Contacts of the strand formed by residues 997 - 1004 (chain A) in PDB entry 3AVS
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 MET 997 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995A GLU 3.5 3.4 + - - +
996A HIS* 1.3 93.0 + - + +
998A VAL* 1.3 67.1 + - - +
999A GLU 4.9 0.2 - - - +
1029A HIS* 3.8 34.1 - - + -
1030A THR 3.5 11.0 - - - +
1031A THR* 5.5 0.4 - - - -
1088A ILE* 3.8 9.7 - - - +
1089A ASP 4.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 998 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997A MET* 1.3 84.3 - - - +
999A GLU* 1.3 74.8 + - - +
1000A VAL* 3.6 7.0 + - + +
1029A HIS* 3.4 3.1 - - - -
1030A THR* 2.9 42.0 + - + +
1031A THR 3.7 1.3 - - - +
1032A ILE* 3.5 41.3 - - + +
1035A TYR* 4.5 9.0 - - + -
1085A GLY* 3.7 13.7 - - - -
1088A ILE* 3.7 30.3 - - + +
1136A MET* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 999 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997A MET* 4.3 0.8 - - - +
998A VAL* 1.3 74.2 - - - +
1000A VAL* 1.3 63.0 + - - +
1001A ARG* 2.9 35.2 + - - -
1027A ARG* 3.9 21.7 + - + -
1028A SER 3.7 11.0 - - - +
1029A HIS* 3.8 17.2 + - + +
1084A PHE 3.5 0.2 - - - +
1085A GLY* 3.5 3.6 - - - -
1086A THR* 2.8 52.7 + - + +
1087A ASN* 3.5 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1000 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998A VAL* 3.9 6.3 - - + +
999A GLU* 1.3 78.5 - - - +
1001A ARG* 1.3 68.1 + - - +
1002A THR* 4.1 3.6 - - - +
1026A ASN 3.2 3.6 - - - +
1027A ARG* 3.4 4.3 - - - +
1028A SER* 2.9 50.9 + - - +
1030A THR* 3.3 36.1 - - + +
1035A TYR* 4.5 7.6 - - + -
1083A LYS* 3.8 37.7 - - + -
1084A PHE 3.4 5.6 - - - +
1510A EDO 4.1 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1001 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999A GLU* 2.9 24.8 + - - -
1000A VAL* 1.3 76.1 - - - +
1002A THR* 1.3 64.1 + - - +
1003A GLN* 3.7 11.3 + - - +
1025A SER* 3.0 47.2 + - - +
1026A ASN* 3.3 5.6 - - - +
1027A ARG* 3.7 28.1 - - - +
1083A LYS* 3.5 1.2 - - - -
1084A PHE* 2.9 45.0 + - + +
1086A THR* 4.0 17.9 - - + +
1087A ASN* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1002 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000A VAL* 4.0 6.6 - - - +
1001A ARG* 1.3 70.9 - - - +
1003A GLN* 1.3 63.7 + - - +
1024A GLU* 3.8 7.6 - - - +
1025A SER* 3.5 3.6 + - - -
1026A ASN* 2.9 44.1 + - - +
1028A SER* 4.8 4.2 + - - -
1081A THR* 3.6 30.5 - - + +
1082A ILE 3.4 4.9 - - - +
1083A LYS* 3.7 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1003 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A ARG* 3.9 15.5 - - - +
1002A THR* 1.3 79.3 - - - +
1004A LEU* 1.3 70.5 + - - +
1023A CYS* 4.8 7.1 - - - -
1024A GLU* 3.5 21.8 - - - +
1025A SER* 3.0 25.3 + - - +
1081A THR* 3.5 7.2 + - - -
1082A ILE* 2.9 37.7 + - + +
1084A PHE* 4.1 5.8 - - - +
1140A GLY 3.8 6.8 - - - +
1141A SER* 3.8 4.7 - - - -
1142A ARG* 2.9 50.9 + - - +
1144A PRO* 5.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1004 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003A GLN* 1.3 81.6 - - - +
1005A LEU* 1.3 64.4 + - - +
1006A GLN* 3.1 29.0 + - - +
1012A TRP 5.3 0.4 - - - +
1014A PRO* 3.9 31.4 - - + +
1024A GLU* 3.9 34.0 + - + +
1079A PHE* 4.0 35.2 - - + +
1080A LYS 3.8 1.6 - - - +
1081A THR* 3.8 20.9 - - - +
1082A ILE* 4.5 3.2 - - - +
1140A GLY 5.0 2.6 - - - +
1142A ARG* 5.8 1.7 - - - -
----------------------------------------------------------
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