Contacts of the strand formed by residues 277 - 280 (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 GLN 277 (chain 5).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354 THR* 3.2 16.9 + - - +
1364 HIS* 2.9 32.4 - - - -
1384 ASN 3.8 5.7 + - - -
1394 GLY* 2.9 19.4 - - - -
1404 ALA* 3.6 13.0 - - + +
685 SER* 3.5 4.2 - - - -
695 LEU* 2.8 27.2 + - - +
2285 GLU 5.5 2.1 - - - +
2695 LEU* 3.0 36.0 - - + +
2705 PHE 2.9 9.2 - - - +
2715 THR* 3.8 18.8 + - + +
2755 GLY 3.6 3.6 - - - +
2765 THR* 1.3 76.5 - - - +
2785 GLN* 1.3 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 278 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585 PRO* 4.2 1.4 - - - +
625 GLN* 3.8 26.6 + - - +
655 LEU* 3.3 33.0 - - + +
665 SER* 2.6 39.4 + - - +
675 LYS 3.6 6.0 - - - +
685 SER* 4.4 9.6 + - - +
695 LEU* 3.3 5.8 - - - -
2695 LEU* 3.3 5.5 - - - +
2705 PHE* 2.8 41.9 + - + +
2725 ASN* 2.8 30.4 + - - +
2775 GLN* 1.3 78.0 - - - +
2795 TRP* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 279 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264 LEU* 3.8 38.3 + - + -
1284 LEU* 3.9 30.5 - - + -
555 MET* 3.0 23.0 - - + +
655 LEU* 3.2 9.2 - - - +
665 SER* 2.8 52.0 + - - -
695 LEU* 3.3 28.0 - - + +
845 GLN 3.9 0.4 + - - -
865 PRO* 3.0 36.6 - - + +
1475 SER* 4.3 15.0 - - - -
2065 GLU* 5.8 0.6 + - - -
2665 ILE* 3.3 27.4 - - + -
2685 GLY 3.4 6.7 - - - +
2695 LEU* 3.2 35.0 - - + +
2785 GLN* 1.3 71.5 - - - +
2805 LYS* 1.3 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 280 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651 LEU 4.8 1.0 + - - -
1661 ALA* 4.3 28.4 - - + +
1871 GLN* 3.4 25.9 + - - +
555 MET* 4.0 3.1 - - - -
635 LYS 5.2 0.8 + - - -
645 GLY* 3.5 14.0 + - - -
655 LEU* 4.2 24.5 - - + -
1245 ALA* 5.2 4.4 - - + +
1255 MET* 5.6 4.9 - - + -
1445 ILE* 3.6 36.1 - - + -
2665 ILE* 3.5 5.9 - - - -
2675 CYS* 2.8 38.2 + - + -
2685 GLY 2.7 14.2 + - - +
2705 PHE* 5.0 4.5 - - + -
2785 GLN 3.4 1.7 + - - +
2795 TRP* 1.3 74.1 - - - +
2815 GLY* 1.3 75.5 + - - +
2825 LEU* 4.3 13.0 - - + +
----------------------------------------------------------
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