Contacts of the strand formed by residues 148 - 155 (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 ASN 148 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1466 GLY 3.8 5.3 + - - +
1476 SER* 1.3 76.5 - - - +
1496 PHE* 1.3 62.1 + - - +
1506 HIS* 4.1 16.4 + - - +
2236 THR 3.8 0.7 - - - +
2246 TYR* 3.6 4.4 - - - -
2256 THR* 3.0 50.9 + - - +
2306 VAL* 4.7 3.9 - - - +
2316 PRO 4.6 2.0 + - - -
2326 PRO* 3.5 30.9 - - - +
2336 VAL 4.6 2.4 - - - +
2666 ILE* 3.2 19.5 - - - +
2676 CYS 3.3 15.9 + - - +
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Residues in contact with PHE 149 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886 TYR* 4.8 13.7 - - - -
1486 ASN* 1.3 75.6 - - - +
1506 HIS* 1.3 62.8 + - - +
1516 PHE* 3.5 34.5 - + + -
2056 VAL* 4.9 8.5 - - + -
2096 VAL* 6.4 1.8 - - + -
2106 PRO* 5.9 2.9 - - + -
2226 GLY* 4.5 3.4 - - - -
2236 THR 3.4 31.4 - - - -
2246 TYR* 3.9 19.7 - + + -
2646 VAL* 3.4 33.0 - - + +
2656 ASP* 3.3 2.4 - - - -
2666 ILE* 2.8 48.4 + - + +
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Residues in contact with HIS 150 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196 VAL* 5.1 4.1 - - + +
1486 ASN* 4.1 21.0 + - - -
1496 PHE* 1.3 77.8 + - - +
1516 PHE* 1.3 60.3 + - - +
2226 GLY* 3.1 19.2 - - - -
2236 THR* 3.1 19.1 + - + +
2326 PRO* 5.5 0.4 - - - +
2336 VAL 5.7 0.2 - - - -
2346 LEU* 3.7 30.5 - - + +
2646 VAL 3.1 3.8 - - - -
2656 ASP* 3.0 25.0 + - + +
2666 ILE 3.5 9.3 + - - -
2676 CYS* 3.4 42.7 - - + +
2846 ARG* 4.9 7.6 - - - +
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Residues in contact with PHE 151 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886 TYR* 4.1 15.5 - + - -
1496 PHE* 3.5 31.4 - + + -
1506 HIS* 1.3 77.4 - - - +
1526 PHE* 1.3 77.8 + - - +
1536 ALA* 3.7 19.5 - - + -
1596 LEU* 3.8 18.6 - - + -
2106 PRO* 4.1 20.4 - - + -
2206 TYR* 3.8 22.2 - + + -
2216 PHE 3.1 22.4 - - - +
2226 GLY* 3.9 2.7 - - - -
2626 SER 3.8 11.7 - - - -
2636 ALA* 3.3 5.9 - - - +
2646 VAL* 2.7 45.0 + - + +
2656 ASP* 4.3 1.0 + - - -
2846 ARG* 4.1 4.4 + - - +
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Residues in contact with PHE 152 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156 VAL* 4.4 16.4 - - + -
1176 THR* 3.6 23.1 - - + -
1516 PHE* 1.3 84.2 - - - +
1536 ALA* 1.3 71.8 + - - +
1546 VAL* 4.2 15.5 - - + -
2206 TYR* 3.3 0.7 - - - +
2216 PHE* 2.7 79.7 + + + +
2426 THR* 5.1 6.3 - - + -
2626 SER 3.2 12.8 - - - +
2636 ALA* 4.1 0.2 - - + -
2846 ARG* 3.8 36.6 - - - +
2866 PHE* 4.0 11.4 - + + -
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Residues in contact with ALA 153 (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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1516 PHE* 3.7 11.2 - - + -
1526 PHE* 1.3 84.2 - - - +
1546 VAL* 1.3 68.7 + - - +
1596 LEU* 4.7 5.4 - - + -
2186 THR* 4.1 7.6 - - - +
2196 ARG 3.0 15.9 - - - +
2206 TYR* 3.6 13.5 - - + -
2606 TYR 4.6 0.2 - - - -
2616 VAL* 3.5 2.9 - - - +
2626 SER* 2.8 40.5 + - - +
2866 PHE* 4.4 1.4 - - - -
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Residues in contact with VAL 154 (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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1126 ALA* 4.4 7.6 - - + -
1156 VAL* 4.2 26.5 - - + -
1526 PHE* 4.2 11.8 - - + -
1536 ALA* 1.3 80.7 - - - +
1556 GLY* 1.3 62.5 + - - +
2186 THR* 3.4 4.5 - - - -
2196 ARG* 2.9 27.6 + - - +
2216 PHE* 6.2 0.2 - - + -
2446 LEU* 3.9 27.8 - - + -
2526 PRO* 3.8 6.5 - - + +
2596 LEU* 4.2 19.1 - - + -
2606 TYR 3.5 4.5 - - - +
2616 VAL* 4.5 4.9 - - + -
2866 PHE* 4.3 10.8 - - + -
2886 ILE* 4.4 9.6 - - + -
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Residues in contact with GLY 155 (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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1546 VAL* 1.3 78.4 - - - +
1566 GLY* 1.3 57.0 + - - -
1576 GLU 3.4 7.6 - - - -
2176 ASN 3.5 11.2 - - - -
2186 THR* 3.5 10.0 + - - -
2526 PRO* 3.8 9.4 - - - -
2546 CYS* 5.1 0.2 - - - -
2596 LEU* 3.7 7.1 - - - +
2606 TYR* 2.7 43.4 + - - +
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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