Contacts of the strand formed by residues 258 - 266 (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 SER 258 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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924 ARG* 3.4 39.4 + - - -
934 ILE 3.2 6.5 - - - -
944 PRO* 4.2 0.2 - - - -
954 LEU* 4.5 0.9 - - - -
1564 GLY 4.0 1.6 - - - +
2544 CYS* 3.2 24.2 - - - +
2564 ALA* 2.5 19.8 + - - +
2574 ASP* 1.3 80.6 + - - +
2594 LEU* 1.3 61.8 + - - +
2604 TYR* 3.5 26.9 + - - -
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Residues in contact with LEU 259 (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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474 VAL* 5.6 3.6 - - + -
914 ALA 3.8 0.2 - - - +
924 ARG* 3.1 6.8 - - - +
934 ILE* 2.5 60.8 + - + +
954 LEU* 4.1 9.2 - - + -
1124 ALA* 5.0 5.6 - - + -
1544 VAL* 4.6 8.7 - - + -
1554 GLY 3.4 17.9 - - - +
2544 CYS* 4.1 12.6 - - - -
2584 SER* 1.3 74.4 - - - +
2604 TYR* 1.3 76.0 + - - +
2614 VAL* 4.8 0.2 - - + -
2884 ILE* 3.8 32.1 - - + -
2904 LEU* 3.9 27.4 - - + -
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Residues in contact with TYR 260 (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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904 VAL* 5.4 7.9 - - + -
914 ALA 3.6 5.8 - - - +
924 ARG* 4.1 23.7 - - + -
1534 ALA 3.8 0.7 - - - +
1544 VAL* 3.3 6.4 - - - -
1554 GLY 2.9 47.5 + - - +
1564 GLY 3.8 3.8 - - - -
1574 GLU* 3.4 30.0 - - - +
1584 PRO* 3.5 39.7 - - + +
1594 LEU 5.4 1.1 - - - +
1974 LEU 5.9 0.7 - - - -
2564 ALA* 4.9 8.7 - - + +
2584 SER* 3.5 32.5 + - - -
2594 LEU* 1.3 77.1 - - - +
2614 VAL* 1.3 66.0 + - - +
2624 SER* 4.6 4.4 + - - +
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Residues in contact with VAL 261 (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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494 CYS* 4.7 6.3 - - - -
514 LEU* 3.9 15.2 - - + +
904 VAL* 3.4 4.0 - - - +
914 ALA* 3.0 34.8 + - + +
934 ILE* 4.3 18.4 - - + -
1534 ALA 3.5 4.3 - - - +
1544 VAL* 4.9 1.3 - - + -
2594 LEU* 4.8 1.8 - - + -
2604 TYR* 1.3 81.5 - - - +
2624 SER* 1.3 66.4 + - - +
2864 PHE* 3.3 42.2 - - + -
2884 ILE* 3.9 27.8 - - + -
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Residues in contact with SER 262 (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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514 LEU* 4.2 1.1 - - - -
884 TYR* 5.9 0.2 - - - -
894 SER 3.2 13.5 - - - -
904 VAL* 4.2 5.0 - - - +
1514 PHE* 4.5 3.1 - - - -
1524 PHE* 3.1 3.8 - - - +
1534 ALA* 2.8 44.3 + - - +
1594 LEU* 4.4 18.3 + - - +
1974 LEU* 4.1 20.6 - - - -
2604 TYR* 4.6 4.2 + - - +
2614 VAL* 1.3 84.3 + - - +
2634 ALA* 1.3 62.9 + - - +
2864 PHE* 4.1 1.7 - - - -
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Residues in contact with ALA 263 (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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514 LEU* 4.3 7.8 - - + +
884 TYR* 4.2 0.7 - - - +
894 SER* 3.2 28.3 + - - +
1514 PHE* 3.1 16.3 - - - +
1524 PHE* 3.6 2.5 - - + +
2624 SER* 1.3 79.0 - - - +
2644 VAL* 1.3 72.7 + - - +
2654 ASP* 4.3 4.5 - - - +
2844 ARG* 3.6 30.5 - - + -
2864 PHE* 4.0 6.1 - - + -
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Residues in contact with VAL 264 (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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554 MET* 6.2 0.2 - - - -
874 CYS 4.8 3.4 - - - +
884 TYR* 3.3 39.0 - - + -
894 SER* 5.3 3.6 - - - -
1494 PHE* 3.8 16.4 - - + -
1504 HIS* 3.1 2.9 - - - -
1514 PHE* 2.7 38.3 + - + -
2054 VAL* 3.5 22.2 - - + -
2634 ALA* 1.3 85.6 - - - +
2654 ASP* 1.3 68.6 + - - +
2664 ILE* 3.2 27.6 - - + -
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Residues in contact with ASP 265 (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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534 PRO* 5.6 5.2 - - + +
554 MET* 4.4 2.5 - - - -
1194 VAL* 3.4 15.5 - - + +
1494 PHE 3.4 0.4 - - - -
1504 HIS* 2.9 29.9 + - + +
2634 ALA* 4.3 1.2 - - - +
2644 VAL* 1.3 84.1 + - - +
2664 ILE* 1.3 62.9 + - - +
2674 CYS* 2.8 12.8 + - - -
2814 GLY* 3.2 19.2 - - - -
2824 LEU 3.6 24.1 - - - +
2844 ARG* 2.6 43.2 + - - +
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Residues in contact with ILE 266 (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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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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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