Contacts of the strand formed by residues 22 - 28 (chain B) in PDB entry 3GBN
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 TYR 22 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 3.4 9.2 - - - +
17A TYR* 4.6 0.7 - - + -
320A LEU* 4.7 3.6 - - + -
17B MET* 3.5 4.7 - - - -
20B GLY 3.5 0.2 - - - -
21B TRP* 1.3 100.0 - - + +
23B GLY* 1.3 60.1 + - - +
36B ALA* 3.6 4.2 - - - +
37B ASP* 2.7 23.5 + - - +
40B SER* 3.4 47.3 - - - +
41B THR* 3.7 5.9 + - - -
44B ALA* 3.3 12.1 - - + +
111B HIS* 2.6 46.7 + - + -
114B ASN* 2.9 35.2 + - + -
115B VAL* 3.5 24.9 - - + -
118B LEU* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.4 9.0 - - - +
16A GLY 2.9 32.8 + - - -
14B TRP* 3.9 1.6 - - - -
17B MET* 3.4 9.7 - - - -
22B TYR* 1.3 77.9 - - - +
24B TYR* 1.3 67.7 + - - -
35B ALA 3.4 10.5 - - - -
37B ASP* 3.5 9.9 - - - -
118B LEU* 4.0 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.1 18.4 - - + -
14A CYS 3.1 7.4 - - - +
15A ILE* 3.5 29.8 - - + -
14B TRP* 3.6 8.9 - - - -
17B MET* 4.0 0.5 - - - +
23B GLY* 1.3 72.1 - - - -
25B HIS* 1.3 58.1 - - - +
34B TYR* 3.2 7.6 - - - +
35B ALA 2.8 42.6 + - - +
36B ALA 4.5 1.1 - - - -
37B ASP* 2.8 45.0 + - + -
118B LEU* 3.6 16.5 - - + +
122B VAL* 3.9 15.3 - - + +
152B VAL* 4.6 1.4 + - + -
153B ARG* 3.4 45.9 + - + -
181B GOL 5.1 0.9 - - - -
182B CL 3.6 16.4 - - + -
183B EDO 3.7 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 5.5 1.2 + - - -
13A ILE* 3.3 3.6 - - - +
14A CYS* 2.7 49.7 + - + +
14B TRP* 3.4 23.5 - + + -
24B TYR* 1.3 73.5 - - - +
26B HIS* 1.3 78.1 + - - +
27B GLN* 4.8 5.8 - - + -
32B SER* 4.0 12.4 - - - -
33B GLY* 3.1 30.2 + - - -
34B TYR* 3.4 35.5 + + + -
182B CL 3.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.3 13.5 - - - +
13A ILE* 4.5 3.4 - - + -
25B HIS* 1.3 82.8 - - - +
27B GLN* 1.3 62.2 + - - +
28B ASN* 4.0 19.3 - - - -
31B GLY 3.7 18.4 + - - -
32B SER* 3.1 29.1 - - - -
33B GLY* 3.0 32.9 + - - -
34B TYR 6.0 0.2 - - - -
146B ASP* 3.7 15.7 + - - -
149B MET* 3.7 18.4 - - + -
153B ARG* 3.4 15.8 + - - +
182B CL 2.9 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY 5.4 5.8 - - - +
11A ASP* 3.2 6.9 - - - +
12A THR* 3.0 42.7 + - - +
25B HIS* 5.0 6.1 - - + -
26B HIS* 1.3 76.1 - - - +
28B ASN* 1.3 70.7 + - - +
31B GLY 3.6 4.9 - - - +
32B SER* 3.7 17.3 + - - +
149B MET* 3.9 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.4 10.5 - - - -
26B HIS* 4.0 2.5 - - - -
27B GLN* 1.3 83.6 + - - +
29B GLU* 1.3 58.6 + - - +
30B GLN* 3.1 13.5 + - - +
31B GLY* 2.9 31.6 + - - +
144B CYS 3.2 27.7 + - - +
145B ASP 3.5 7.1 - - - -
146B ASP* 3.0 23.0 + - - +
149B MET* 3.8 11.5 - - + +
185B EDO 3.3 19.1 + - - +
----------------------------------------------------------
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