Contacts of the strand formed by residues 1655 - 1660 (chain A) in PDB entry 5M64
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 ASP1655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1654A PHE* 1.3 80.8 - - - +
1656A VAL* 1.3 67.6 + - - +
1657A LEU* 4.6 1.4 - - - +
134F ILE* 4.4 0.3 - - - -
135F ARG* 2.9 60.6 + - - +
137F TYR* 3.1 34.2 + - - +
106G LYS* 3.8 28.5 - - + +
107G ILE 5.5 1.8 - - - +
109G PRO* 5.9 9.0 - - + -
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Residues in contact with VAL1656 (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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1654A PHE* 4.4 3.6 - - + -
1655A ASP* 1.3 82.3 - - - +
1657A LEU* 1.3 78.3 + - - +
89F GLU* 5.7 0.4 - - - +
92F ARG* 3.6 46.0 - - + +
93F ILE* 5.3 7.4 - - + -
96F THR* 4.5 6.7 - - + +
132F LEU* 3.6 21.5 - - + -
133F VAL 3.3 14.1 - - - +
134F ILE* 5.3 2.5 - - + -
106G LYS* 3.6 2.3 - - - +
107G ILE* 3.0 41.4 + - + +
109G PRO* 5.6 2.6 - - + +
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Residues in contact with LEU1657 (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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1655A ASP* 4.6 1.1 - - - +
1656A VAL* 1.3 82.4 - - - +
1658A ALA* 1.3 62.9 + - - +
132F LEU* 3.2 13.9 - - - +
133F VAL* 2.8 52.8 + - + -
135F ARG* 3.3 59.7 - - + +
145F ASP* 4.5 1.8 - - - +
92G ALA* 5.1 1.6 - - + -
104G LEU* 3.8 28.3 - - + -
105G ILE 3.3 7.0 - - - +
106G LYS* 3.6 27.8 - - + +
107G ILE* 4.5 1.3 - - - -
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Residues in contact with ALA1658 (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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1657A LEU* 1.3 78.9 - - - +
1659A LYS* 1.3 63.1 + - - +
1660A VAL* 3.9 7.2 + - + +
131F PRO 4.1 9.2 - - - +
132F LEU* 4.3 12.3 - - + -
133F VAL 4.6 0.9 - - - +
54G LEU* 5.0 22.0 - - + -
103G LYS 3.8 0.2 - - - +
104G LEU* 3.2 4.7 - - - -
105G ILE* 3.0 34.9 + - + +
107G ILE* 5.1 9.4 - - + -
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Residues in contact with LYS1659 (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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1658A ALA* 1.3 73.7 - - - +
1660A VAL* 1.3 64.2 + - - +
1661A PRO* 4.7 0.7 - - - +
131F PRO* 3.9 23.7 + - + +
133F VAL* 3.5 31.3 - - + +
145F ASP* 5.0 6.4 + - - -
147F SER* 4.3 19.8 - - - -
102G GLU* 3.8 24.5 + - + +
103G LYS 3.0 15.5 - - - +
104G LEU* 4.1 20.2 - - + -
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Residues in contact with VAL1660 (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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1658A ALA* 4.2 9.9 - - + +
1659A LYS* 1.3 78.4 - - - +
1661A PRO* 1.3 69.3 - - + +
1662A ASN* 3.3 28.9 - - - +
54G LEU* 3.2 41.3 - - + +
57G PRO* 3.7 19.1 - - + -
102G GLU* 3.2 22.3 - - - +
103G LYS* 3.3 23.4 + - + -
105G ILE* 5.6 3.1 - - + -
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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