Contacts of the strand formed by residues 1062 - 1069 (chain A) in PDB entry 2OOQ
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 ARG1062 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997A ILE 4.2 0.6 + - - -
998A TRP* 2.9 74.3 + - + +
1001A ASN* 3.3 36.0 + - - +
1002A SER 5.3 7.1 + - - +
1052A THR* 3.2 8.6 - - - -
1053A VAL* 2.8 39.6 + - + +
1060A GLU* 3.0 41.4 + - - +
1061A ILE* 1.3 76.5 - - - +
1063A GLU* 1.3 64.0 + - - +
1064A LEU* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1063 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A B3P 5.2 0.7 - - - -
1002A SER 5.1 0.5 - - - +
1003A ALA* 4.1 17.5 - - - +
1038A ILE* 3.7 14.6 - - + +
1050A THR* 3.7 30.3 - - + +
1051A PHE 3.4 5.2 - - - +
1052A THR* 4.6 3.1 - - + +
1062A ARG* 1.3 79.2 - - - +
1064A LEU* 1.3 63.6 + - - +
1065A ARG* 3.5 25.4 + - + +
1096A PRO* 5.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1064 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A TRP* 4.4 11.2 - - + -
997A ILE* 3.6 32.1 - - + -
1002A SER* 3.6 15.3 - - - +
1003A ALA* 3.3 14.1 - - - +
1005A ILE* 3.7 30.5 - - + -
1050A THR* 3.4 3.5 - - - +
1051A PHE* 2.8 49.3 + - + +
1053A VAL* 3.8 17.7 - - + -
1062A ARG* 4.2 0.6 - - + -
1063A GLU* 1.3 76.6 - - - +
1065A ARG* 1.3 79.6 + - - +
1066A LEU* 4.1 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1065 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A B3P 2.9 35.4 + - - -
1003A ALA 2.9 11.4 + - - +
1004A SER* 3.3 4.9 + - - +
1005A ILE 2.8 31.7 + - - +
1048A ILE* 4.3 7.6 - - + -
1049A ARG 3.3 5.2 - - - +
1050A THR* 3.8 16.8 - - + +
1063A GLU* 3.5 23.7 + - + -
1064A LEU* 1.3 82.0 - - - +
1066A LEU* 1.3 54.8 + - - +
1067A PHE* 3.6 30.7 - - + -
1094A LEU* 2.8 47.1 + - - +
1095A ASN* 4.9 0.4 - - - +
1096A PRO* 4.5 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1066 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005A ILE* 3.4 17.3 - - + +
1007A MET* 3.7 23.1 - - + -
1022A TYR* 3.4 26.2 - - + +
1023A TRP* 3.7 50.0 - - + -
1047A VAL 3.5 3.1 - - - +
1048A ILE* 3.4 4.8 - - - -
1049A ARG* 2.8 41.8 + - + +
1051A PHE* 3.9 19.1 - - + -
1064A LEU* 4.1 3.3 - - + +
1065A ARG* 1.3 71.1 - - - +
1067A PHE* 1.3 65.7 + - - +
1068A HIS* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1067 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004A SER* 3.6 28.0 - - - -
1005A ILE 2.7 18.8 + - - +
1006A VAL* 4.4 3.6 - - + -
1007A MET 2.8 28.4 + - - +
1047A VAL 4.0 2.7 - - - -
1048A ILE* 3.9 34.1 - - + +
1065A ARG* 3.6 33.0 - - + -
1066A LEU* 1.3 72.2 - - - +
1068A HIS* 1.3 59.3 + - - +
1087A PHE* 3.5 24.6 - + + -
1090A GLN* 4.1 13.0 - - + -
1091A VAL* 3.6 30.1 - - + -
1094A LEU* 4.0 22.7 - - + -
1095A ASN 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1068 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A MET* 3.5 34.4 - - + +
1009A THR 2.7 29.6 + - - -
1010A ASN* 3.9 9.5 + - - -
1011A LEU* 5.3 2.9 - - + -
1023A TRP* 4.4 8.9 - + - -
1046A TYR* 3.1 5.5 - - - -
1047A VAL* 2.9 50.3 + - + +
1049A ARG* 3.5 25.3 + - - +
1066A LEU* 3.6 6.0 + - + -
1067A PHE* 1.3 71.9 - - - +
1069A PHE* 1.3 68.0 + - - +
1070A THR* 3.7 21.0 - - + +
1087A PHE* 3.9 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1069 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A MET 2.9 15.9 + - - +
1008A VAL* 3.9 8.6 - - + -
1009A THR* 3.9 13.5 + - - +
1045A GLU* 3.4 26.2 - - + -
1046A TYR* 3.7 2.9 - + + -
1068A HIS* 1.3 80.6 - - - +
1070A THR* 1.3 61.5 + - - +
1071A SER* 3.1 26.0 + - - -
1072A TRP* 3.7 40.3 + + + +
1078A PRO* 4.5 7.6 - - + -
1083A GLY 3.8 7.4 - - - -
1084A LEU* 3.5 42.6 - - + -
1087A PHE* 3.6 35.6 - + + -
----------------------------------------------------------
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