Contacts of the strand formed by residues 1595 - 1600 (chain B) in PDB entry 3RYT
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 SER1595 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1504B ASN* 3.4 22.2 - - - -
1506B VAL* 5.7 6.1 - - - -
1556B TRP* 4.3 1.1 - - - -
1557B ARG* 3.3 37.4 + - - +
1593B GLY 5.2 0.4 - - - -
1594B SER* 1.3 77.3 - - - +
1596B VAL* 1.3 61.1 + - - +
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Residues in contact with VAL1596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1503B LEU* 4.7 12.8 - - + +
1504B ASN 3.7 4.2 + - - -
1505B CYS* 3.2 26.9 - - - +
1506B VAL* 4.8 0.9 - - - -
1554B LEU* 3.9 21.1 - - + +
1555B GLU 3.2 15.3 - - - +
1556B TRP* 4.0 17.3 - - + -
1566B LEU* 6.5 0.2 - - + -
1594B SER 4.1 1.6 + - - -
1595B SER* 1.3 74.2 - - - +
1597B ALA* 1.3 59.3 + - - +
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Residues in contact with ALA1597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505B CYS* 4.2 6.1 - - - -
1506B VAL* 3.8 36.1 - - + +
1508B PRO* 6.0 1.1 - - + -
1554B LEU* 3.8 5.9 - - - +
1555B GLU* 2.8 38.3 + - + +
1557B ARG* 5.8 1.0 - - - +
1595B SER 4.4 0.4 + - - -
1596B VAL* 1.3 75.2 - - - +
1598B LEU* 1.3 65.4 + - - +
1599B VAL* 5.2 2.5 - - + -
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Residues in contact with LEU1598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505B CYS* 4.7 6.3 - - - -
1508B PRO* 4.6 20.3 - - + +
1530B LYS* 6.0 4.0 - - + -
1533B LEU* 6.0 5.4 - - + -
1534B LEU* 6.1 4.5 - - + -
1552B MET* 3.8 28.8 - - + +
1553B ASP 3.6 8.3 - - - +
1554B LEU* 4.7 4.9 - - + +
1597B ALA* 1.3 77.1 - - - +
1599B VAL* 1.3 68.8 + - - +
1600B PRO* 4.7 0.5 - - - +
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Residues in contact with VAL1599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1552B MET* 3.3 7.2 - - - -
1553B ASP* 2.8 56.7 + - + +
1555B GLU* 4.9 15.3 - - + -
1597B ALA* 5.2 2.2 - - + -
1598B LEU* 1.3 81.6 - - - +
1600B PRO* 1.3 73.7 - - + +
1601B LYS 3.2 0.7 + - - -
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Residues in contact with PRO1600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1551B ASP 4.0 7.6 - - - +
1552B MET* 3.8 12.3 - - + -
1598B LEU 4.7 1.1 - - - +
1599B VAL* 1.3 89.5 - - + +
1601B LYS* 1.3 64.3 + - - +
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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