Contacts of the strand formed by residues 26 - 33 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLN* 3.9 0.2 - - - +
24B GLU 3.7 7.9 - - - +
25B LYS* 1.3 79.4 - - - +
27B GLN* 1.3 70.5 + - - +
46B THR* 3.3 6.9 - - - +
47B LEU* 2.8 36.6 + - + +
49B SER 3.4 36.8 - - - +
50B GLU* 3.5 7.0 - - + +
51B PRO* 4.4 11.7 - - + -
93B PRO* 3.1 44.2 - - + +
94B ASN* 3.7 7.0 - - - -
95B LYS* 4.7 1.8 - - + +
184C LEU* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 6.3 0.2 - - - +
22B GLN* 4.2 1.2 - - - +
26B VAL* 1.3 75.7 - - - +
28B ALA* 1.3 61.2 + - - +
29B MET 4.2 0.4 - - - -
44B THR* 3.9 1.6 - - + -
45B ARG 3.7 3.1 - - - -
46B THR* 6.0 0.2 - - - -
90B ARG* 3.7 37.5 + - - +
94B ASN* 2.7 37.2 + - + +
95B LYS 2.9 26.2 + - - +
177C GLU* 4.7 3.0 + - - -
180C TYR* 3.3 59.6 - - + +
181C ARG* 3.8 18.0 + - - +
184C LEU* 4.4 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL 4.1 0.2 + - - -
27B GLN* 1.3 73.2 - - - +
29B MET* 1.3 61.4 + - - +
30B TYR* 3.7 24.5 - - + -
44B THR* 3.3 3.6 - - - -
45B ARG* 2.9 38.4 + - + +
47B LEU* 3.5 30.3 - - + -
57B LEU* 4.4 6.7 - - + -
95B LYS* 3.7 9.4 - - + +
97B VAL* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN 4.2 0.6 - - - -
28B ALA* 1.3 70.3 - - - +
30B TYR* 1.3 62.9 + - - +
31B ILE* 3.7 4.3 + - + +
42B CYS* 3.7 24.0 - - + -
43B LYS 3.5 5.4 - - - +
44B THR* 3.4 21.3 - - - +
87B ASP* 5.2 0.9 - - - +
89B PHE* 6.1 1.3 - - - -
90B ARG* 3.8 25.4 - - - +
95B LYS 3.0 13.6 + - - +
96B LEU* 3.6 16.4 - - + -
97B VAL 2.9 26.4 + - - +
223B PHE* 3.6 33.4 - - - -
227B ARG* 5.3 6.3 - - - +
701B CL 3.7 15.0 - - + -
173C ARG* 4.4 10.5 - - - +
177C GLU* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 3.7 27.1 - - + -
29B MET* 1.3 73.2 - - - +
31B ILE* 1.3 60.0 + - - +
32B TRP* 3.3 5.7 - - + -
42B CYS* 3.1 5.2 - - - -
43B LYS 2.8 33.9 + - - +
45B ARG* 3.6 21.6 + - - -
57B LEU* 3.8 7.4 - - + +
58B PRO* 2.5 50.2 + - - +
60B TRP* 3.6 39.5 - + + -
79B LEU* 4.3 11.7 - - + -
81B PRO* 4.2 10.8 - - + -
97B VAL* 3.5 13.9 - - + -
99B CYS* 3.4 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 4.1 5.2 - - + +
30B TYR* 1.3 76.8 - - - +
32B TRP* 1.3 68.0 + - - +
40B LEU* 3.6 27.6 - - + -
41B ARG 3.2 9.0 - - - +
42B CYS* 4.2 1.8 - - + -
96B LEU* 4.1 27.1 - - + -
97B VAL 2.8 19.1 + - - +
98B LEU* 3.7 14.8 - - + +
99B CYS* 2.8 30.8 + - - +
219B TRP 5.8 0.2 - - - +
220B VAL* 5.0 9.4 - - + -
223B PHE* 3.7 53.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR 3.3 23.3 - - - -
31B ILE* 1.3 79.1 - - - +
33B ILE* 1.3 78.5 + - - +
40B LEU* 3.4 5.8 - - - +
41B ARG* 2.8 58.6 + - + +
42B CYS* 3.7 11.4 - - - -
43B LYS* 3.9 17.7 - - + -
62B PHE* 3.3 53.4 - + + -
67B THR* 4.3 0.8 - - + +
69B GLN* 4.2 3.1 - - - +
79B LEU* 3.6 32.5 - - + -
98B LEU* 4.7 2.5 - - - -
99B CYS 4.1 7.9 - - - +
101B VAL* 3.7 24.0 - - + -
162C TYR* 4.7 2.0 - + - -
163C CYS* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TRP* 1.3 84.3 - - - +
34B ASP* 1.3 71.0 + - - +
37B GLY* 3.9 28.5 - - - +
39B GLY 3.6 6.5 - - - +
40B LEU* 4.1 13.2 - - + -
69B GLN* 3.4 12.0 - - - +
98B LEU* 5.1 6.5 - - + -
99B CYS 5.0 3.8 + - - +
101B VAL* 3.9 8.4 - - + +
111B THR* 3.9 20.0 + - - +
219B TRP* 3.3 48.9 - - + +
347B ASP* 4.6 6.1 - - - +
349B PHE* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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