Contacts of the strand formed by residues 25 - 32 (chain B) in PDB entry 3QS1
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 GLN 25 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLN* 3.3 3.1 - - - -
20B ILE 3.0 31.0 + - - +
23B ASN* 3.1 39.3 + - - +
24B LYS* 1.3 71.4 - - - +
26B LYS* 1.3 59.9 + - - +
27B PHE* 3.1 21.8 - - + -
54B ASN* 6.2 0.7 - - - +
55B LEU 4.1 3.8 - - - +
56B TYR* 3.5 24.2 - - - -
57B ASP* 3.1 46.6 + - - +
60B LYS* 4.3 2.5 - - - +
61B SER* 4.2 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.2 27.0 + - - +
18B ALA 3.9 2.2 - - - -
19B GLN* 4.3 16.6 - - + +
24B LYS 3.4 17.0 - - - +
25B GLN* 1.3 70.4 - - - +
27B PHE* 1.3 77.5 + - - +
54B ASN* 3.3 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.1 10.2 + - - +
18B ALA 2.9 33.5 + - - -
20B ILE* 3.7 23.6 - - + -
25B GLN* 3.1 45.3 - - + -
26B LYS* 1.3 82.5 - - - +
28B ALA* 1.3 60.3 + - - +
29B PHE* 3.5 22.2 - - + -
40B VAL* 3.8 20.9 - - + -
54B ASN* 3.1 35.4 - - + -
55B LEU 4.3 1.3 - - - -
56B TYR* 3.6 33.9 - - + -
118B ASP* 3.2 14.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
15B TYR* 3.7 29.6 - - + -
16B GLY 3.6 7.0 - - - +
17B GLU* 4.4 3.4 - - + +
27B PHE* 1.3 74.9 - - - +
29B PHE* 1.3 61.8 + - - +
116B GLN 4.1 2.0 - - - +
117B PHE* 3.8 13.7 - - - -
118B ASP* 2.5 38.9 + - - +
119B GLY 3.1 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 3.3 9.1 - - - +
16B GLY 3.0 29.0 + - - +
18B ALA* 3.3 42.6 - - + -
20B ILE* 4.7 9.0 - - + -
27B PHE* 3.5 30.7 - + + -
28B ALA* 1.3 76.9 - - - +
30B ILE* 1.3 59.5 + - - +
31B PHE* 3.5 11.3 - + + -
38B LEU* 4.5 8.5 - - + -
39B TRP 3.4 20.2 - - - -
40B VAL* 3.5 15.3 - - + -
89B VAL* 6.2 0.9 - - + -
117B PHE* 4.7 1.1 - - - -
119B GLY* 3.0 24.5 - - - +
120B ILE 3.6 4.0 - - - -
121B VAL* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B MET* 3.3 38.6 - - + -
14B TYR 3.7 17.3 - - - +
29B PHE* 1.3 71.0 - - - +
31B PHE* 1.3 66.4 + - - +
32B ASP* 4.9 2.9 - - + +
117B PHE* 3.6 38.4 - - + -
119B GLY 3.1 3.6 + - - -
120B ILE* 3.4 19.6 - - + +
121B VAL 2.7 33.7 + - - +
216B SER 5.4 1.3 - - - +
217B GLY* 4.7 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 4.4 8.7 - - + -
6B LEU* 3.9 21.1 - - + -
14B TYR 4.5 2.4 + - - -
15B TYR* 5.2 0.4 - - - -
16B GLY* 3.6 26.0 - - - -
17B GLU 4.2 11.2 - - - -
18B ALA* 4.8 2.7 - - + -
29B PHE* 3.5 26.9 - + + -
30B ILE* 1.3 74.8 - - - +
32B ASP* 1.3 54.1 + - - +
33B THR 4.0 0.2 - - - -
91B ILE* 4.4 13.5 - - + -
121B VAL* 3.4 36.3 - - + -
123B LEU* 3.8 15.0 - - + -
153B PHE* 3.7 14.2 - - + -
165B LEU* 3.5 23.1 - - + -
216B SER* 2.7 30.9 + - - +
217B GLY 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.4 4.5 - - + +
31B PHE* 1.3 73.7 - - - +
33B THR* 1.3 54.3 + - - +
34B GLY* 2.9 29.6 + - - +
35B SER* 3.2 31.3 + - - +
75B TYR* 4.7 5.7 - - - -
120B ILE* 4.2 15.6 - - + +
121B VAL 3.0 11.5 + - - +
123B LEU* 2.7 30.5 + - - +
215B ASP* 2.9 16.8 - - - +
216B SER* 3.3 1.6 - - - -
217B GLY* 3.6 13.2 - - - +
----------------------------------------------------------
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