Contacts of the strand formed by residues 258 - 266 (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 SER 258 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923 ARG* 3.7 25.9 + - - -
933 ILE 3.4 7.0 - - - -
943 PRO* 5.1 0.8 - - - +
953 LEU* 4.5 1.6 - - - +
1563 GLY 3.8 7.8 - - - +
2543 CYS* 3.0 26.8 - - - +
2563 ALA* 2.3 35.1 + - - +
2573 ASP* 1.3 74.5 + - - +
2593 LEU* 1.3 61.2 + - - +
2603 TYR* 3.5 22.5 + - - -
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Residues in contact with LEU 259 (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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473 VAL* 5.3 3.4 - - + -
913 ALA 4.0 0.2 - - - +
923 ARG* 3.4 4.3 - - - +
933 ILE* 2.7 62.8 + - + +
953 LEU* 4.1 10.8 - - + -
1123 ALA* 4.6 11.2 - - + -
1543 VAL* 4.5 19.1 - - + -
1553 GLY 4.0 8.7 - - - +
2543 CYS* 4.1 13.0 - - - -
2583 SER* 1.3 76.8 - - - +
2603 TYR* 1.3 65.5 + - - +
2613 VAL* 4.7 3.1 - - + -
2883 ILE* 3.8 27.6 - - + -
2903 LEU* 4.2 22.4 - - + -
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Residues in contact with TYR 260 (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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903 VAL* 5.6 7.0 - - + -
913 ALA 3.6 4.7 - - - +
923 ARG* 4.0 26.2 - - + -
1533 ALA 3.9 0.9 - - - +
1543 VAL* 3.5 5.7 - - - +
1553 GLY 3.0 34.9 + - - +
1563 GLY 3.7 7.2 - - - -
1573 GLU* 3.4 40.6 - - - +
1583 PRO* 3.5 36.9 - - + +
1593 LEU 5.4 0.2 - - - +
1973 LEU 5.8 0.2 - - - -
2563 ALA* 4.6 9.5 - - + +
2583 SER* 3.5 30.9 + - - -
2593 LEU* 1.3 77.2 - - - +
2613 VAL* 1.3 67.8 + - - +
2623 SER* 4.4 4.9 + - - +
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Residues in contact with VAL 261 (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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493 CYS* 4.7 6.1 - - - -
513 LEU* 3.7 11.9 - - + +
903 VAL* 3.3 2.9 - - - +
913 ALA* 2.8 39.3 + - + +
933 ILE* 4.6 16.8 - - + -
1533 ALA 3.7 2.5 - - - -
1543 VAL* 4.5 5.4 - - + -
2593 LEU* 4.7 2.5 - - + -
2603 TYR* 1.3 80.2 - - - +
2623 SER* 1.3 66.1 + - - +
2863 PHE* 3.3 43.1 - - + -
2883 ILE* 3.9 28.5 - - + -
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Residues in contact with SER 262 (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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513 LEU* 4.3 1.1 - - - -
883 TYR* 5.9 0.2 - - - -
893 SER 3.2 9.0 - - - -
903 VAL* 3.7 18.7 - - - +
1513 PHE* 4.6 1.8 - - - -
1523 PHE* 3.3 1.5 - - - +
1533 ALA* 2.9 41.5 + - - +
1593 LEU* 4.1 23.8 + - - +
1973 LEU* 4.2 11.2 - - - -
2603 TYR* 4.4 4.5 + - - +
2613 VAL* 1.3 81.2 + - - +
2633 ALA* 1.3 65.9 + - - +
2863 PHE* 4.2 1.9 - - - -
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Residues in contact with ALA 263 (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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513 LEU* 4.2 9.6 - - + +
883 TYR* 4.1 0.8 - - - -
893 SER* 2.9 36.9 + - - +
1513 PHE* 3.2 16.5 - - - +
1523 PHE* 3.7 11.0 - - + +
2623 SER* 1.3 77.1 - - - +
2643 VAL* 1.3 66.7 + - - +
2653 ASP* 4.5 3.4 - - - +
2843 ARG* 3.8 11.0 - - + -
2863 PHE* 3.8 15.9 - - + -
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Residues in contact with VAL 264 (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* 6.0 1.1 - - - -
873 CYS 5.1 3.4 - - - +
883 TYR* 3.4 43.5 - - + -
893 SER* 5.2 2.7 - - - -
1493 PHE* 3.8 16.6 - - + -
1503 HIS* 3.1 2.4 - - - -
1513 PHE* 2.7 43.0 + - + +
2053 VAL* 3.7 14.8 - - + -
2633 ALA* 1.3 84.1 - - - +
2653 ASP* 1.3 70.4 + - - +
2663 ILE* 3.4 28.0 - - + -
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Residues in contact with ASP 265 (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* 5.4 6.2 - - + +
553 MET* 4.5 3.9 - - - -
1193 VAL* 3.8 11.2 - - + +
1493 PHE 3.3 3.6 - - - -
1503 HIS* 2.7 32.0 + - + +
2633 ALA* 4.5 0.7 - - - +
2643 VAL* 1.3 89.0 + - - +
2663 ILE* 1.3 60.6 + - - +
2673 CYS* 2.7 13.8 + - - -
2813 GLY* 3.1 18.7 - - - -
2823 LEU 3.8 20.3 - - - +
2843 ARG* 2.5 45.7 + - - +
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Residues in contact with ILE 266 (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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1262 LEU* 4.5 10.3 - - + -
553 MET* 3.3 21.3 - - + -
863 PRO* 4.5 9.4 - - + -
1473 SER 4.0 4.9 - - - +
1483 ASN* 3.0 8.5 - - - +
1493 PHE* 2.7 42.9 + - + +
1503 HIS* 3.4 2.5 - - - -
2053 VAL* 4.3 16.8 - - + -
2643 VAL* 3.4 26.0 - - + -
2653 ASP* 1.3 69.3 - - - +
2673 CYS* 1.3 57.0 + - - +
2683 GLY* 3.4 18.2 - - - +
2793 TRP* 3.4 35.9 - - + -
2803 LYS 3.4 6.3 - - - +
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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