Contacts of the strand formed by residues 61 - 65 (chain 4) in PDB entry 1G6Q
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 ILE 61 (chain 4).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604 LYS* 1.3 78.5 - - - +
624 VAL* 1.3 60.9 + - - +
824 LYS* 4.7 13.2 - - + -
834 HIS* 3.3 26.7 - - + +
854 ILE* 4.0 11.2 - - + -
1234 PHE* 3.5 40.4 - - + -
1254 LYS* 3.6 19.7 - - + +
1264 VAL* 3.7 2.7 - - - +
1274 ASP* 2.8 53.8 + - - +
1284 ILE 3.2 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574 PHE* 3.5 22.9 - - + -
604 LYS 5.9 0.2 - - - -
614 ILE* 1.3 71.5 - - - +
634 LEU* 1.3 60.1 + - - +
764 ALA* 3.9 16.6 - - + -
774 ALA 4.9 0.2 - - - +
814 ALA* 3.9 16.8 - - + -
834 HIS 3.2 7.5 + - - +
844 VAL* 3.4 30.1 - - + +
854 ILE* 2.9 32.1 + - - +
1264 VAL* 3.8 3.4 - - - -
1284 ILE* 3.2 37.7 - - + +
1304 ILE* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624 VAL* 1.3 75.7 - - - +
644 ASP* 1.3 61.6 + - - +
654 VAL* 3.1 37.2 + - + +
854 ILE* 3.4 23.3 - - + +
874 VAL* 3.9 22.4 - - + -
1164 LEU* 4.7 4.9 - - + -
1264 VAL* 3.9 15.0 - - + -
1284 ILE 2.9 10.1 + - - -
1294 ILE* 3.6 19.6 - - + -
1304 ILE* 2.8 26.9 + - - +
1504 ALA* 4.3 4.5 - - + -
1544 TYR* 4.2 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634 LEU* 1.3 70.8 - - - +
654 VAL* 1.3 62.5 + - - +
674 CYS* 3.2 34.2 + - - +
704 GLY 3.8 2.1 - - - +
714 ILE* 5.5 0.9 - - - +
724 LEU* 3.2 32.4 + - - +
734 SER* 3.1 36.6 + - - -
844 VAL* 4.5 0.8 - - - +
854 ILE 2.7 12.9 + - - +
864 GLY* 4.1 2.9 - - - -
874 VAL 3.0 19.0 + - - -
1304 ILE* 3.1 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634 LEU* 3.1 32.5 + - + +
644 ASP* 1.3 73.6 - - - +
664 GLY* 1.3 66.2 + - - +
874 VAL* 4.3 3.6 - - + -
1164 LEU* 3.7 26.2 - - + -
1294 ILE* 4.7 7.0 - - + -
1304 ILE 3.2 2.6 + - - +
1314 SER* 3.0 35.5 + - - +
1324 GLU 4.0 2.6 + - - -
1434 MET* 5.5 0.4 - - + -
1464 THR* 3.8 17.7 - - + +
1474 VAL* 3.8 22.2 - - + -
1504 ALA* 4.0 16.2 - - + -
----------------------------------------------------------
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