Contacts of the strand formed by residues 218 - 225 (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 THR 218 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2382 ASN* 2.9 19.9 + - - -
1533 ALA* 4.2 3.8 - - - +
1543 VAL 3.5 10.1 + - - -
1553 GLY* 3.4 13.9 - - - -
1573 GLU* 4.2 8.5 - - + +
1583 PRO 4.2 13.7 - - - +
1593 LEU* 4.2 15.0 - - + +
1603 GLU* 5.0 2.0 - - - +
2153 ASN* 3.1 39.4 + - + +
2163 GLU 3.5 0.4 - - - -
2173 ASN* 1.3 85.0 - - + +
2193 ARG* 1.3 77.9 + - - +
2203 TYR* 5.2 0.5 - - - +
2523 PRO* 4.4 0.4 - - - -
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Residues in contact with ARG 219 (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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2382 ASN* 3.4 12.5 - - - +
2392 THR* 4.4 13.5 - - + -
1533 ALA* 2.9 3.6 - - - +
1543 VAL 2.8 31.7 + - - +
2153 ASN 4.9 0.4 + - - -
2163 GLU 3.7 19.2 + - - -
2173 ASN* 4.5 1.4 + - - -
2183 THR* 1.3 90.5 + - - +
2203 TYR* 1.3 62.1 + - - +
2213 PHE* 3.7 19.7 - - + -
2433 VAL 5.9 0.2 - - - +
2443 LEU* 2.7 37.0 + - + +
2453 LEU 4.1 4.6 + - - -
2463 ASP* 3.4 20.1 + - - +
2503 VAL* 3.0 28.5 + - - +
2513 GLY* 3.4 14.1 + - - -
2523 PRO* 4.0 18.3 - - + +
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Residues in contact with TYR 220 (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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1182 GLU* 2.6 26.2 + - - -
2362 ILE* 3.5 7.9 - - + -
2372 THR* 2.9 50.7 - - - +
2382 ASN* 2.8 45.5 + - + +
1513 PHE* 3.4 13.7 - + + -
1523 PHE 3.2 5.4 - - - -
1533 ALA* 3.3 18.2 - - + -
1593 LEU* 5.1 2.5 - - + -
2103 PRO* 3.7 36.5 + - + -
2123 PRO* 3.8 17.3 - - + +
2153 ASN* 4.5 19.3 - - + -
2183 THR* 5.3 0.7 - - - -
2193 ARG* 1.3 76.2 - - - +
2213 PHE* 1.3 72.1 + - - +
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Residues in contact with PHE 221 (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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2362 ILE 3.3 9.6 - - - -
2372 THR* 3.4 14.6 - - + +
2392 THR* 3.4 23.3 - - + -
1513 PHE* 3.0 7.4 - - - -
1523 PHE* 2.8 74.2 + + + -
1543 VAL 5.1 0.2 - - - -
2193 ARG* 3.7 24.2 - - + -
2203 TYR* 1.3 92.3 - - - +
2223 GLY* 1.3 58.9 + - - +
2423 THR* 4.2 25.4 - - + -
2433 VAL 5.1 1.8 - - - -
2443 LEU* 4.5 7.6 - - + -
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Residues in contact with GLY 222 (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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2352 HIS* 3.2 7.4 - - - +
2362 ILE* 2.9 36.2 + - - +
2372 THR* 4.1 0.6 + - - -
1493 PHE* 4.5 0.7 - - - -
1503 HIS 3.1 14.6 - - - -
1513 PHE* 3.7 10.1 - - - -
2213 PHE* 1.3 78.1 - - - +
2233 THR* 1.3 65.4 + - - +
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Residues in contact with THR 223 (chain 3).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1222 VAL* 6.0 0.2 - - - -
2332 VAL* 4.8 3.1 - - - +
2342 LEU 3.1 7.0 - - - -
2352 HIS* 3.2 34.4 + - + +
2362 ILE* 5.4 0.4 - - - -
1483 ASN* 3.8 1.2 - - - +
1493 PHE* 3.1 20.3 - - - -
1503 HIS* 3.0 22.9 + - + +
2223 GLY* 1.3 79.1 - - - +
2243 TYR* 1.3 62.7 + - - +
2253 THR* 3.6 14.0 + - - -
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Residues in contact with TYR 224 (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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1222 VAL* 3.7 33.4 - - + -
1232 THR* 5.1 0.7 - - - -
1252 MET* 3.2 50.3 + - + +
1262 LEU* 3.3 35.7 - - + -
1432 PRO* 4.6 3.5 - - - +
2322 PRO* 4.0 7.0 - - + -
2332 VAL* 3.1 5.0 - - - +
2342 LEU* 2.7 43.8 + - + +
1473 SER* 3.4 7.9 + - - -
1483 ASN 3.5 9.2 - - - -
1493 PHE* 3.8 10.0 - + + -
2233 THR* 1.3 74.3 - - - +
2253 THR* 1.3 69.6 + - - +
2263 GLY* 2.9 36.2 - - - -
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Residues in contact with THR 225 (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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2312 PRO* 5.0 3.1 - - + -
2322 PRO 3.2 6.3 - - - +
2332 VAL* 3.6 22.0 - - + +
1473 SER* 3.2 3.5 - - - -
1483 ASN* 2.9 45.5 + - - +
2233 THR* 3.6 11.3 + - - -
2243 TYR* 1.3 82.0 + - - +
2263 GLY* 1.3 67.0 + - - +
2303 VAL* 4.1 17.9 - - + +
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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