Contacts of the strand formed by residues 218 - 225 (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 THR 218 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2383 ASN* 3.0 19.5 + - - -
1534 ALA* 4.3 2.9 - - - +
1544 VAL 3.4 7.5 + - - -
1554 GLY* 3.4 16.6 - - - -
1574 GLU* 4.0 23.6 - - + +
1584 PRO 4.2 6.1 - - - +
1594 LEU* 4.1 16.7 - - - +
1604 GLU* 4.7 0.9 - - - +
2154 ASN* 3.4 31.3 + - + +
2164 GLU 3.5 0.4 + - - -
2174 ASN* 1.3 85.9 - - - +
2194 ARG* 1.3 77.3 + - - +
2204 TYR* 5.1 0.7 - - - +
2524 PRO* 4.3 1.3 - - - -
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Residues in contact with ARG 219 (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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2383 ASN* 3.6 8.0 - - - +
2393 THR* 4.2 17.3 - - + -
1534 ALA* 3.1 4.3 - - - +
1544 VAL 2.9 30.5 + - - +
2154 ASN 5.1 0.2 + - - -
2164 GLU 3.5 23.0 + - - -
2174 ASN* 4.3 3.6 + - - +
2184 THR* 1.3 87.8 + - - +
2204 TYR* 1.3 61.6 + - - +
2214 PHE* 3.8 23.3 - - + -
2444 LEU* 2.8 41.3 + - + +
2454 LEU 4.6 1.4 + - - -
2464 ASP* 3.3 21.8 - - - +
2504 VAL* 2.8 31.1 + - - +
2514 GLY* 3.6 10.9 + - - -
2524 PRO* 4.3 10.3 - - + +
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Residues in contact with TYR 220 (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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1183 GLU* 2.6 28.4 + - - -
2363 ILE* 3.5 11.7 - - + -
2373 THR* 2.8 49.4 - - - +
2383 ASN* 2.9 48.1 + - + +
1514 PHE* 3.8 11.4 - + + -
1524 PHE 3.4 5.8 - - - +
1534 ALA* 3.6 16.2 - - + -
1594 LEU* 5.0 2.7 - - + -
2104 PRO* 3.5 38.0 + - + -
2124 PRO* 3.7 18.0 - - + +
2154 ASN* 4.6 16.2 - - + -
2184 THR* 5.3 0.2 - - - -
2194 ARG* 1.3 77.1 - - - +
2214 PHE* 1.3 69.9 + - - +
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Residues in contact with PHE 221 (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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2363 ILE 3.5 7.6 - - - -
2373 THR* 3.6 11.2 - - + +
2393 THR* 3.5 34.5 - - + -
1514 PHE* 3.0 8.1 - - - -
1524 PHE* 2.7 78.0 + + + +
2194 ARG* 3.8 20.2 - - + -
2204 TYR* 1.3 98.3 - - - +
2224 GLY* 1.3 56.1 + - - +
2424 THR* 4.1 24.5 - - + -
2434 VAL 4.9 1.8 - - - -
2444 LEU* 4.7 5.4 - - + -
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Residues in contact with GLY 222 (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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2353 HIS* 3.3 2.6 - - - +
2363 ILE* 2.9 41.4 + - - +
2373 THR* 4.6 0.5 + - - -
1494 PHE* 4.3 0.7 - - - -
1504 HIS 3.1 13.7 - - - -
1514 PHE* 3.6 9.4 - - - -
2214 PHE* 1.3 75.5 - - - +
2234 THR* 1.3 71.5 + - - +
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Residues in contact with THR 223 (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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2333 VAL* 5.7 1.3 - - - -
2343 LEU 3.1 7.0 - - - -
2353 HIS* 3.2 31.6 - - + -
2363 ILE* 5.4 0.2 - - - -
1484 ASN* 3.8 1.4 + - - +
1494 PHE* 3.6 20.3 - - - -
1504 HIS* 3.1 16.6 + - - +
2224 GLY* 1.3 82.3 - - - +
2244 TYR* 1.3 63.9 + - - +
2254 THR* 3.4 11.9 + - - -
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Residues in contact with TYR 224 (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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1223 VAL* 3.2 37.8 - - + +
1233 THR* 5.2 0.2 - - - -
1253 MET* 3.1 61.0 + - + +
1263 LEU* 3.4 29.6 - - + +
1433 PRO* 4.6 3.1 - - - +
2323 PRO* 4.2 3.8 - - + -
2333 VAL* 3.2 3.1 - - - +
2343 LEU* 2.6 46.7 + - + +
1474 SER* 3.3 10.6 + - - -
1484 ASN 3.6 10.5 - - - -
1494 PHE* 3.7 15.5 - + + -
2234 THR* 1.3 70.1 - - - +
2254 THR* 1.3 70.0 + - - +
2264 GLY* 3.1 34.8 - - - -
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Residues in contact with THR 225 (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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2313 PRO* 5.6 0.4 - - + -
2323 PRO 3.3 4.3 - - - +
2333 VAL* 3.5 24.8 - - + +
1474 SER* 3.5 2.4 - - - -
1484 ASN* 3.0 46.6 + - - +
2234 THR* 3.4 12.8 + - - -
2244 TYR* 1.3 81.8 + - - +
2264 GLY* 1.3 64.6 + - - +
2304 VAL* 3.6 23.2 - - + +
2314 PRO 6.1 0.2 - - - +
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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