Contacts of the strand formed by residues 159 - 163 (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 LEU 159 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886 TYR* 4.9 2.7 - - + -
906 VAL* 6.2 0.9 - - + -
1516 PHE* 3.8 27.1 - - + -
1536 ALA* 4.7 6.3 - - + -
1576 GLU 3.8 0.2 + - - -
1586 PRO* 1.3 72.9 - - - +
1606 GLU* 1.3 64.8 + - - +
1616 LEU* 3.7 22.3 + - + +
1966 VAL* 3.4 2.4 - - - +
1976 LEU* 2.9 48.5 + - + +
2106 PRO* 4.2 10.8 - - + -
2156 ASN* 3.5 24.2 - - - +
2186 THR* 4.3 15.7 - - - +
2206 TYR* 5.1 2.9 - - + -
2606 TYR* 5.4 1.6 - - - +
2626 SER* 4.1 24.0 + - - +
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Residues in contact with GLU 160 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3453 ASP* 4.7 7.8 - - - +
1576 GLU* 4.5 14.6 - - - +
1586 PRO 3.3 6.0 + - - +
1596 LEU* 1.3 71.6 - - - +
1616 LEU* 1.3 62.0 + - - +
1956 ALA 3.6 8.3 - - - +
1966 VAL* 4.4 6.3 - - + +
2106 PRO* 3.5 4.5 - - - +
2116 ASP* 2.8 9.4 + - - -
2146 LYS* 2.5 62.9 + - + +
2156 ASN* 2.7 43.7 + - - +
2166 GLU 4.3 1.0 + - - -
2176 ASN 5.6 0.2 + - - -
2186 THR* 5.4 0.5 - - - +
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Residues in contact with LEU 161 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886 TYR* 5.0 8.7 - - + -
1596 LEU* 3.7 33.2 - - + +
1606 GLU* 1.3 81.9 - - - +
1626 GLN* 1.3 59.6 + - - +
1936 HIS 4.3 0.2 - - - -
1946 LYS* 3.5 4.7 - - - +
1956 ALA 2.7 33.8 + - - +
1966 VAL* 4.2 2.9 - - - +
1976 LEU* 3.8 23.8 - - + +
2036 TYR* 4.0 24.9 - - + -
2086 TRP* 3.9 29.4 - - + -
2096 VAL 3.3 16.8 - - - +
2106 PRO* 4.0 3.8 - - + -
2116 ASP* 3.4 11.7 - - - +
2146 LYS* 5.3 0.3 - - - +
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Residues in contact with GLN 162 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1616 LEU* 1.3 75.6 - - - +
1636 GLY* 1.3 87.5 + - - +
1646 VAL* 3.8 8.4 + - + -
1896 MET* 3.5 25.7 - - + +
1906 ASN 3.1 22.1 + - - +
1916 THR* 4.5 1.2 - - - +
1936 HIS* 3.1 10.1 - - - +
1946 LYS* 2.9 39.8 - - - +
2086 TRP* 3.4 5.0 - - - -
2096 VAL* 2.9 39.1 + - + +
2116 ASP* 3.8 19.1 - - + -
2126 PRO* 5.4 1.8 - - + -
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Residues in contact with GLY 163 (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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1626 GLN* 1.3 95.5 - - - +
1646 VAL* 1.3 66.6 + - - +
1796 PRO* 4.6 3.6 - - - -
1886 GLN 4.5 1.9 - - - +
1906 ASN 4.4 0.3 - - - +
1936 HIS* 2.7 34.5 + - - +
2076 CYS 3.0 12.3 - - - -
2086 TRP* 3.2 15.1 - - - -
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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