Contacts of the strand formed by residues 2100 - 2105 (chain A) in PDB entry 5V6Y
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 LYS2100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2083A GLU* 4.8 6.3 + - - -
2085A MET* 3.9 34.3 - - + -
2086A GLN 3.3 4.9 - - - -
2087A LEU* 4.6 0.2 - - - +
2088A CYS* 3.5 11.1 - - - -
2099A GLU* 1.3 85.3 - - + +
2101A VAL* 1.3 62.9 + - - +
2102A THR* 3.8 24.5 - - + +
2123A ASN 4.6 2.3 - - - +
2126A GLN* 3.8 26.3 + - + +
2127A CYS* 4.0 2.1 - - - -
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Residues in contact with VAL2101 (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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2073A LEU* 4.2 8.1 - - + -
2075A TRP* 3.8 10.4 - - + -
2084A SER 3.7 0.3 - - - +
2085A MET* 3.2 5.7 - - - -
2086A GLN* 2.5 36.8 + - + +
2087A LEU 3.9 3.4 - - - +
2088A CYS* 3.5 29.8 - - - +
2100A LYS* 1.3 78.5 - - - +
2102A THR* 1.3 64.0 + - - +
2122A THR* 3.7 17.9 - - + -
2123A ASN 3.4 14.8 - - - +
2124A TYR* 3.7 27.4 - - + -
2127A CYS* 3.6 14.1 - - - -
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Residues in contact with THR2102 (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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2075A TRP* 4.4 0.2 - - - -
2083A GLU* 3.7 28.6 - - - +
2084A SER 3.3 9.2 - - - +
2085A MET* 5.0 4.3 - - + -
2100A LYS* 3.8 33.7 - - + +
2101A VAL* 1.3 78.3 - - - +
2103A LYS* 1.3 61.4 + - - +
2104A ILE* 5.4 4.3 - - - +
2122A THR* 3.5 3.1 - - - +
2123A ASN* 2.9 55.2 + - - +
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Residues in contact with LYS2103 (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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2068A THR* 4.6 3.6 - - - -
2070A ASP* 4.4 5.2 - - - -
2075A TRP* 3.5 49.7 - - + +
2082A THR 4.1 0.2 - - - +
2083A GLU* 3.7 0.8 - - - -
2084A SER* 2.9 33.7 + - - -
2102A THR* 1.3 75.1 - - - +
2104A ILE* 1.3 65.5 + - - +
2105A CYS 4.1 0.3 + - - -
2111A TRP* 3.6 42.6 - - + +
2112A PHE 4.7 1.4 + - - +
2120A THR* 3.4 27.1 - - - +
2121A TRP 3.4 15.0 + - - +
2122A THR* 3.2 27.4 + - + +
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Residues in contact with ILE2104 (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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51A GLN* 3.3 50.5 - - + +
54A ALA* 4.1 15.3 - - + -
55A THR* 3.8 28.0 - - + -
2082A THR 3.9 3.1 - - - +
2083A GLU* 4.2 22.4 - - + +
2102A THR* 5.4 4.5 - - - +
2103A LYS* 1.3 79.9 - - - +
2105A CYS* 1.3 64.2 + - - +
2111A TRP* 3.5 9.0 - - - -
2112A PHE* 2.8 50.6 + - + +
2121A TRP* 5.4 1.9 + - + -
2123A ASN* 6.5 1.3 - - + -
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Residues in contact with CYS2105 (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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54A ALA 4.4 0.3 - - - +
2065A CYS* 2.0 55.9 - - + -
2078A VAL* 4.1 5.8 - - + -
2079A ALA 3.8 17.7 - - - +
2080A ALA* 4.1 2.9 - - - -
2081A GLY* 3.0 14.0 + - - -
2082A THR 2.9 22.3 + - - +
2104A ILE* 1.3 78.1 - - - +
2106A ASP* 1.3 75.1 + - - +
2109A GLY* 4.1 1.8 - - - -
2110A ASN 3.7 3.4 - - - -
2111A TRP* 4.1 8.5 - - + -
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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