Contacts of the helix formed by residues 2075 - 2086 (chain A) in PDB entry 5NP1
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 HIS2075 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2074A CYS* 1.3 79.5 - - - +
2076A ILE* 1.3 51.6 + - - +
2078A SER* 3.0 10.5 + - - -
2079A VAL* 2.3 36.3 + - - +
2106A ASN* 4.7 6.0 - - + +
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Residues in contact with ILE2076 (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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2074A CYS 3.2 2.8 - - - +
2075A HIS* 1.3 74.4 - - - +
2077A LEU* 1.3 56.3 + - - +
2079A VAL* 3.0 10.0 + - - +
2080A TYR* 2.4 37.0 + - - +
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Residues in contact with LEU2077 (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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2074A CYS* 3.0 26.3 + - - +
2076A ILE* 1.3 76.7 - - - +
2078A SER* 1.3 51.8 + - - +
2080A TYR* 2.8 11.0 + - - +
2081A LEU* 2.3 40.2 + - - +
2102A ALA* 5.0 9.9 - - + -
2105A ARG* 5.9 0.9 - - + -
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Residues in contact with SER2078 (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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2074A CYS 2.2 28.4 + - - -
2075A HIS* 3.1 16.6 - - - -
2077A LEU* 1.3 65.9 - - - +
2079A VAL* 1.3 51.3 + - - +
2081A LEU* 3.1 9.8 - - - +
2082A LYS* 2.3 36.4 + - - +
2102A ALA* 4.9 7.0 - - - +
2106A ASN* 4.4 15.0 - - - -
2111A HIS* 5.9 3.4 - - - -
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Residues in contact with VAL2079 (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 HIS 2.3 26.5 + - - +
2076A ILE* 3.1 14.8 - - - +
2078A SER* 1.3 64.6 - - - +
2080A TYR* 1.3 59.9 + - - +
2082A LYS* 2.7 32.9 + - - +
2083A GLY 3.3 2.9 + - - -
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Residues in contact with TYR2080 (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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2076A ILE 2.4 27.6 + - - +
2077A LEU* 3.2 12.8 - - - +
2079A VAL* 1.3 68.6 - - - +
2081A LEU* 1.3 59.3 + - - +
2083A GLY* 3.4 10.0 + - - -
2084A LEU* 3.7 5.7 + - - +
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Residues in contact with LEU2081 (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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2077A LEU 2.3 29.3 + - - +
2078A SER* 3.3 11.9 - - - +
2080A TYR* 1.3 66.1 - - - +
2082A LYS* 1.3 51.4 + - - +
2083A GLY 3.0 2.2 - - - -
2084A LEU* 2.6 17.3 + - + +
2085A ASP* 2.2 41.5 + - + +
2098A LEU 6.1 0.4 - - - -
2099A HIS* 5.3 10.3 - - + -
2102A ALA* 4.8 12.6 - - + -
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Residues in contact with LYS2082 (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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2078A SER 2.3 25.8 + - - +
2079A VAL* 2.7 20.4 + - - +
2081A LEU* 1.3 66.3 - - - +
2083A GLY* 1.3 54.6 + - - +
2085A ASP* 3.6 11.0 - - - -
2086A TYR* 2.4 36.5 + - - +
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Residues in contact with GLY2083 (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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2079A VAL 3.3 6.9 + - - -
2080A TYR 3.4 6.0 + - - -
2081A LEU 3.0 0.8 - - - -
2082A LYS* 1.3 78.8 - - - +
2084A LEU* 1.3 61.5 + - - +
2086A TYR* 3.8 10.9 - - - +
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Residues in contact with LEU2084 (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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2080A TYR 3.7 4.3 + - - +
2081A LEU* 2.6 21.7 + - + +
2083A GLY* 1.3 71.5 - - - +
2085A ASP* 1.3 67.2 + - - +
2086A TYR* 4.2 1.9 - - - +
2095A LEU* 6.0 6.3 - - + -
2099A HIS* 6.4 2.2 - - + -
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Residues in contact with ASP2085 (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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2081A LEU* 2.2 33.7 + - + +
2082A LYS* 3.6 10.8 - - - -
2084A LEU* 1.3 71.1 - - - +
2086A TYR* 1.3 68.9 + - - +
2099A HIS* 6.1 5.8 - - + +
2114A SER* 4.2 34.8 - - - +
2116A SER 5.9 3.1 - - - -
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Residues in contact with TYR2086 (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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2082A LYS* 2.4 27.4 + - - +
2083A GLY* 3.8 11.9 - - - +
2084A LEU 4.2 1.8 - - - +
2085A ASP* 1.3 78.2 - - - +
2116A SER* 6.4 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