 4.1 15.7 - - + -
97F VAL* 3.3 12.3 - - + -
99F CYS* 3.4 22.2 - - - -
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Residues in contact with ILE 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F MET* 4.1 4.7 - - + +
30F TYR* 1.3 77.1 - - - +
32F TRP* 1.3 67.1 + - - +
40F LEU* 3.8 24.9 - - + -
41F ARG 3.3 8.1 - - - +
42F CYS* 4.1 3.1 - - + -
96F LEU* 4.0 27.8 - - + -
97F VAL 2.7 22.3 + - - +
98F LEU* 3.8 15.9 - - + +
99F CYS* 2.9 29.1 + - - +
219F TRP 5.7 0.4 - - - +
220F VAL* 5.3 8.3 - - + -
223F PHE* 3.8 49.8 - - + -
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Residues in contact with TRP 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F TYR* 3.4 24.7 - - + -
31F ILE* 1.3 77.6 - - - +
33F ILE* 1.3 78.0 + - - +
40F LEU* 3.3 7.3 - - - +
41F ARG* 2.7 64.0 + - + +
42F CYS* 3.7 9.0 - - - -
43F LYS* 3.9 23.6 - - + -
62F PHE* 3.3 59.5 - + + -
67F THR* 4.3 1.0 - - - +
69F GLN* 4.3 3.4 - - - +
79F LEU* 3.4 35.9 - - + -
98F LEU* 5.1 1.8 - - - -
99F CYS 4.4 8.5 - - - +
101F VAL* 3.8 11.0 - - + -
162G TYR* 4.5 1.8 - + - -
163G CYS* 4.0 18.6 - - + -
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Residues in contact with ILE 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F TRP* 1.3 84.7 - - - +
34F ASP* 1.3 72.1 + - - +
37F GLY* 3.7 29.8 - - - +
39F GLY 3.3 5.8 - - - +
40F LEU* 4.1 16.2 - - + -
69F GLN* 3.1 13.3 - - - +
98F LEU* 5.4 6.7 - - + -
99F CYS 5.1 5.0 + - - +
101F VAL* 3.9 8.2 - - + +
111F THR* 3.7 20.3 + - - +
113F LEU 6.3 0.2 - - - +
219F TRP* 3.6 42.6 - - + +
347F ASP* 4.5 6.7 - - - +
349F PHE* 4.6 8.7 - - + -
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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