Contacts of the strand formed by residues 218 - 225 (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 THR 218 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1536 ALA* 4.1 7.4 - - - +
1546 VAL 3.3 14.9 + - - -
1556 GLY* 3.5 12.7 - - - -
1576 GLU* 4.5 9.0 - - + +
1586 PRO 4.4 11.9 - - - +
1596 LEU* 4.3 9.8 - - + +
1606 GLU* 5.4 0.7 - - - +
2156 ASN* 3.1 51.0 - - + +
2166 GLU 3.6 0.8 + - - -
2176 ASN* 1.3 83.4 - - + +
2196 ARG* 1.3 79.8 + - - +
2206 TYR* 4.2 2.3 + - - +
2526 PRO* 4.6 1.6 - - - -
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Residues in contact with ARG 219 (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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1536 ALA* 3.0 4.5 - - - +
1546 VAL 2.9 35.2 + - - +
2156 ASN 4.8 0.8 + - - -
2166 GLU 3.5 23.0 + - - -
2176 ASN* 4.3 1.6 + - - +
2186 THR* 1.3 88.1 + - - +
2206 TYR* 1.3 61.7 + - - +
2216 PHE* 4.0 23.0 - - + -
2436 VAL 5.3 0.7 - - - +
2446 LEU* 2.7 44.7 + - + +
2456 LEU 4.7 0.8 + - - -
2466 ASP* 3.2 35.0 + - - +
2506 VAL* 3.3 10.5 + - - +
2516 GLY 3.7 12.7 + - - -
2526 PRO* 3.9 9.1 - - + +
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Residues in contact with TYR 220 (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* 3.8 10.5 - + + -
1526 PHE 3.3 5.4 - - - +
1536 ALA* 3.6 15.5 - - + -
1596 LEU* 5.1 3.1 - - + -
2106 PRO* 3.7 37.4 + - + -
2126 PRO* 3.7 32.3 - - + +
2156 ASN* 4.4 25.1 - - + -
2186 THR 4.9 1.6 - - - -
2196 ARG* 1.3 80.6 - - - +
2216 PHE* 1.3 82.5 - - - +
2226 GLY 5.1 0.9 - - - -
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Residues in contact with PHE 221 (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* 3.1 7.5 - - - -
1526 PHE* 2.7 80.0 + + + +
1546 VAL 5.6 0.2 - - - -
2196 ARG* 4.0 26.5 - - + -
2206 TYR* 1.3 94.2 - - - +
2226 GLY* 1.3 58.3 + - - +
2426 THR* 4.0 24.5 - - + -
2436 VAL 5.2 2.9 - - - -
2446 LEU* 4.7 6.1 - - + -
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Residues in contact with GLY 222 (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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1496 PHE* 4.5 5.8 - - - -
1506 HIS 3.1 14.4 - - - -
1516 PHE* 3.7 10.7 - - - -
2206 TYR* 5.1 1.4 - - - -
2216 PHE* 1.3 78.0 - - - +
2236 THR* 1.3 70.8 + - - +
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Residues in contact with THR 223 (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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1486 ASN* 3.8 1.6 - - - +
1496 PHE* 3.4 10.6 - - - -
1506 HIS* 3.1 32.5 + - + +
2226 GLY* 1.3 81.3 - - - +
2246 TYR* 1.3 61.1 + - - +
2256 THR* 3.8 12.1 + - - -
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Residues in contact with TYR 224 (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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1476 SER* 3.3 17.5 + - - -
1486 ASN 3.6 10.8 - - - -
1496 PHE* 3.9 19.4 - + + -
2236 THR* 1.3 75.1 + - - +
2256 THR* 1.3 70.2 + - - +
2266 GLY* 3.1 40.0 - - - -
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Residues in contact with THR 225 (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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1476 SER* 3.4 1.9 - - - -
1486 ASN* 3.0 46.7 + - - +
2236 THR* 3.8 11.3 + - - -
2246 TYR* 1.3 81.9 + - - +
2266 GLY* 1.3 65.4 + - - +
2306 VAL* 3.9 20.7 - - + +
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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