Contacts of the strand formed by residues 277 - 281 (chain 3) 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 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352 THR* 3.4 16.5 + - - +
1362 HIS* 3.3 18.6 - - - -
1382 ASN 3.9 4.8 + - - -
1392 GLY* 3.3 4.4 - - - -
1402 ALA* 2.9 39.1 - - + +
683 SER* 3.8 1.8 - - - -
693 LEU* 2.8 31.2 + - - +
1423 LYS* 5.5 2.9 + - - -
2283 GLU 5.4 2.4 - - - +
2693 LEU* 4.0 26.9 - - + +
2703 PHE 2.9 7.9 - - - +
2713 THR* 3.5 29.7 + - + +
2723 ASN* 4.9 0.2 - - - -
2753 GLY 3.8 3.6 + - - +
2763 THR* 1.3 78.8 - - - +
2783 GLN* 1.3 63.0 + - - +
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Residues in contact with GLN 278 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583 PRO* 4.7 0.2 - - - +
623 GLN* 3.2 31.9 + - - +
653 LEU* 3.7 26.0 - - + +
663 SER* 2.5 45.5 + - - +
673 LYS* 3.7 8.9 - - - +
683 SER* 4.2 10.3 + - - +
693 LEU* 3.9 4.3 - - - -
2693 LEU* 3.4 6.0 - - - -
2703 PHE* 2.6 47.7 + - + +
2723 ASN* 2.9 27.3 + - - +
2773 GLN* 1.3 77.7 - - - +
2793 TRP* 1.3 60.6 + - - +
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Residues in contact with TRP 279 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262 LEU* 4.0 45.4 + - + -
1282 LEU* 4.1 25.6 - - + -
553 MET* 3.7 17.3 - - + +
643 GLY 3.5 0.2 - - - +
653 LEU* 3.2 10.5 - - - +
663 SER* 2.7 41.3 + - - +
693 LEU* 3.4 30.9 - - + +
843 GLN 4.2 0.4 + - - -
863 PRO* 3.1 36.1 - - + +
1473 SER* 3.7 22.9 - - - -
2663 ILE* 3.4 21.8 - - + -
2683 GLY 3.2 10.1 - - - -
2693 LEU* 3.2 31.8 - - + +
2783 GLN* 1.3 70.8 - - - +
2803 LYS* 1.3 59.3 + - - +
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Residues in contact with LYS 280 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553 MET* 3.4 7.0 - - - +
633 LYS 4.4 6.9 + - - -
643 GLY 3.2 13.2 - - - +
653 LEU* 4.5 16.2 - - + -
1243 ALA* 5.7 3.4 - - + +
1253 MET* 5.1 7.0 - - + -
1443 ILE* 3.5 34.8 - - + -
2663 ILE* 3.4 0.5 - - - -
2673 CYS* 2.7 34.8 + - + -
2683 GLY 2.7 12.9 + - - +
2703 PHE* 5.2 0.4 - - + -
2783 GLN 3.7 1.7 + - - +
2793 TRP* 1.3 75.3 - - - +
2813 GLY* 1.3 75.2 + - - +
2823 LEU* 3.9 19.1 - - + +
1644 VAL* 5.8 0.2 - - - +
1654 LEU 4.4 1.0 + - - -
1664 ALA* 4.3 27.9 - - + +
1874 GLN* 3.1 32.2 + - - -
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Residues in contact with GLY 281 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533 PRO* 3.6 12.8 - - - +
553 MET* 3.3 18.5 - - - +
643 GLY* 3.2 13.4 + - - +
2653 ASP 3.1 13.5 - - - -
2673 CYS* 3.9 0.9 - - - -
2803 LYS* 1.3 83.1 + - - +
2823 LEU* 1.3 77.3 + - - +
1874 GLN 5.0 0.9 - - - +
1884 GLN* 6.0 0.5 - - - +
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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
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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