Contacts of the helix formed by residues 2107 - 2117 (chain B) in PDB entry 3NBN
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 HIS2107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2070B ALA 3.4 7.1 + - - -
2071B ARG 2.5 31.2 + - - -
2072B GLU* 3.5 3.6 + - - -
2073B GLY* 3.1 23.6 - - - +
2102B ALA* 3.6 6.8 + - - +
2105B ARG* 3.6 30.0 + - + +
2106B MET* 1.3 74.2 - - - +
2108B HIS* 1.3 60.3 + - - +
2109B ASP* 3.1 5.2 - - + +
2110B ILE* 4.2 17.3 - - + +
2111B VAL* 3.1 27.1 + - - +
40C ARG* 3.3 34.4 - - - +
44C VAL* 5.4 4.2 - - + +
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Residues in contact with HIS2108 (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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2103B GLN* 5.5 6.3 - - - +
2106B MET* 2.5 43.5 + - - -
2107B HIS* 1.3 70.8 - - - +
2109B ASP* 1.3 64.9 + - - +
2111B VAL* 3.6 12.2 - - + +
2112B ARG* 2.9 27.4 + - - +
44C VAL* 5.0 1.4 - - + +
47C GLU* 3.2 38.5 + - - -
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Residues in contact with ASP2109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2075B TYR* 3.9 21.3 - - + -
2107B HIS* 3.1 1.7 - - + -
2108B HIS* 1.3 77.8 - - - +
2110B ILE* 1.3 57.4 - - - +
2111B VAL 3.0 0.9 - - - -
2112B ARG* 2.5 69.6 + - - +
2113B LEU* 2.9 9.5 + - - +
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Residues in contact with ILE2110 (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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2070B ALA* 3.5 24.5 - - + +
2073B GLY* 3.2 41.7 - - - +
2074B SER 3.8 10.1 - - - +
2075B TYR* 3.8 24.1 - - + -
2078B ALA* 4.3 9.2 - - + -
2102B ALA* 3.6 17.0 - - + -
2107B HIS* 3.8 11.2 + - + +
2109B ASP* 1.3 76.1 - - - +
2111B VAL* 1.3 62.3 + - - +
2113B LEU* 3.4 4.8 + - + +
2114B LEU* 3.0 42.0 + - + +
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Residues in contact with VAL2111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2099B ARG* 4.0 21.8 - - - +
2102B ALA* 3.4 6.7 - - + -
2103B GLN* 3.3 43.1 - - - +
2107B HIS 3.1 18.1 + - - +
2108B HIS* 3.6 12.6 - - + +
2109B ASP 2.8 1.6 + - - -
2110B ILE* 1.3 76.1 - - - +
2112B ARG* 1.3 66.0 + - - +
2114B LEU* 2.7 19.2 + - - +
2115B ASP* 2.8 32.8 + - - +
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Residues in contact with ARG2112 (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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2075B TYR* 4.6 12.1 + - - -
2108B HIS 2.9 12.5 + - - +
2109B ASP* 2.5 49.5 + - - +
2111B VAL* 1.3 76.3 - - - +
2113B LEU* 1.3 54.7 + - - +
2115B ASP* 3.8 6.5 - - - +
2116B GLU* 3.1 47.7 + - - +
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Residues in contact with LEU2113 (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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2075B TYR* 3.9 39.7 - - + +
2078B ALA* 4.3 9.2 - - + +
2079B LYS* 3.8 38.1 - - + +
2082B LEU* 4.8 9.0 - - + +
2088B ARG* 3.8 2.8 + - - -
2109B ASP 2.9 8.2 + - - +
2110B ILE* 3.5 9.4 - - - +
2112B ARG* 1.3 78.0 - - - +
2114B LEU* 1.3 62.3 + - + +
2117B TYR* 3.0 71.1 + - + +
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Residues in contact with LEU2114 (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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2066B LEU* 3.8 19.7 - - + -
2070B ALA* 4.0 9.4 - - + -
2078B ALA* 6.3 1.1 - - + -
2082B LEU* 3.7 27.4 - - + -
2088B ARG* 2.9 41.8 + - + +
2098B PRO* 4.1 2.9 - - + -
2099B ARG* 3.6 45.6 - - + +
2102B ALA* 4.6 1.3 - - + -
2110B ILE* 3.0 37.1 + - + +
2111B VAL* 2.7 11.7 + - - +
2113B LEU* 1.3 72.3 - - + +
2115B ASP* 1.3 60.6 + - - +
2119B LEU* 4.6 1.0 - - - +
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Residues in contact with ASP2115 (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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2088B ARG* 4.7 0.9 - - - -
2099B ARG* 2.7 47.4 + - - +
2111B VAL* 2.8 31.0 + - - +
2112B ARG* 3.8 8.6 - - - +
2114B LEU* 1.3 74.7 - - - +
2116B GLU* 1.3 69.6 + - + +
2117B TYR 4.1 0.4 - - - -
2119B LEU* 4.2 10.7 - - - +
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Residues in contact with GLU2116 (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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2112B ARG* 3.1 34.1 + - + +
2113B LEU 3.8 0.2 - - - -
2115B ASP* 1.3 91.6 - - + +
2117B TYR* 1.3 62.9 + - - +
2118B ASN 4.2 0.7 + - - -
2119B LEU* 3.8 11.5 - - - +
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Residues in contact with TYR2117 (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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2079B LYS* 3.6 46.1 + - + +
2082B LEU* 3.6 20.4 - - + +
2083B ASP* 2.7 31.7 + - - -
2088B ARG* 3.0 18.0 + - - +
2113B LEU* 3.0 46.5 + - + +
2116B GLU* 1.3 75.0 - - - +
2118B ASN* 1.3 74.8 + - + +
2119B LEU* 3.7 3.2 - - - +
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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
------------------------------------------------------------
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