Contacts of the strand formed by residues 89 - 94 (chain 1) 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 89 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511 LEU* 3.5 13.2 - - - +
521 ASN 3.2 26.3 + - - -
531 PRO* 4.0 2.1 - - - +
541 GLN* 3.5 17.3 + - - +
871 CYS 3.4 9.9 + - - -
881 TYR* 1.3 72.1 - - - +
901 VAL* 1.3 59.6 + - - +
2001 ASP* 3.7 10.8 - - - -
2621 SER* 3.3 3.8 - - - -
2631 ALA* 3.0 39.8 + - - -
2641 VAL* 5.1 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511 LEU* 4.0 7.0 - - - +
891 SER* 1.3 76.3 - - - +
911 ALA* 1.3 81.2 + - - +
1581 PRO* 6.6 0.2 - - + -
1591 LEU* 6.3 1.1 - - + +
1971 LEU* 4.1 33.7 - - + +
1981 ASP* 4.7 4.0 - - - +
1991 LYS* 3.8 10.8 - - - +
2001 ASP* 3.0 48.1 + - + +
2601 TYR* 5.5 8.3 - - + -
2611 VAL 3.1 18.6 - - - +
2621 SER* 4.5 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511 LEU* 3.6 20.6 - - + -
901 VAL* 1.3 86.9 - - - +
921 ARG* 1.3 62.0 + - - +
931 ILE* 4.1 5.5 + - + +
2601 TYR* 3.6 3.8 - - - +
2611 VAL* 3.0 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911 ALA* 1.3 75.8 - - - +
931 ILE* 1.3 61.7 + - - +
941 PRO* 3.0 28.1 - - - +
2581 SER* 3.2 40.4 - - - +
2591 LEU 3.2 5.6 - - - +
2601 TYR* 4.0 22.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 ILE* 4.4 11.2 - - + -
471 VAL* 3.9 27.4 - - + -
491 CYS* 3.7 32.5 - - + -
911 ALA* 4.1 4.7 - - + -
921 ARG* 1.3 73.1 - - - +
941 PRO* 1.3 69.3 - - + +
951 LEU* 3.2 22.5 - - + +
2581 SER* 3.4 0.7 - - - -
2591 LEU* 2.8 57.7 + - + -
2611 VAL* 4.9 11.0 - - + -
2881 ILE* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 94 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 ILE* 4.3 13.6 - - + +
351 LEU* 4.1 10.4 - - - +
921 ARG* 3.0 25.3 - - + +
931 ILE* 1.3 89.2 - - + +
951 LEU* 1.3 68.1 + - - +
961 PRO* 4.4 0.2 - - - +
2571 ASP 4.0 6.3 - - - +
2581 SER* 4.6 4.3 - - - +
----------------------------------------------------------
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