Contacts of the helix formed by residues 122 - 126 (chain 2) in PDB entry 1SVA
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 VAL 122 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192 VAL* 3.7 25.8 - - + +
1212 GLY* 1.3 74.2 - - - +
1232 THR* 1.3 64.8 + - + +
1242 ALA 2.8 6.2 + - - -
1252 MET* 3.0 22.4 + - - +
2342 LEU* 3.6 39.3 - - + +
2352 HIS 5.4 1.1 - - - +
2362 ILE* 4.2 21.6 - - + +
2822 LEU* 3.8 8.1 - - - -
1493 PHE* 4.3 12.6 - - + -
2093 VAL* 4.1 2.2 - - + +
2243 TYR* 3.7 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222 VAL* 1.3 79.8 - - + +
1242 ALA* 1.3 61.4 + - - +
1252 MET 3.1 1.5 + - - -
1262 LEU* 3.2 28.6 - - + +
883 TYR* 3.5 10.5 - - - +
1493 PHE* 3.6 35.0 - - + -
2053 VAL* 2.9 23.6 + - + +
2063 GLU* 3.5 6.6 - - - -
2073 CYS 5.0 0.2 - - - -
2083 TRP 2.6 25.4 + - - +
2093 VAL* 2.8 18.0 - - + +
2103 PRO* 6.0 0.2 - - + -
2243 TYR* 5.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212 GLY 2.9 14.8 + - - +
1222 VAL 2.8 0.8 + - - -
1232 THR* 1.3 76.6 + - - +
1252 MET* 1.3 59.1 + - + +
1262 LEU 2.8 11.7 + - - -
1272 ASN* 3.5 16.1 + - - +
2802 LYS* 5.6 4.9 - - - +
2822 LEU* 5.5 3.4 - - + -
1643 VAL* 4.1 12.1 - - + +
1653 LEU* 4.1 29.6 - - - -
1663 ALA* 4.5 11.6 + - + +
2063 GLU 3.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 125 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222 VAL 3.0 14.5 + - - +
1242 ALA* 1.3 78.4 - - + +
1262 LEU* 1.3 61.3 + - - +
1272 ASN 3.4 5.3 + - - +
1282 LEU* 4.1 14.2 - - - +
1432 PRO* 4.9 1.9 - - - +
1442 ILE* 3.6 55.8 + - + +
2322 PRO* 3.8 10.3 - - + -
2342 LEU* 5.1 6.5 - - - -
2672 CYS* 4.2 24.7 - - + -
2802 LYS* 5.2 5.6 - - + -
2822 LEU* 5.0 9.9 - - + -
1473 SER* 4.9 0.5 + - - -
2243 TYR* 3.2 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232 THR* 3.2 22.0 - - + +
1242 ALA 2.8 1.8 + - - -
1252 MET* 1.3 80.5 - - - +
1272 ASN* 1.3 59.1 + - - +
1282 LEU* 3.4 8.1 + - + -
1292 HIS* 4.8 0.7 + - - -
863 PRO* 6.1 0.3 - - - +
1473 SER* 4.3 11.0 - - - -
1483 ASN 5.3 1.1 - - - +
1493 PHE* 4.4 22.0 - - + -
2053 VAL* 4.0 22.2 - - + -
2063 GLU* 2.9 22.5 - - + +
2243 TYR* 3.3 33.2 - - + -
2663 ILE* 4.5 12.3 - - + -
2793 TRP* 4.0 37.5 + - + -
----------------------------------------------------------
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