Contacts of the strand formed by residues 258 - 266 (chain 1) 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 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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921 ARG* 3.2 34.5 - - - +
931 ILE 3.4 7.2 - - - -
941 PRO* 4.8 1.9 - - - +
951 LEU* 4.4 2.4 - - - +
1561 GLY* 4.2 0.3 - - - -
2541 CYS* 2.8 29.7 - - - +
2561 ALA* 2.2 29.1 + - - +
2571 ASP* 1.3 74.8 + - - +
2591 LEU* 1.3 59.2 + - - +
2601 TYR* 3.5 24.4 + - - -
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Residues in contact with LEU 259 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471 VAL* 5.2 2.5 - - + -
921 ARG* 3.2 5.4 - - - -
931 ILE* 2.8 65.6 + - + +
951 LEU* 4.2 5.2 - - + -
1121 ALA* 4.3 11.4 - - + -
1541 VAL* 4.8 5.6 - - + -
1551 GLY 4.0 6.7 - - - +
2541 CYS* 3.5 20.4 - - - -
2581 SER* 1.3 74.1 - - - +
2601 TYR* 1.3 68.5 + - - +
2611 VAL* 4.9 3.8 - - + +
2881 ILE* 4.1 30.3 - - + -
2901 LEU* 4.1 28.3 - - + -
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Residues in contact with TYR 260 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901 VAL* 5.5 7.6 - - + -
911 ALA 3.6 4.0 - - - +
921 ARG* 4.0 26.5 - - + -
1541 VAL* 3.4 7.8 - - - +
1551 GLY 2.9 41.4 + - - +
1561 GLY 3.3 21.5 - - - -
1571 GLU* 3.3 26.6 - - - +
1581 PRO* 3.7 33.3 - - + +
1591 LEU 5.5 0.4 - - - +
2561 ALA* 3.6 19.0 + - - +
2581 SER* 3.5 28.1 + - - -
2591 LEU* 1.3 76.7 - - - +
2611 VAL* 1.3 67.0 + - - +
2621 SER* 4.5 3.7 + - - +
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Residues in contact with VAL 261 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491 CYS* 5.3 3.1 - - - -
511 LEU* 3.5 21.3 - - + -
901 VAL* 3.1 7.3 - - - +
911 ALA* 3.0 36.2 + - + +
931 ILE* 4.9 16.6 - - + -
1531 ALA 3.7 3.8 - - - +
1541 VAL* 4.7 3.8 - - + -
2591 LEU* 4.9 5.6 - - + +
2601 TYR* 1.3 81.8 - - - +
2621 SER* 1.3 67.1 + - - +
2861 PHE* 3.4 50.3 - - + -
2881 ILE* 4.6 13.0 - - + -
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Residues in contact with SER 262 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511 LEU* 4.1 1.6 - - - -
891 SER 3.3 9.2 - - - -
901 VAL* 4.5 9.3 - - - +
1511 PHE* 4.1 13.5 - - - -
1521 PHE* 3.0 4.1 - - - +
1531 ALA* 2.8 44.8 + - - +
1541 VAL* 5.3 0.2 - - - -
1591 LEU* 4.4 18.9 - - - +
1971 LEU* 4.6 8.1 - - - -
2601 TYR* 4.5 3.5 + - - +
2611 VAL* 1.3 82.3 + - - +
2631 ALA* 1.3 63.5 + - - +
2861 PHE* 4.2 1.0 - - - -
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Residues in contact with ALA 263 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511 LEU* 4.0 11.2 - - + +
881 TYR* 4.0 1.3 - - - +
891 SER* 3.0 31.9 + - - +
1511 PHE* 3.2 16.5 - - - +
1521 PHE* 3.8 1.8 - - + +
2621 SER* 1.3 79.5 - - - +
2641 VAL* 1.3 72.7 + - - +
2651 ASP* 4.3 3.6 - - - +
2841 ARG* 3.8 26.9 - - + -
2861 PHE* 4.0 5.2 - - + -
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Residues in contact with VAL 264 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871 CYS 5.5 2.0 - - - +
881 TYR* 3.9 32.1 - - + -
891 SER* 5.1 3.1 - - - -
1491 PHE* 3.7 20.9 - - + -
1501 HIS* 3.1 1.0 - - - -
1511 PHE* 2.7 46.9 + - + -
2051 VAL* 3.7 13.7 - - + -
2631 ALA* 1.3 83.4 - - - +
2651 ASP* 1.3 74.0 + - - +
2661 ILE* 3.2 28.5 - - + -
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Residues in contact with ASP 265 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531 PRO* 5.7 3.8 - - + +
551 MET* 4.9 3.0 - - - -
1191 VAL* 3.6 11.2 - - + +
1491 PHE 3.3 4.5 - - - -
1501 HIS* 2.8 27.1 + - + +
2631 ALA* 4.3 1.4 - - - +
2641 VAL* 1.3 93.8 + - - +
2661 ILE* 1.3 62.0 + - - +
2671 CYS* 2.9 13.3 + - - -
2811 GLY* 3.4 18.9 - - - -
2821 LEU 3.6 24.9 - - - +
2841 ARG* 2.6 42.6 + - - +
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Residues in contact with ILE 266 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551 MET* 3.8 16.4 - - + -
861 PRO* 4.5 14.6 - - + -
1471 SER 3.9 7.0 - - - +
1481 ASN* 3.0 8.7 - - - +
1491 PHE* 2.7 44.6 + - + +
1501 HIS* 3.3 3.2 + - - -
2051 VAL* 4.4 13.5 - - + -
2641 VAL* 3.2 28.3 - - + -
2651 ASP* 1.3 69.6 - - - +
2671 CYS* 1.3 56.7 + - - +
2681 GLY 3.4 15.5 - - - +
2791 TRP* 3.6 35.7 - - + -
2801 LYS 3.7 5.8 - - - +
1265 LEU* 4.9 10.8 - - + -
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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