Contacts of the strand formed by residues 23 - 32 (chain A) in PDB entry 2XWA
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 ALA 23 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 3.2 5.8 - - - -
20A LEU* 2.9 35.3 + - - +
21A ASN 3.3 2.9 - - - +
22A GLY* 1.3 79.7 - - - +
24A HIS* 1.3 66.7 + - - +
25A LEU* 3.2 1.0 + - - +
137A ARG* 5.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 2.7 29.4 + - - +
18A VAL 4.0 0.9 - - - -
19A GLN* 4.2 6.0 - - - +
23A ALA* 1.3 73.7 - - - +
25A LEU* 1.3 61.7 + - - +
26A CYS 3.2 29.6 + - - -
27A GLY* 3.9 1.8 - - - -
60A LEU* 3.8 26.0 - - + +
128A TRP* 3.7 43.7 - + + +
137A ARG* 4.8 11.8 + - - +
181A GLY* 2.8 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 2.9 18.9 + - + +
19A GLN 5.3 0.2 - - - -
20A LEU* 4.0 41.1 - - + +
23A ALA 3.2 6.1 + - - +
24A HIS* 1.3 79.0 - - - +
26A CYS* 1.3 70.8 + - + +
42A CYS* 3.0 37.0 - - + +
43A LEU* 5.3 3.8 - - + -
45A ASP* 5.8 2.7 - - - +
51A VAL* 6.4 2.0 - - + -
181A GLY* 3.7 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 2.7 44.3 + - + -
24A HIS* 3.2 17.1 + - - -
25A LEU* 1.3 91.6 - - + +
27A GLY* 1.3 63.5 + - - +
38A SER* 4.2 0.4 - - - +
41A HIS* 5.2 1.1 - - - -
42A CYS* 2.0 55.9 - - + -
181A GLY 4.0 1.8 - - - -
183A SER* 3.3 15.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
15A MET* 4.3 8.1 - - - -
16A ALA 3.5 8.1 - - - -
18A VAL* 3.6 2.9 - - - +
24A HIS* 4.4 4.3 - - - -
26A CYS* 1.3 75.7 - - - +
28A GLY* 1.3 52.2 + - - -
38A SER* 2.6 28.6 + - - -
128A TRP* 5.4 1.1 - - - -
181A GLY 3.8 6.8 + - - -
182A ASP* 4.5 2.0 - - - -
183A SER 2.7 14.5 + - - -
184A GLY* 3.2 11.9 - - - -
185A GLY* 3.8 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MET* 3.9 10.8 - - - +
16A ALA* 2.9 38.6 + - - +
18A VAL* 4.3 1.6 - - - -
27A GLY* 1.3 73.9 - - - -
29A VAL* 1.3 62.1 + - - +
36A VAL* 4.1 4.7 - - - -
37A LEU 3.1 13.2 - - - -
38A SER* 4.1 2.0 - - - -
184A GLY 3.3 7.0 + - - -
185A GLY* 4.0 1.6 - - - -
186A PRO* 4.2 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.6 27.8 - - + -
28A GLY* 1.3 76.1 - - - +
30A LEU* 1.3 74.6 + - - +
31A VAL* 3.2 4.4 + - + +
36A VAL* 3.9 3.9 - - - +
37A LEU* 2.7 54.8 + - + +
108A LEU* 4.1 16.8 - - + -
184A GLY 5.2 1.6 - - - +
186A PRO* 3.9 15.0 - - + -
193A LEU* 3.6 32.5 - - + -
196A VAL* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO 5.0 1.3 - - - +
14A TYR* 3.0 21.2 + - - +
16A ALA* 4.7 0.8 - - - +
29A VAL* 1.3 76.7 - - - +
31A VAL* 1.3 57.8 + - - +
32A ALA 3.2 22.7 - - - +
33A GLU* 4.4 8.7 - - - +
35A TRP 3.5 10.8 - - - +
36A VAL* 3.9 19.4 - - + +
55A LEU* 4.1 19.1 - - + -
95A LEU* 4.4 4.3 - - + -
99A ALA* 4.6 3.4 - - + -
101A LEU* 4.5 5.2 - - + -
105A VAL* 4.0 21.8 - - + -
106A ARG 3.8 6.1 - - - +
107A PRO* 3.4 31.1 - - + +
108A LEU* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.2 29.4 + - + +
30A LEU* 1.3 75.2 - - - +
32A ALA* 1.3 63.7 + - - +
35A TRP* 3.0 22.3 + - + +
37A LEU* 4.2 17.9 - - + +
92A LEU* 4.5 8.5 - - + -
107A PRO* 4.0 9.5 - - - +
108A LEU 4.0 13.3 - - - +
110A TRP* 3.9 29.9 + - + +
112A ARG* 5.6 1.0 + - - -
193A LEU* 3.9 16.4 - - + -
223A ILE* 5.1 4.5 - - + -
227A LEU* 4.7 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.2 15.6 - - - +
31A VAL* 1.3 76.7 - - - +
33A GLU* 1.3 67.8 + - - +
34A GLN 3.0 2.9 + - - +
35A TRP* 3.2 27.2 + - + -
107A PRO* 4.2 9.0 - - - -
227A LEU* 3.8 25.8 - - + -
----------------------------------------------------------
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