Contacts of the strand formed by residues 159 - 163 (chain 3) 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 LEU 159 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883 TYR* 4.9 3.6 - - + -
903 VAL* 5.3 1.6 - - + +
1513 PHE* 3.8 31.6 - - + -
1533 ALA* 4.6 5.6 - - + -
1573 GLU 3.8 0.2 + - - -
1583 PRO* 1.3 72.9 - - - +
1603 GLU* 1.3 60.6 + - - +
1613 LEU* 3.5 19.8 - - + +
1963 VAL* 3.2 2.6 - - - -
1973 LEU* 2.7 51.2 + - + -
2103 PRO* 4.4 9.6 - - + -
2153 ASN* 3.4 28.9 - - - +
2183 THR* 4.2 15.0 - - - +
2203 TYR* 5.1 2.0 - - + -
2603 TYR* 5.4 1.2 - - - +
2623 SER* 4.1 25.0 + - - +
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Residues in contact with GLU 160 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1573 GLU* 4.2 16.5 - - - +
1583 PRO 4.0 7.2 - - - +
1593 LEU* 1.3 71.0 - - - +
1613 LEU* 1.3 64.3 + - - +
1953 ALA 3.5 8.5 - - - +
1963 VAL* 4.3 7.0 - - + +
2103 PRO* 3.6 0.7 - - - +
2113 ASP* 2.9 8.7 + - - -
2143 LYS* 2.5 59.2 + - + +
2153 ASN* 2.8 47.6 + - - +
2163 GLU 4.1 2.3 + - - -
2183 THR* 5.0 1.7 - - - +
3456 ASP* 4.4 11.4 - - - +
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Residues in contact with LEU 161 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883 TYR* 5.4 5.4 - - + -
1593 LEU* 3.5 35.2 - - + +
1603 GLU* 1.3 82.9 - - - +
1623 GLN* 1.3 62.9 + - - +
1943 LYS* 3.5 5.5 - - - +
1953 ALA* 2.7 33.7 + - + +
1963 VAL 4.2 2.0 - - - +
1973 LEU* 3.8 26.5 - - + +
2033 TYR* 4.0 26.2 - - + -
2083 TRP* 3.7 28.7 - - + -
2093 VAL 3.5 9.0 - - - +
2103 PRO* 4.2 9.4 - - + -
2113 ASP* 3.4 13.3 - - - +
2143 LYS* 5.4 0.5 - - - +
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Residues in contact with GLN 162 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202 ILE* 4.6 6.7 - - + -
1613 LEU* 1.3 77.7 - - - +
1633 GLY* 1.3 85.7 + - - +
1643 VAL* 3.9 5.9 + - + +
1893 MET* 3.1 29.8 - - + +
1903 ASN 3.2 19.1 - - - +
1913 THR* 4.4 3.0 - - - +
1933 HIS* 3.0 12.1 - - - +
1943 LYS* 2.9 43.2 - - - +
2083 TRP* 3.3 3.8 - - - -
2093 VAL* 2.9 32.8 + - + +
2103 PRO 5.0 0.4 - - - +
2113 ASP* 3.7 16.8 - - + +
2123 PRO* 5.2 2.0 - - + -
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Residues in contact with GLY 163 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1623 GLN* 1.3 86.6 - - - +
1643 VAL* 1.3 69.7 + - - +
1793 PRO* 4.7 3.6 - - - -
1883 GLN 4.7 0.2 - - - +
1903 ASN 4.6 4.3 + - - -
1933 HIS* 2.6 35.8 + - - +
2073 CYS 3.2 13.2 - - - -
2083 TRP* 3.1 12.9 - - - -
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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