Contacts of the strand formed by residues 13 - 18 (chain A) in PDB entry 1GQ5
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 ARG 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 3.5 2.5 + - - -
12A PRO* 1.3 72.9 - - - +
14A LEU* 1.3 62.1 + - - +
15A CYS* 3.5 21.5 - - - -
51A ALA 5.2 0.4 - - - -
52A GLY* 3.0 38.0 + - - -
54A LEU* 4.2 16.0 - - - +
57A ASP* 5.0 2.7 - - - -
89A LEU* 3.6 3.1 - - - +
90A VAL* 3.1 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO 3.3 3.8 + - - +
13A ARG* 1.3 74.2 - - - +
15A CYS* 1.3 63.1 + - - +
16A CYS* 4.0 26.7 + - - -
51A ALA 4.6 2.4 - - - +
87A ARG* 4.3 20.6 - - + +
88A LEU 3.8 15.5 - - - +
89A LEU* 3.7 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 3.5 32.1 - - - -
14A LEU* 1.3 70.6 - - - +
16A CYS* 1.3 62.0 + - - +
17A LEU* 3.3 20.5 - - + +
51A ALA* 3.5 23.3 - - + +
52A GLY 3.7 13.5 - - - -
53A LEU* 3.7 20.6 - - + -
87A ARG* 3.4 1.0 - - - -
88A LEU* 2.8 41.5 + - + +
90A VAL* 4.3 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.0 25.0 + - - -
15A CYS* 1.3 73.9 - - - +
17A LEU* 1.3 62.1 + - - +
18A GLU* 4.1 1.9 + - - +
51A ALA* 3.6 13.1 + - - +
85A ALA* 6.1 0.2 - - - -
86A VAL 3.7 5.2 - - - -
87A ARG* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS* 3.3 26.5 - - + +
16A CYS* 1.3 74.5 - - - +
18A GLU* 1.3 63.2 + - - +
19A LYS 3.8 0.2 + - - -
24A TYR* 3.8 22.5 - - + -
26A PHE* 3.9 21.3 - - + -
47A PRO* 4.0 14.1 - - + -
48A ALA* 3.7 25.8 - - + +
51A ALA* 3.5 23.3 - - + -
53A LEU* 4.6 2.9 - - + -
85A ALA* 3.2 26.0 - - - +
86A VAL* 3.1 21.3 + - + +
88A LEU* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS 5.5 1.3 - - - +
17A LEU* 1.3 74.5 - - - +
19A LYS* 1.3 66.7 + - - +
20A GLY* 3.2 3.6 + - - -
24A TYR* 4.0 1.1 - - - -
47A PRO* 3.3 20.4 - - + +
84A ASN* 3.7 7.4 - - - +
85A ALA* 4.6 5.4 - - + +
----------------------------------------------------------
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