Contacts of the strand formed by residues 266 - 271 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1263 LEU* 4.8 11.7 - - + -
554 MET* 3.4 26.2 - - + -
864 PRO* 4.7 7.6 - - + -
1474 SER 3.8 9.9 - - - +
1484 ASN* 3.1 3.3 - - - +
1494 PHE* 2.7 39.2 + - + +
1504 HIS* 3.2 3.3 - - - -
2054 VAL* 4.5 13.9 - - + -
2644 VAL* 3.2 28.9 - - + -
2654 ASP* 1.3 70.0 - - - +
2674 CYS* 1.3 60.2 + - - +
2684 GLY 3.4 14.6 - - - +
2794 TRP* 3.4 36.6 - - + -
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Residues in contact with CYS 267 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194 VAL* 4.9 1.3 - - - -
1254 MET* 4.1 20.9 - - - -
1444 ILE* 4.7 3.2 - - + +
1464 GLY 4.5 0.3 - - - +
1484 ASN* 3.3 12.5 + - - +
1504 HIS* 3.2 18.6 + - + -
2324 PRO* 3.6 22.6 - - + +
2344 LEU* 4.9 9.2 - - + -
2654 ASP* 2.8 16.1 + - - -
2664 ILE* 1.3 71.6 - - - +
2684 GLY* 1.3 55.2 + - - +
2804 LYS* 2.7 22.0 + - + +
2814 GLY 4.2 0.2 - - - -
2824 LEU* 3.7 40.6 - - - -
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Residues in contact with GLY 268 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1444 ILE* 3.7 7.6 - - - +
1454 GLN 4.2 2.2 - - - -
1464 GLY 3.8 6.1 - - - -
1474 SER 3.4 20.4 - - - -
2664 ILE* 3.1 4.7 - - - +
2674 CYS* 1.3 82.9 - - - +
2694 LEU* 1.3 63.1 + - - -
2794 TRP* 3.5 10.7 - - - -
2804 LYS 3.1 21.9 + - - -
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Residues in contact with LEU 269 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283 LEU* 4.5 8.1 - - + -
1353 THR* 6.1 0.2 - - - +
1403 ALA* 4.2 23.3 - - + -
1413 GLY 6.0 0.2 - - - +
694 LEU* 3.6 9.6 - - + -
1434 PRO 4.1 0.7 - - - +
1444 ILE* 3.2 11.3 - - - +
1454 GLN* 2.8 39.6 + - - +
1464 GLY* 5.3 5.6 - - - -
1474 SER* 5.2 3.8 - - - +
2284 GLU 5.8 2.2 - - - +
2684 GLY* 1.3 72.8 - - - -
2704 PHE* 1.3 60.5 + - - +
2714 THR* 3.7 6.5 + - - +
2774 GLN* 4.3 22.7 - - + +
2784 GLN 3.4 26.5 - - - +
2794 TRP* 3.3 37.0 - - + +
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Residues in contact with PHE 270 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654 LEU* 4.7 22.7 - - + -
1274 ASN 6.0 2.2 - - - -
1304 SER* 4.6 7.2 - - - -
1314 GLY* 3.6 10.8 - - - -
1324 THR* 3.5 29.8 - - + -
1424 LYS 5.6 2.7 - - - -
1434 PRO 5.8 0.4 - - - -
1444 ILE* 4.1 22.1 - - + +
2694 LEU* 1.3 70.9 - - - +
2714 THR* 1.3 83.9 + - - +
2724 ASN* 3.4 22.4 + - - -
2764 THR 3.6 1.0 - - - +
2774 GLN* 3.0 25.7 - - - -
2784 GLN* 2.9 27.2 + - + +
2804 LYS* 5.2 6.3 - - + +
755 PHE* 4.6 13.7 - + - -
1665 ALA* 5.8 7.0 - - + -
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Residues in contact with THR 271 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1363 HIS* 4.0 17.0 - - + +
1334 GLN* 3.6 24.0 + - - +
1424 LYS* 3.7 40.7 + - - +
1434 PRO 5.0 1.5 + - - -
1454 GLN* 5.5 1.0 + - - +
2694 LEU* 3.7 7.9 + - - +
2704 PHE* 1.3 86.9 - - - +
2724 ASN* 1.3 68.4 + - - +
2754 GLY* 4.3 4.7 - - - +
2764 THR 3.5 3.8 - - - +
2774 GLN* 3.1 33.6 + - + +
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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