Contacts of the strand formed by residues 159 - 163 (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 LEU 159 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882 TYR* 4.8 3.6 - - + -
902 VAL* 5.9 0.9 - - + -
1512 PHE* 4.1 23.6 - - + -
1532 ALA* 4.6 9.0 - - + -
1572 GLU 3.6 2.1 + - - -
1582 PRO* 1.3 72.1 - - - +
1602 GLU* 1.3 60.0 + - - +
1612 LEU* 3.8 21.0 - - + +
1962 VAL* 3.4 2.6 - - - +
1972 LEU* 2.8 58.8 + - + -
2102 PRO* 4.2 12.3 - - + -
2152 ASN* 3.6 25.8 - - + +
2182 THR* 4.3 13.7 - - - +
2202 TYR* 5.2 1.8 - - + -
2602 TYR* 5.2 2.4 - - - +
2622 SER* 4.3 19.5 + - - +
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Residues in contact with GLU 160 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1572 GLU* 4.1 13.9 - - - +
1582 PRO 3.9 9.6 - - - +
1592 LEU* 1.3 71.2 - - - +
1612 LEU* 1.3 64.4 + - - +
1952 ALA 3.7 8.5 - - - +
1962 VAL* 4.4 5.8 - - + +
2102 PRO* 3.7 0.7 - - - +
2112 ASP* 3.0 8.5 + - - -
2142 LYS* 3.1 61.7 + - + +
2152 ASN* 2.6 45.5 + - - +
2162 GLU 4.1 1.7 + - - -
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Residues in contact with LEU 161 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882 TYR* 5.1 7.2 - - + +
1592 LEU* 3.8 28.7 - - + +
1602 GLU* 1.3 81.3 - - - +
1622 GLN* 1.3 61.4 + - - +
1942 LYS* 3.7 3.5 - - - +
1952 ALA 2.9 29.8 + - - +
1962 VAL 4.3 0.7 - - - -
1972 LEU* 3.9 20.2 - - + +
2032 TYR* 3.8 32.3 - - + -
2082 TRP* 3.7 28.9 - - + -
2092 VAL* 3.5 20.9 - - - +
2102 PRO* 3.9 2.2 - - + -
2112 ASP* 3.1 19.0 - - - +
2142 LYS* 4.6 2.1 - - - +
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Residues in contact with GLN 162 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201 ILE* 4.3 17.9 - - + -
1612 LEU* 1.3 76.3 - - - +
1632 GLY* 1.3 94.8 + - - +
1642 VAL* 3.9 0.5 - - - +
1892 MET* 3.3 25.3 - - + +
1902 ASN 3.7 12.0 + - - +
1912 THR* 4.2 1.0 - - - +
1932 HIS* 3.1 14.5 + - - +
1942 LYS* 2.9 40.3 - - + +
2082 TRP* 3.5 1.8 - - - -
2092 VAL* 3.0 33.7 + - + +
2112 ASP* 3.4 25.6 - - + +
2122 PRO* 5.4 0.7 - - + -
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Residues in contact with GLY 163 (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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1622 GLN* 1.3 94.8 + - - +
1642 VAL* 1.3 67.7 + - - +
1792 PRO* 4.3 4.0 - - - -
1862 SER 4.8 0.2 - - - +
1902 ASN 4.4 1.0 + - - +
1932 HIS* 2.7 33.9 + - - +
2072 CYS 2.9 13.7 - - - -
2082 TRP* 3.2 15.3 - - - -
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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