Contacts of the strand formed by residues 26 - 33 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 3.9 0.2 - - - +
24A GLU 3.8 8.5 - - - +
25A LYS* 1.3 79.2 - - - +
27A GLN* 1.3 71.6 + - - +
28A ALA 4.1 0.2 - - - -
46A THR* 3.2 6.2 - - - -
47A LEU* 2.6 42.0 + - + +
49A SER* 3.5 32.3 - - - +
50A GLU* 3.5 6.7 - - + +
51A PRO* 4.2 16.6 - - + -
93A PRO* 3.1 42.0 - - + +
94A ASN* 3.9 3.6 - - - -
95A LYS* 4.8 2.0 - - + -
184B LEU* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 5.7 0.4 - - - +
22A GLN* 4.1 2.3 + - - +
26A VAL* 1.3 77.5 - - - +
28A ALA* 1.3 61.5 + - - +
29A MET 4.1 0.4 - - - -
44A THR* 3.8 9.4 - - + -
45A ARG 3.6 4.0 - - - -
46A THR* 5.4 0.2 - - - +
90A ARG* 3.6 31.0 - - - +
94A ASN* 2.9 36.2 + - + +
95A LYS 3.0 25.1 + - - +
177B GLU* 4.7 2.8 + - - -
180B TYR* 3.5 52.0 - - + +
181B ARG* 4.0 17.5 + - - +
184B LEU* 4.3 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL 4.0 0.4 + - - -
27A GLN* 1.3 73.0 - - - +
29A MET* 1.3 62.5 + - - +
30A TYR* 3.7 24.8 + - + -
43A LYS 3.7 0.2 - - - +
44A THR* 3.2 3.7 - - - -
45A ARG* 2.9 37.3 + - + +
47A LEU* 3.7 27.8 - - + -
57A LEU* 4.0 8.5 - - + -
95A LYS* 3.7 8.1 - - + -
97A VAL* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN 4.1 0.6 - - - -
28A ALA* 1.3 70.7 - - - +
30A TYR* 1.3 59.8 + - - +
31A ILE* 3.8 4.5 + - + +
42A CYS* 3.6 34.5 - - + -
43A LYS 3.4 4.9 - - - +
44A THR* 3.4 24.9 - - - +
87A ASP* 5.1 1.1 - - - +
89A PHE* 6.0 1.8 - - - -
90A ARG* 3.5 27.6 - - - +
95A LYS 2.9 16.0 + - - +
96A LEU* 3.5 16.1 - - + -
97A VAL* 2.8 31.4 + - - +
223A PHE* 3.7 20.4 - - - -
227A ARG* 5.4 6.5 - - - +
173B ARG* 4.1 13.0 - - - +
177B GLU* 4.4 2.9 - - - +
705B CL 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 3.8 26.5 - - + -
29A MET* 1.3 74.3 - - - +
31A ILE* 1.3 59.1 + - - +
32A TRP* 3.5 4.5 - - + -
42A CYS* 3.0 7.3 - - - +
43A LYS 2.8 36.3 + - - +
45A ARG* 3.8 24.3 + - - -
57A LEU* 3.7 7.0 - - + +
58A PRO* 2.6 46.4 + - - +
60A TRP* 3.7 37.0 - + + -
79A LEU* 4.3 13.5 - - + -
81A PRO* 4.0 15.0 - - + -
97A VAL* 3.4 13.5 - - + -
99A CYS* 3.3 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 4.1 4.5 - - + +
30A TYR* 1.3 78.1 - - - +
32A TRP* 1.3 66.7 + - - +
40A LEU* 3.8 26.2 - - + -
41A ARG 3.3 8.1 - - - +
42A CYS* 4.3 1.6 - - + -
96A LEU* 3.9 27.4 - - + -
97A VAL 2.7 18.7 + - - +
98A LEU* 3.6 15.4 - - + +
99A CYS* 2.9 27.6 + - - +
219A TRP 5.7 0.7 - - - +
220A VAL* 4.8 10.8 - - + -
223A PHE* 3.8 50.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR 3.5 22.4 - - - -
31A ILE* 1.3 78.8 - - - +
33A ILE* 1.3 79.4 + - - +
34A ASP 4.5 0.2 - - - -
40A LEU* 3.3 7.8 - - - -
41A ARG* 2.8 64.5 + - + +
42A CYS* 3.6 7.0 - - - -
43A LYS* 3.8 12.1 - - + -
62A PHE* 3.3 51.8 - + + -
67A THR* 4.4 0.8 - - + +
69A GLN* 4.3 3.5 - - - +
79A LEU* 3.5 37.7 - - + -
98A LEU* 4.7 2.0 - - - -
99A CYS 4.3 7.2 - - - +
101A VAL* 3.6 18.8 - - + -
162B TYR* 4.6 2.5 - + - -
163B CYS* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 1.3 83.8 - - - +
34A ASP* 1.3 70.9 + - - +
37A GLY* 3.8 28.0 - - - +
38A GLU 4.5 0.2 - - - +
39A GLY 3.5 5.2 - - - +
40A LEU* 4.1 15.9 - - + -
69A GLN* 3.4 12.1 - - - +
98A LEU* 5.3 7.4 - - + +
99A CYS 5.1 3.6 + - - +
101A VAL* 4.0 8.8 - - + +
111A THR* 3.8 20.7 + - - +
113A LEU 6.2 0.4 - - - +
219A TRP* 3.5 42.2 - - + +
347A ASP* 4.4 8.5 - - - +
349A PHE* 4.7 8.5 - - + -
----------------------------------------------------------
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