Contacts of the strand formed by residues 218 - 225 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2384 ASN* 2.9 19.6 + - - -
1535 ALA* 4.4 3.6 - - - +
1545 VAL 3.4 8.1 + - - -
1555 GLY* 3.4 16.4 - - - -
1575 GLU* 4.1 23.8 - - - +
1585 PRO 4.2 5.8 - - - +
1595 LEU* 4.2 17.2 - - - +
2155 ASN* 3.3 33.0 + - + +
2175 ASN* 1.3 82.1 - - - +
2195 ARG* 1.3 78.9 + - - +
2205 TYR* 4.8 1.0 - - - +
2525 PRO* 4.3 1.8 - - - -
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Residues in contact with ARG 219 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2384 ASN* 3.4 9.6 - - - +
2394 THR* 4.0 15.9 - - + -
1535 ALA* 3.1 3.5 - - - +
1545 VAL 2.9 29.0 + - - +
2165 GLU 3.9 17.6 + - - -
2175 ASN* 4.4 2.8 + - - +
2185 THR* 1.3 89.8 + - - +
2205 TYR* 1.3 63.4 + - - +
2215 PHE* 3.5 23.5 - - + -
2445 LEU* 2.6 48.8 + - + +
2455 LEU 4.3 3.0 + - - -
2465 ASP* 3.4 20.4 + - - +
2505 VAL 3.0 21.0 + - - -
2515 GLY* 3.5 11.1 + - - -
2525 PRO* 4.0 12.1 - - + +
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Residues in contact with TYR 220 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184 GLU* 2.6 27.0 + - - -
2364 ILE* 3.5 25.1 - - + +
2374 THR* 2.8 24.9 - - - +
2384 ASN* 2.7 50.2 + - + +
1515 PHE* 3.7 12.3 - + + -
1525 PHE 3.2 6.5 - - - +
1535 ALA* 3.2 21.3 - - + -
1595 LEU* 5.0 1.6 - - + -
2105 PRO* 3.3 41.5 + - + +
2125 PRO* 4.1 13.9 - - + +
2155 ASN* 4.6 15.9 - - + -
2185 THR* 4.8 2.7 - - - +
2195 ARG* 1.3 79.3 - - - +
2215 PHE* 1.3 72.7 + - - +
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Residues in contact with PHE 221 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2364 ILE 3.3 8.1 - - - -
2374 THR* 3.5 18.4 - - + +
2394 THR* 3.6 23.8 - - + -
1515 PHE* 3.3 5.0 - - - -
1525 PHE* 2.8 76.2 + + + +
2195 ARG* 3.5 25.4 - - + -
2205 TYR* 1.3 88.5 - - - +
2225 GLY* 1.3 55.8 - - - +
2425 THR* 4.3 24.2 - - + -
2435 VAL 4.9 3.1 - - - -
2445 LEU* 4.4 9.0 - - + -
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Residues in contact with GLY 222 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2354 HIS* 3.2 5.4 - - - +
2364 ILE* 2.8 41.5 + - - +
2374 THR* 4.3 0.5 + - - -
1495 PHE* 4.6 0.4 - - - -
1505 HIS 3.2 13.0 - - - -
1515 PHE* 3.5 11.0 - - - -
2215 PHE* 1.3 76.2 - - - +
2235 THR* 1.3 65.9 + - - +
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Residues in contact with THR 223 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2334 VAL* 4.9 4.2 - - - +
2344 LEU 3.2 6.1 + - - -
2354 HIS* 3.2 32.1 + - + -
2364 ILE* 5.4 0.4 - - - -
1485 ASN* 4.2 0.7 - - - +
1495 PHE* 3.4 7.4 - - - -
1505 HIS* 2.8 36.0 + - + +
2225 GLY* 1.3 79.6 - - - +
2245 TYR* 1.3 62.5 + - - +
2255 THR* 4.0 11.4 + - - -
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Residues in contact with TYR 224 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1224 VAL* 4.1 23.8 - - + -
1234 THR* 5.2 0.7 - - - -
1254 MET* 3.0 55.6 + - + +
1264 LEU* 3.7 29.6 - - + -
1434 PRO* 4.6 3.3 - - - +
2324 PRO* 4.0 7.2 - - + -
2334 VAL* 3.1 5.9 - - - +
2344 LEU* 2.8 53.9 + - + +
1475 SER* 4.1 5.9 + - - -
1485 ASN 3.6 10.5 - - - -
1495 PHE* 3.7 21.0 - + + -
2235 THR* 1.3 74.4 - - - +
2255 THR* 1.3 65.2 + - - +
2265 GLY* 3.2 32.0 - - - -
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Residues in contact with THR 225 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2314 PRO* 5.5 2.5 - - + -
2324 PRO 3.5 6.5 - - - +
2334 VAL* 3.3 25.5 - - + +
1475 SER* 3.4 2.4 - - - -
1485 ASN* 2.8 55.7 + - - +
2235 THR* 4.0 10.0 + - - -
2245 TYR* 1.3 78.0 - - - +
2265 GLY* 1.3 61.0 + - - +
2305 VAL* 3.7 17.7 - - + +
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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