Contacts of the strand formed by residues 266 - 271 (chain 6) 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 ILE 266 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556 MET* 3.7 24.5 - - + -
866 PRO* 4.5 11.4 - - + -
1476 SER 3.9 4.5 - - - +
1486 ASN* 3.2 5.4 - - - +
1496 PHE* 2.8 43.9 + - + +
1506 HIS* 3.5 2.5 - - - -
2056 VAL* 4.5 10.8 - - + -
2646 VAL* 3.6 23.8 - - + -
2656 ASP* 1.3 70.3 - - - +
2676 CYS* 1.3 56.7 + - - +
2686 GLY* 3.3 18.6 - - - +
2796 TRP* 3.4 40.2 - - + -
2806 LYS 3.5 6.3 - - - +
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Residues in contact with CYS 267 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196 VAL* 5.2 0.7 - - - -
1256 MET* 3.5 22.0 - - + -
1446 ILE* 4.4 3.0 - - - +
1466 GLY 4.5 1.0 - - - +
1486 ASN* 3.3 12.9 - - - +
1506 HIS* 3.4 20.2 - - + +
2326 PRO* 3.6 22.9 - - + +
2346 LEU* 4.8 7.0 - - + -
2656 ASP* 2.8 16.3 + - - -
2666 ILE* 1.3 72.2 - - - +
2686 GLY* 1.3 56.3 + - - +
2806 LYS* 2.8 16.7 + - + +
2816 GLY* 4.1 0.9 - - - -
2826 LEU* 3.7 40.6 - - - -
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Residues in contact with GLY 268 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1446 ILE* 3.8 7.3 - - - +
1456 GLN 3.8 5.4 - - - -
1466 GLY 4.0 2.0 - - - -
1476 SER 3.3 19.3 - - - -
2666 ILE* 3.2 5.4 - - - -
2676 CYS* 1.3 82.4 - - - +
2696 LEU* 1.3 64.2 + - - -
2796 TRP* 3.3 12.1 - - - -
2806 LYS 2.9 24.3 + - - -
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Residues in contact with LEU 269 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696 LEU* 3.6 14.4 - - + -
1436 PRO 4.6 1.2 - - - +
1446 ILE* 3.4 9.5 - - - +
1456 GLN* 2.7 36.6 + - - +
1466 GLY* 5.4 4.7 - - - -
1476 SER* 5.2 3.6 - - - +
2286 GLU 5.9 1.3 - - - +
2686 GLY* 1.3 74.3 - - - -
2706 PHE* 1.3 60.1 + - - +
2716 THR* 3.6 5.5 + - - -
2776 GLN* 3.1 35.4 - - + +
2786 GLN 3.5 6.5 - - - +
2796 TRP* 3.2 57.7 - - + +
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Residues in contact with PHE 270 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656 LEU* 4.3 22.0 - - + -
1276 ASN 5.9 2.9 - - - -
1306 SER* 4.5 9.0 - - - -
1316 GLY* 3.7 31.0 - - - -
1326 THR* 3.9 4.5 - - - -
1446 ILE* 4.0 29.0 - - + +
2686 GLY 4.2 0.6 + - - -
2696 LEU* 1.3 70.4 - - - +
2716 THR* 1.3 65.7 + - - +
2726 ASN* 3.4 41.8 + - - -
2766 THR 3.8 0.2 - - - +
2776 GLN* 3.0 4.7 - - - -
2786 GLN* 2.9 43.5 + - + +
2806 LYS* 5.0 4.2 - - + +
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Residues in contact with THR 271 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326 THR* 4.3 1.7 - - - -
1336 GLN* 3.7 32.2 + - + +
1426 LYS* 4.0 37.8 + - + +
1436 PRO 5.7 0.8 + - - -
1446 ILE* 5.6 0.4 - - - +
2696 LEU 3.6 6.7 + - - -
2706 PHE* 1.3 80.9 - - - +
2726 ASN* 1.3 71.4 + - - +
2756 GLY* 4.1 12.6 - - - +
2766 THR 3.6 2.5 - - - -
2776 GLN* 3.2 31.6 + - + +
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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