Contacts of the strand formed by residues 258 - 266 (chain 5) 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 SER 258 (chain 5).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925 ARG* 3.4 42.8 + - - -
935 ILE 3.3 7.9 - - - -
945 PRO* 4.8 0.3 - - - +
955 LEU* 4.3 1.9 - - - +
1565 GLY* 3.8 1.7 - - - +
2545 CYS* 3.2 24.4 - - - +
2565 ALA* 2.5 14.8 + - - +
2575 ASP* 1.3 81.6 + - - +
2595 LEU* 1.3 60.4 - - - +
2605 TYR* 3.4 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475 VAL* 5.4 3.1 - - + -
915 ALA 3.9 0.2 - - - +
925 ARG* 3.5 2.3 - - - -
935 ILE* 2.6 59.6 + - + +
955 LEU* 4.1 8.7 - - + -
1125 ALA* 4.9 7.2 - - + -
1545 VAL* 4.1 22.7 - - + -
1555 GLY 3.7 11.7 - - - +
2545 CYS* 4.0 13.5 - - - -
2585 SER* 1.3 75.3 - - - +
2605 TYR* 1.3 72.8 + - - +
2615 VAL* 4.3 6.2 + - + -
2885 ILE* 4.0 22.4 - - + -
2905 LEU* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 260 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905 VAL* 5.5 7.2 - - + -
915 ALA 3.5 7.0 - - - +
925 ARG* 3.7 27.3 - - + -
1535 ALA 3.8 0.3 - - - +
1545 VAL* 3.4 5.4 - - - -
1555 GLY 2.8 47.1 + - - +
1565 GLY 3.7 2.7 - - - -
1575 GLU* 3.4 30.5 - - - +
1585 PRO* 3.6 39.0 - - + +
1595 LEU 5.4 0.7 - - - +
1975 LEU 5.9 0.2 - - - -
2565 ALA* 4.4 11.2 - - + +
2585 SER* 3.4 37.0 + - - -
2595 LEU* 1.3 78.0 - - - +
2615 VAL* 1.3 65.2 + - - +
2625 SER* 4.5 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495 CYS* 5.1 1.6 - - - -
515 LEU* 3.4 30.5 - - + -
905 VAL* 3.3 5.2 - - - +
915 ALA* 3.0 36.2 + - + +
935 ILE* 4.6 18.6 - - + -
1535 ALA 3.6 3.6 - - - -
1545 VAL* 4.4 8.5 - - + -
2595 LEU* 4.8 6.3 - - + -
2605 TYR* 1.3 79.3 - - - +
2625 SER* 1.3 66.8 + - - +
2865 PHE* 3.5 39.3 - - + -
2885 ILE* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515 LEU* 3.9 3.1 - - - -
895 SER 3.3 12.1 - - - -
905 VAL* 3.9 13.3 - - - +
1515 PHE* 4.4 4.9 - - - -
1525 PHE* 3.3 1.8 - - - +
1535 ALA* 3.0 39.3 + - - +
1595 LEU* 4.4 18.3 - - - +
1975 LEU* 4.1 13.7 - - - -
2605 TYR* 4.5 3.5 + - - +
2615 VAL* 1.3 81.4 + - - +
2635 ALA* 1.3 67.8 + - - +
2865 PHE* 4.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515 LEU* 4.4 8.3 - - + -
885 TYR* 4.1 0.6 - - - -
895 SER* 3.1 30.3 + - - +
1515 PHE* 3.3 17.8 - - - +
1525 PHE* 3.8 9.0 - - + +
2625 SER* 1.3 80.2 - - - +
2645 VAL* 1.3 73.9 + - - +
2655 ASP* 4.4 2.9 - - - +
2845 ARG* 4.3 11.7 - - + +
2865 PHE* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555 MET* 6.1 0.7 - - - -
865 PRO* 6.0 0.2 - - + -
875 CYS 5.2 2.2 - - - +
885 TYR* 3.6 32.5 - - + -
895 SER* 5.3 2.7 - - - -
1495 PHE* 3.7 18.6 - - + -
1505 HIS* 2.9 4.7 - - - -
1515 PHE* 2.8 41.1 + - + -
2055 VAL* 3.7 24.0 - - + -
2635 ALA* 1.3 86.2 - - - +
2655 ASP* 1.3 65.2 + - - +
2665 ILE* 3.1 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535 PRO* 5.8 4.5 - - + +
555 MET* 4.9 3.2 - - - -
1195 VAL* 3.5 12.7 - - + +
1495 PHE 3.4 3.6 - - - -
1505 HIS* 3.0 33.2 + - + +
2635 ALA* 4.4 1.2 - - - +
2645 VAL* 1.3 82.2 + - - +
2665 ILE* 1.3 55.9 + - - +
2675 CYS* 2.6 20.1 + - - -
2815 GLY* 3.4 18.0 - - - -
2825 LEU 3.8 17.8 - - - +
2845 ARG* 2.7 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264 LEU* 4.7 12.6 - - + -
555 MET* 3.6 21.8 - - + -
865 PRO* 4.4 12.8 - - + -
1475 SER 4.3 4.3 - - - +
1485 ASN* 3.1 5.2 - - - +
1495 PHE* 2.8 36.5 + - + +
1505 HIS* 3.7 1.6 - - - -
2055 VAL* 4.3 13.7 - - + -
2645 VAL* 3.1 29.8 - - + -
2655 ASP* 1.3 69.3 - - - +
2675 CYS* 1.3 60.5 + - - +
2685 GLY* 3.6 13.9 - - - +
2795 TRP* 3.3 37.0 - - + -
2805 LYS 3.5 6.5 - - - +
----------------------------------------------------------
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