Contacts of the strand formed by residues 194 - 197 (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 LYS 194 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1615 LEU 3.6 4.0 - - - +
1625 GLN* 2.8 30.6 - - - +
1895 MET* 4.2 9.1 - - - +
1915 THR* 3.4 29.8 - - - +
1925 ASP 2.8 12.6 + - - +
1935 HIS* 1.3 74.5 - - - +
1955 ALA* 1.3 65.4 + - - +
2085 TRP* 4.5 1.0 - - - -
2115 ASP* 2.8 38.8 + - - +
2135 SER* 3.8 10.5 + - - -
2145 LYS* 4.6 18.8 - - + +
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Residues in contact with ALA 195 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1605 GLU* 3.5 7.8 - - - +
1615 LEU* 2.9 28.0 + - + +
1775 VAL* 6.3 0.2 - - + -
1945 LYS* 1.3 78.6 - - - +
1965 VAL* 1.3 69.8 + - - +
2035 TYR* 4.9 8.3 - - + -
2085 TRP* 3.5 32.1 - - + -
2145 LYS* 5.7 1.2 - - - +
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Residues in contact with VAL 196 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1585 PRO* 3.2 39.5 - - + +
1595 LEU 3.4 10.5 - - - +
1605 GLU* 4.6 6.7 - - + +
1615 LEU* 4.3 0.6 - - - +
1955 ALA* 1.3 84.6 - - - +
1975 LEU* 1.3 59.9 + - - +
1985 ASP* 3.0 17.5 + - + +
2035 TYR* 2.9 23.7 + - - +
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Residues in contact with LEU 197 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885 TYR* 3.5 41.5 - - + +
895 SER 4.7 0.2 - - - +
905 VAL* 3.7 36.4 - - + +
1585 PRO* 3.8 17.2 - - - +
1595 LEU* 3.0 28.8 + - + +
1615 LEU* 4.1 14.4 - - + +
1965 VAL* 1.3 67.3 - - - +
1985 ASP* 1.3 57.9 + - - +
1995 LYS 3.5 14.6 - - - +
2035 TYR* 3.1 33.9 - - + -
2605 TYR* 5.9 0.5 - - - -
2625 SER* 4.1 12.8 - - - -
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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
------------------------------------------------------------
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