Contacts of the strand formed by residues 277 - 281 (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 GLN 277 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351 THR* 3.2 19.2 + - - +
1361 HIS* 2.8 23.4 - - + -
1381 ASN 3.4 5.9 + - - -
1391 GLY* 2.8 28.7 - - - -
1401 ALA* 3.1 16.6 - - + +
682 SER* 3.6 1.8 - - - -
692 LEU* 2.7 36.1 + - - +
2282 GLU 5.1 4.0 - - - +
2692 LEU* 3.4 32.6 - - + +
2702 PHE 3.3 4.7 - - - +
2712 THR* 3.1 23.9 + - - +
2762 THR* 1.3 76.5 - - - +
2782 GLN* 1.3 57.0 + - - +
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Residues in contact with GLN 278 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582 PRO* 4.3 0.4 - - - +
622 GLN* 3.5 30.3 + - - +
652 LEU* 3.5 29.6 - - + +
662 SER* 2.7 38.4 + - - +
672 LYS 3.6 5.8 - - - +
682 SER* 3.9 14.8 + - - +
692 LEU* 3.8 5.4 - - - -
2692 LEU* 3.4 4.0 - - - +
2702 PHE* 2.8 35.7 + - + +
2722 ASN* 3.1 27.2 + - - +
2772 GLN* 1.3 76.9 - - - +
2792 TRP* 1.3 62.6 + - - +
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Residues in contact with TRP 279 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261 LEU* 3.7 41.0 + - + -
1281 LEU* 4.3 19.7 - - + -
552 MET* 3.6 16.7 - - + +
652 LEU* 3.2 12.1 - - - +
662 SER* 2.6 47.9 + - - +
692 LEU* 3.4 25.2 - - + +
842 GLN 4.1 1.0 + - - -
862 PRO* 3.2 34.5 - - + +
1472 SER* 3.7 25.8 - - - -
2062 GLU* 5.5 1.8 + - - -
2662 ILE* 3.3 22.2 - - + -
2682 GLY 3.3 8.7 - - - -
2692 LEU* 3.2 36.2 - - + +
2782 GLN* 1.3 71.2 - - - +
2802 LYS* 1.3 58.8 + - - +
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Residues in contact with LYS 280 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552 MET* 3.0 9.3 - - - +
632 LYS 4.9 3.2 + - - -
642 GLY* 3.3 19.0 - - - +
652 LEU* 4.2 17.7 - - + -
1242 ALA* 5.6 3.6 - - - +
1252 MET* 5.2 5.6 - - + -
1442 ILE* 3.5 38.4 - - + -
2672 CYS* 2.7 37.4 + - + +
2682 GLY 2.9 12.1 + - - +
2702 PHE* 5.0 7.0 - - + -
2782 GLN 3.7 0.2 + - - -
2792 TRP* 1.3 72.8 - - - +
2812 GLY* 1.3 63.2 + - - +
2822 LEU* 4.1 17.9 - - + +
1653 LEU 4.1 10.1 + - - -
1663 ALA* 4.2 20.0 - - + +
1873 GLN* 3.6 24.1 + - - +
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Residues in contact with GLY 281 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532 PRO* 3.7 13.2 - - - +
552 MET* 3.5 17.0 - - - +
642 GLY* 3.2 13.6 + - - +
2652 ASP 3.2 13.0 - - - -
2672 CYS* 4.3 0.4 - - - -
2802 LYS* 1.3 85.0 + - - +
2822 LEU* 1.3 76.5 + - - +
2832 PRO* 4.7 0.2 - - - +
1873 GLN 5.0 1.2 - - - +
1883 GLN* 6.0 0.2 - - - +
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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
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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) + - + + + + + -
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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