Contacts of the strand formed by residues 218 - 226 (chain 2) 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 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2381 ASN* 2.9 19.1 + - - -
1532 ALA* 4.2 8.5 - - - +
1542 VAL 3.5 7.2 + - - -
1552 GLY* 3.3 18.2 - - - -
1572 GLU* 3.9 24.2 - - - +
1582 PRO 4.4 4.5 - - - +
1592 LEU* 4.3 8.9 - - - +
2152 ASN* 3.5 34.9 + - + +
2172 ASN* 1.3 85.6 - - - +
2192 ARG* 1.3 75.6 + - - +
2202 TYR* 5.0 1.1 - - - +
2522 PRO* 4.3 1.3 - - - -
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Residues in contact with ARG 219 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2381 ASN* 3.4 12.8 - - - +
2391 THR* 4.4 15.4 - - + +
1532 ALA* 3.1 5.5 - - - +
1542 VAL 2.9 30.3 + - - +
2152 ASN 5.5 0.2 + - - -
2162 GLU 3.7 21.2 + - - -
2172 ASN* 4.4 3.8 + - - +
2182 THR* 1.3 87.3 + - - +
2202 TYR* 1.3 61.1 + - - +
2212 PHE* 3.8 22.6 - - + -
2442 LEU* 2.7 47.7 + - + +
2452 LEU 4.4 1.8 + - - -
2462 ASP* 3.2 21.6 + - - +
2502 VAL* 2.9 29.3 + - - +
2512 GLY* 3.4 11.3 - - - -
2522 PRO* 4.2 9.1 - - + +
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Residues in contact with TYR 220 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181 GLU* 2.7 25.3 + - - -
2361 ILE* 3.4 18.6 - - + +
2371 THR* 3.0 37.4 - - - +
2381 ASN* 2.7 51.5 + - + +
1512 PHE* 3.5 12.8 - + + -
1522 PHE 3.3 4.3 - - - -
1532 ALA* 3.4 19.1 - - + -
1592 LEU* 5.2 1.1 - - + -
2102 PRO* 3.4 40.0 + - + -
2122 PRO* 3.8 18.6 - - + +
2152 ASN* 4.8 16.4 - - + -
2182 THR* 4.9 2.0 - - - +
2192 ARG* 1.3 77.2 - - - +
2212 PHE* 1.3 71.3 + - - +
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Residues in contact with PHE 221 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2361 ILE 3.6 6.7 - - - -
2371 THR* 3.7 8.5 - - + +
2391 THR* 3.3 27.6 - - + -
1512 PHE* 3.0 8.2 - - - -
1522 PHE* 2.8 73.2 + + + -
1542 VAL 5.5 0.4 - - - -
2192 ARG* 3.8 23.8 - - + -
2202 TYR* 1.3 92.7 - - - +
2222 GLY* 1.3 60.3 + - - +
2422 THR* 4.1 23.1 - - + -
2432 VAL 5.1 0.9 - - - -
2442 LEU* 4.4 6.5 - - + -
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Residues in contact with GLY 222 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2351 HIS* 3.3 5.7 - - - +
2361 ILE* 2.9 39.9 + - - +
2371 THR* 4.1 0.9 + - - -
1492 PHE* 4.6 0.4 - - - -
1502 HIS 3.0 13.5 - - - -
1512 PHE* 3.7 10.5 - - - -
2212 PHE* 1.3 78.5 - - - +
2232 THR* 1.3 67.4 - - - +
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Residues in contact with THR 223 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2331 VAL* 4.5 3.6 - - - +
2341 LEU 3.0 5.2 + - - -
2351 HIS* 3.0 38.2 + - + +
2361 ILE* 5.3 0.2 - - - -
1482 ASN* 4.8 0.2 - - - +
1492 PHE* 3.5 10.6 - - - -
1502 HIS* 3.0 33.4 + - + +
2222 GLY* 1.3 78.1 - - - +
2242 TYR* 1.3 61.3 + - - +
2252 THR* 3.5 15.4 + - - -
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Residues in contact with TYR 224 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221 VAL* 3.7 36.1 - - + +
1251 MET* 3.2 60.0 + - + +
1261 LEU* 3.8 28.4 - - + -
1431 PRO* 4.6 3.6 - - - +
2321 PRO* 4.4 5.6 - - + -
2331 VAL* 3.2 6.1 - - - +
2341 LEU* 2.6 45.7 + - + +
1472 SER* 3.8 14.0 + - - -
1482 ASN 3.8 10.1 - - - -
1492 PHE* 3.8 15.5 - + + -
2232 THR* 1.3 71.1 - - - +
2252 THR* 1.3 64.4 + - - +
2262 GLY* 3.4 27.9 - - - -
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Residues in contact with THR 225 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2311 PRO* 5.8 2.5 - - + -
2321 PRO 3.5 3.4 - - - +
2331 VAL* 3.5 25.8 - - + -
1472 SER* 3.5 2.4 - - - -
1482 ASN* 2.9 49.7 + - - +
1502 HIS* 5.7 0.3 - - - -
2232 THR* 3.5 13.3 + - - -
2242 TYR* 1.3 76.0 - - - +
2262 GLY* 1.3 60.0 + - - +
2302 VAL* 3.7 16.4 - - + +
2312 PRO 6.1 0.9 - - - +
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Residues in contact with GLY 226 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1441 ILE 4.7 3.6 - - - -
2311 PRO* 2.8 32.2 - - - +
2321 PRO* 3.0 21.8 + - - +
1472 SER* 3.9 2.0 - - - -
2242 TYR* 3.4 31.4 - - - -
2252 THR* 1.3 74.8 - - - +
2272 GLY* 1.3 57.4 + - - -
2302 VAL* 3.8 2.7 - - - -
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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