Contacts of the strand formed by residues 31 - 37 (chain A) in PDB entry 1XSK
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 GLU 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 3.7 2.8 - - - -
28A GLN 2.9 35.4 + - - +
29A ASP* 3.3 0.6 - - - -
30A ASN* 1.3 94.7 + - - +
32A MET* 1.3 60.8 + - - +
33A VAL* 4.1 1.1 + - - -
56A ARG* 3.0 43.9 + - + +
57A PHE 3.5 5.4 - - - +
58A PHE* 3.4 31.1 - - + +
88A GLN* 4.7 10.4 - - - +
94A ILE* 3.7 6.2 - - - +
103A PHE* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 4.3 15.9 - - + -
26A GLU 3.7 4.5 - - - +
27A GLN* 4.7 0.7 - - - +
31A GLU* 1.3 73.7 - - - +
33A VAL* 1.3 62.6 + - - +
34A VAL* 3.9 13.5 - - + -
56A ARG* 3.6 0.7 - - - -
57A PHE* 2.8 69.6 + - + +
94A ILE* 3.9 22.8 - - + +
95A GLU 5.3 0.4 - - - +
101A ALA* 4.0 26.2 - - + +
102A GLU 3.8 26.7 - - - -
103A PHE* 3.9 25.8 - - + +
110A ALA 4.6 3.1 - - - +
112A VAL* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU 4.0 0.5 - - - +
25A VAL* 3.4 4.2 - - - +
26A GLU* 2.7 47.6 + - + +
28A GLN* 3.3 38.8 - - + +
31A GLU 4.8 0.7 - - - +
32A MET* 1.3 75.3 - - - +
34A VAL* 1.3 67.1 + - - +
35A TYR* 3.8 29.8 - - + +
54A THR* 3.9 21.1 - - + -
55A LEU 3.6 4.9 - - - +
56A ARG* 3.4 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.0 33.9 - - + -
24A GLU 3.6 2.7 - - - +
25A VAL* 4.4 11.2 - - + -
32A MET* 3.9 18.2 - - + -
33A VAL* 1.3 79.4 - - - +
35A TYR* 1.3 68.9 + - - +
36A ALA* 4.9 0.7 - - + +
53A PHE 3.5 2.3 - - - +
54A THR* 3.7 1.2 - - - -
55A LEU* 2.8 49.0 + - + +
57A PHE* 3.8 23.6 - - + -
101A ALA* 4.9 1.1 - - + -
112A VAL* 4.5 11.7 - - + -
118A TRP* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.7 3.6 - - - +
23A PHE* 2.8 35.3 + - + -
24A GLU* 2.9 32.8 + - + +
26A GLU* 3.8 29.4 + - + -
28A GLN* 4.3 7.8 + - - -
33A VAL* 3.8 21.5 - - + +
34A VAL* 1.3 73.2 - - - +
36A ALA* 1.3 61.7 + - - +
52A LEU* 3.6 27.1 - - + -
53A PHE 3.5 2.2 - - - -
54A THR* 3.9 28.8 - - + +
353F LYS* 3.7 46.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 3.5 27.6 - - + -
21A GLN 3.1 11.7 - - - +
34A VAL* 5.0 0.4 - - + -
35A TYR* 1.3 75.1 - - - +
37A ALA* 1.3 61.9 + - - +
38A PRO 4.2 0.2 - - - -
52A LEU* 3.2 7.5 - - - +
53A PHE* 2.9 39.5 + - - +
55A LEU* 4.2 8.1 - - + -
118A TRP* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS 4.2 0.9 - - - -
19A PRO* 4.4 0.4 - - - -
20A LEU 2.9 23.1 + - - -
21A GLN 2.9 15.2 + - - +
23A PHE* 4.9 2.1 - - + +
36A ALA* 1.3 72.4 - - - +
38A PRO* 1.3 67.0 - - + +
39A ARG 3.0 24.3 + - - +
41A VAL* 3.6 31.0 - - + -
50A THR* 5.2 2.0 - - + +
51A PRO 4.8 0.4 - - - +
52A LEU* 3.8 10.7 - - + +
313F PHE* 5.5 1.1 - - + -
----------------------------------------------------------
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