Contacts of the strand formed by residues 1595 - 1600 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1504A ASN* 3.6 16.3 + - - -
1506A VAL* 5.4 4.7 - - - +
1556A TRP* 3.3 3.5 - - - -
1557A ARG* 2.9 49.1 + - - +
1593A GLY 3.5 2.7 + - - -
1594A SER* 1.3 72.7 - - - +
1596A VAL* 1.3 69.3 + - - +
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Residues in contact with VAL1596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1503A LEU* 3.9 25.8 - - + -
1504A ASN 3.5 4.4 + - - -
1505A CYS* 3.0 11.1 - - + +
1506A VAL* 2.7 34.1 + - - +
1533A LEU* 3.8 17.0 - - + -
1554A LEU* 3.4 35.7 - - + -
1555A GLU 3.7 12.8 - - - +
1556A TRP* 4.0 14.6 - - + -
1557A ARG* 4.2 3.8 - - - +
1594A SER* 3.9 2.6 + - - +
1595A SER* 1.3 86.0 + - - +
1597A ALA* 1.3 61.5 + - - +
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Residues in contact with ALA1597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505A CYS* 4.5 1.6 - - - -
1506A VAL* 4.1 20.6 - - + +
1554A LEU* 4.3 0.7 - - - -
1555A GLU* 3.3 36.8 + - - +
1557A ARG* 3.7 32.3 - - + +
1596A VAL* 1.3 81.6 - - - +
1598A LEU* 1.3 65.8 + - - +
1599A VAL 3.7 1.2 + - - -
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Residues in contact with LEU1598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505A CYS* 4.7 3.9 - - - -
1508A PRO* 3.9 34.6 - - + +
1530A LYS* 4.2 29.6 - - + +
1533A LEU* 4.2 25.4 - - + -
1534A LEU* 3.8 35.9 - - + +
1537A VAL* 5.2 4.5 - - + -
1552A MET* 3.6 30.5 - - + +
1553A ASP 4.0 4.3 - - - +
1554A LEU* 4.3 13.9 - - + -
1597A ALA* 1.3 74.8 - - - +
1599A VAL* 1.3 59.9 + - - +
1600A PRO* 4.5 1.6 - - - +
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Residues in contact with VAL1599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1552A MET* 3.5 6.8 - - - -
1553A ASP* 2.8 36.0 + - + +
1555A GLU* 3.1 40.4 - - - +
1597A ALA* 3.7 0.6 + - + -
1598A LEU* 1.3 74.8 - - - +
1600A PRO* 1.3 73.7 - - + +
1601A LYS 3.2 0.2 + - - -
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Residues in contact with PRO1600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1551A ASP 4.0 6.7 - - - +
1552A MET* 4.8 7.3 - - + -
1553A ASP* 4.6 1.7 - - - +
1555A GLU* 5.6 0.2 - - - +
1565A ILE* 5.8 2.4 - - - +
1598A LEU 4.5 2.2 - - - +
1599A VAL* 1.3 90.4 - - + +
1601A LYS* 1.3 66.5 + - - +
1602A GLN* 3.3 8.4 + - + +
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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