Contacts of the strand formed by residues 268 - 271 (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 GLY 268 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1445 ILE* 3.6 9.6 - - - +
1455 GLN 3.8 3.8 - - - -
1465 GLY 4.3 0.4 - - - -
1475 SER 3.4 19.3 - - - -
1485 ASN* 4.1 0.4 - - - -
2665 ILE* 3.0 5.2 - - - -
2675 CYS* 1.3 83.8 - - - +
2695 LEU* 1.3 61.9 + - - -
2795 TRP* 3.4 8.1 - - - -
2805 LYS* 2.7 32.8 + - - +
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Residues in contact with LEU 269 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1284 LEU* 4.4 7.0 - - + -
1404 ALA* 4.3 15.9 - - + -
695 LEU* 3.7 9.2 - - + -
1435 PRO 4.5 0.5 - - - +
1445 ILE* 3.4 8.5 - - - +
1455 GLN* 2.7 37.0 + - - +
1465 GLY* 5.0 6.5 - - - -
1475 SER 4.4 3.8 + - - +
2285 GLU 5.7 2.0 - - - +
2685 GLY* 1.3 70.4 - - - -
2705 PHE* 1.3 62.4 + - - +
2715 THR* 3.7 6.3 + - - +
2775 GLN* 3.0 29.8 - - + +
2785 GLN 3.3 27.6 - - - +
2795 TRP* 3.2 41.5 - - + +
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Residues in contact with PHE 270 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751 PHE* 4.4 18.2 - + - -
1661 ALA* 5.6 8.5 - - + -
655 LEU* 4.1 27.6 - - + -
1305 SER* 4.6 5.2 - - - -
1315 GLY* 3.9 11.9 - - - -
1325 THR* 3.8 32.3 - - + -
1425 LYS 5.5 2.0 - - - -
1435 PRO 6.6 0.2 - - - -
1445 ILE* 4.3 25.3 - - + +
2685 GLY 3.9 1.0 + - - -
2695 LEU* 1.3 72.1 - - - +
2715 THR* 1.3 100.6 + - - +
2725 ASN* 3.6 14.6 + - - -
2775 GLN* 2.9 6.6 - - - +
2785 GLN* 2.8 44.8 + - + +
2805 LYS* 4.8 5.3 - - + +
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Residues in contact with THR 271 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1364 HIS* 4.2 13.1 - - + +
1325 THR* 4.3 0.2 - - - -
1335 GLN* 3.5 27.7 + - + +
1425 LYS* 4.5 33.1 + - + +
1435 PRO 5.1 2.9 + - - -
1445 ILE* 5.7 0.2 - - - +
1455 GLN* 5.8 2.6 - - - +
2695 LEU* 3.7 7.4 + - - +
2705 PHE* 1.3 89.0 - - - +
2725 ASN* 1.3 71.9 + - - +
2755 GLY* 4.1 11.9 - - - +
2765 THR 3.6 2.5 - - - -
2775 GLN* 3.8 25.2 + - + +
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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
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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