Contacts of the strand formed by residues 23 - 31 (chain A) in PDB entry 2ZPS
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 HIS 23 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 2.7 29.5 + - - +
18A LEU 3.5 6.3 - - - -
19A ASN* 3.6 7.3 - - - +
22A TYR* 1.3 81.6 - - - +
24A PHE* 1.3 61.2 + - - +
25A CYS 3.2 30.2 + - - -
26A GLY* 4.1 1.8 - - - -
55A ILE* 3.9 24.0 - - + -
121A TRP* 3.8 43.1 - + + +
174A GLY* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.0 48.4 + - + -
19A ASN 3.8 2.7 - - - -
20A SER* 3.6 35.4 - - - +
22A TYR 3.8 2.5 - - - +
23A HIS* 1.3 78.5 - - - +
25A CYS* 1.3 88.3 + - + +
41A CYS* 3.2 26.9 - - + -
43A LYS* 3.4 31.0 - - + +
46A VAL* 3.9 11.9 - - + -
174A GLY* 4.4 12.9 + - - -
176A SER* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 2.8 33.5 + - + -
23A HIS* 3.2 13.2 - - - -
24A PHE* 1.3 100.0 - - + +
26A GLY* 1.3 64.8 + - - +
40A HIS* 5.1 1.6 - - - -
41A CYS* 2.0 54.7 - - + -
174A GLY 4.1 5.2 - - - -
176A SER* 3.2 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 3.9 10.1 - - - -
16A VAL 3.4 11.4 - - - -
18A LEU* 3.7 6.5 - - - +
23A HIS* 4.1 5.3 - - - -
25A CYS* 1.3 75.8 - - - +
27A GLY* 1.3 57.4 + - - -
37A SER* 2.8 21.8 + - - -
174A GLY 4.1 3.8 + - - -
175A ASP* 4.4 2.5 - - - -
176A SER 2.8 12.4 + - - +
177A GLY* 3.2 10.7 - - - +
178A GLY* 3.9 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS 3.7 0.5 - - - +
15A GLN* 3.7 7.3 + - - +
16A VAL* 3.0 42.1 + - - +
18A LEU* 5.0 0.7 - - - -
26A GLY* 1.3 74.6 - - - -
28A SER* 1.3 64.7 + - - -
35A VAL* 4.1 4.5 - - - -
36A VAL 3.3 13.0 - - - -
37A SER* 4.3 1.8 - - - -
177A GLY 3.4 5.8 + - - -
178A GLY* 3.9 2.4 - - - -
179A PRO* 3.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.3 6.1 - - - -
27A GLY* 1.3 73.6 + - - -
29A LEU* 1.3 62.6 + - - +
30A VAL* 3.4 3.1 + - - +
35A VAL* 3.3 6.7 - - - +
36A VAL* 2.8 40.0 + - - -
103A VAL* 4.2 10.8 - - - -
177A GLY 5.0 0.2 + - - -
178A GLY 4.3 0.9 - - - -
179A PRO* 2.9 36.3 - - - +
186A LEU* 3.5 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO 5.1 0.7 - - - +
14A HIS* 2.8 20.1 + - - +
16A VAL* 4.4 8.3 - - + +
27A GLY 4.4 0.2 - - - -
28A SER* 1.3 70.7 - - - +
30A VAL* 1.3 58.1 + - - +
31A ASN 3.0 26.2 - - - +
34A TRP 3.6 9.0 - - - +
35A VAL* 3.9 12.1 - - + -
50A LEU* 3.8 17.9 - - + -
90A LEU* 4.2 11.4 - - + -
94A ALA* 4.5 3.6 - - + -
96A LEU* 3.9 18.6 - - + -
100A VAL* 3.6 30.7 - - + -
101A GLN 4.0 12.3 - - - +
102A PRO* 3.1 3.8 - - + +
103A VAL* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 3.9 4.7 - - - +
29A LEU* 1.3 76.4 - - - +
31A ASN* 1.3 65.8 + - - +
34A TRP* 3.0 19.5 + - + +
36A VAL* 3.7 29.8 - - + -
102A PRO* 3.4 11.7 - - - +
103A VAL* 3.7 19.8 - - + +
105A LEU* 3.9 22.4 - - + +
186A LEU* 4.2 11.0 - - + -
219A MET* 3.7 32.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.0 22.9 - - - +
30A VAL* 1.3 77.1 + - - +
32A GLU* 1.3 78.1 + - - +
33A ASN* 2.6 31.9 + - - +
34A TRP* 2.7 28.1 + - - +
102A PRO* 3.5 12.6 - - - +
219A MET* 3.0 37.6 - - - +
----------------------------------------------------------
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