Contacts of the strand formed by residues 233 - 237 (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 VAL 233 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2231 THR* 5.4 2.2 - - - +
2241 TYR 3.3 8.7 - - - +
2251 THR* 4.2 18.2 - - + +
1485 ASN* 5.0 1.0 - - - +
1505 HIS* 5.6 1.2 + - - -
2315 PRO* 3.4 14.3 + - + +
2325 PRO* 1.3 82.2 - - - +
2345 LEU* 1.3 75.1 + - - +
2355 HIS* 3.8 25.8 + - + +
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Residues in contact with LEU 234 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2231 THR* 2.9 4.2 - - - -
2241 TYR* 2.7 51.6 + - + +
1195 VAL* 4.7 20.4 - - + -
1225 VAL* 3.5 42.7 - - + +
1255 MET* 4.6 11.7 - - - -
1505 HIS* 4.1 31.6 - - + +
2325 PRO* 5.0 4.5 - - + -
2335 VAL* 1.3 89.5 - - - +
2355 HIS* 1.3 66.7 + - - +
2365 ILE 4.1 0.3 + - - -
2675 CYS* 5.0 3.8 - - + -
2825 LEU* 4.7 2.7 - - + -
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Residues in contact with HIS 235 (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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2221 GLY 3.1 7.2 - - - +
2231 THR* 3.3 30.0 - - + +
1185 GLU* 4.3 8.1 - - - +
1195 VAL 5.5 1.2 + - - -
1225 VAL* 5.6 0.7 - - - -
2335 VAL* 3.8 29.8 + - + +
2345 LEU* 1.3 77.7 - - - +
2365 ILE* 1.3 62.6 + - - +
2375 THR* 4.0 6.5 + - - +
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Residues in contact with ILE 236 (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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1491 PHE* 4.6 14.1 - - + -
1511 PHE* 4.8 6.3 - - + -
2091 VAL* 4.4 21.1 - - + -
2101 PRO* 4.2 9.9 - - + +
2121 PRO* 5.7 1.3 - - + -
2201 TYR* 3.5 16.6 - - + -
2211 PHE* 3.7 0.5 - - - -
2221 GLY* 2.8 36.9 + - - +
2231 THR* 5.5 0.2 - - - -
1185 GLU* 2.8 30.5 - - + +
1195 VAL 3.4 25.8 - - - +
1205 ILE* 5.0 1.3 - - + -
1225 VAL* 3.6 20.6 - - + -
2345 LEU 4.1 0.8 + - - +
2355 HIS* 1.3 75.1 - - - +
2375 THR* 1.3 69.5 + - - +
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Residues in contact with THR 237 (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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2201 TYR* 3.2 17.8 - - - +
2211 PHE* 3.5 18.2 - - + +
2221 GLY 4.0 1.2 + - - -
1175 THR 5.0 3.5 - - - +
1185 GLU* 2.5 27.4 + - - +
2355 HIS* 4.0 7.1 + - - +
2365 ILE* 1.3 80.9 + - - +
2385 ASN* 1.3 61.1 + - - +
2395 THR* 2.5 37.2 + - - +
2405 ALA* 4.2 16.9 + - + +
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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