Contacts of the helix formed by residues 54 - 63 (chain B) in PDB entry 6NUF
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 LEU 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A PHE* 4.6 2.0 - - + +
357A VAL* 3.9 36.1 - - + -
360A LYS* 4.1 16.6 - - + -
361A VAL* 4.2 19.5 - - + +
364A MET* 5.1 0.4 - - - -
52B ASN* 3.0 12.1 + - - +
53B PRO* 1.3 83.5 - - + +
55B VAL* 1.3 64.8 + - - +
56B GLN 3.3 2.7 - - - -
57B ARG* 3.1 19.7 + - + +
58B VAL* 3.1 23.0 + - + +
98B ILE* 4.2 18.8 - - + -
115B VAL* 4.5 6.5 - - + +
118B MET* 4.9 2.5 - - + -
119B MET* 3.7 28.7 - - + -
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Residues in contact with VAL 55 (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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364A MET* 3.7 27.5 - - + +
40B VAL* 6.0 0.2 - - + -
43B PHE* 4.7 0.4 - - + -
44B MET* 3.9 23.8 - - - -
49B LEU* 3.3 37.5 - - + +
52B ASN* 3.3 33.2 + - + +
53B PRO 3.5 1.2 - - - -
54B LEU* 1.3 77.0 - - - +
56B GLN* 1.3 62.2 + - - +
58B VAL* 3.3 2.6 + - - +
59B ILE* 3.0 36.3 + - + +
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Residues in contact with GLN 56 (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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40B VAL* 3.3 42.6 - - + +
53B PRO 5.0 2.5 + - - +
54B LEU 3.3 0.4 - - - -
55B VAL* 1.3 80.1 - - - +
57B ARG* 1.3 62.4 + - + +
59B ILE* 3.4 13.1 + - - +
60B ASP* 2.9 36.9 + - + +
118B MET* 6.0 5.6 - - + -
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PRO 5.6 0.2 + - - -
54B LEU* 3.1 21.1 + - + +
56B GLN* 1.3 81.7 + - + +
58B VAL* 1.3 62.2 + - - +
60B ASP* 2.9 39.9 + - - +
61B ILE* 3.0 35.9 + - - +
97B ARG 2.9 28.1 + - - -
98B ILE* 2.9 39.5 + - + +
100B ASP 3.9 1.6 + - - -
101B MET* 3.6 34.4 + - - +
103B LYS* 6.0 1.4 - - - +
115B VAL* 4.2 5.8 - - + -
118B MET* 3.8 40.2 - - - -
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A VAL* 3.5 37.5 - - + -
364A MET* 3.6 34.3 - - + -
365A LEU* 4.1 11.4 - - + -
54B LEU 3.1 16.0 + - - +
55B VAL 3.9 0.2 - - - +
57B ARG* 1.3 74.7 - - - +
59B ILE* 1.3 63.2 + - - +
61B ILE* 3.1 6.2 + - - +
62B PHE* 2.9 47.3 + - + -
94B PHE* 4.2 6.5 - - + -
98B ILE* 3.9 8.5 - - + -
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Residues in contact with ILE 59 (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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364A MET* 4.1 8.3 - - + -
38B LEU 5.6 0.9 - - - +
40B VAL* 4.1 29.6 - - + +
43B PHE* 3.3 49.8 - - + -
55B VAL* 3.0 27.8 + - + +
56B GLN* 3.7 16.6 - - - +
58B VAL* 1.3 76.0 - - - +
60B ASP* 1.3 64.5 + - - +
62B PHE* 3.2 8.7 + - - +
63B ASP* 2.9 24.0 + - + +
68B GLY 4.8 8.3 - - - +
70B VAL* 4.1 15.6 - - + +
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Residues in contact with ASP 60 (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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56B GLN* 2.9 25.6 + - + +
57B ARG* 2.9 30.1 + - - +
58B VAL 3.3 0.2 - - - -
59B ILE* 1.3 78.8 - - - +
61B ILE* 1.3 59.9 + - - +
63B ASP* 3.3 17.0 + - - +
66B GLY* 6.1 0.3 - - - -
101B MET 3.8 9.7 - - - +
103B LYS* 2.8 43.0 + - - -
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Residues in contact with ILE 61 (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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57B ARG* 3.0 15.2 + - - +
58B VAL 3.1 5.8 + - - +
60B ASP* 1.3 74.5 - - - +
62B PHE* 1.3 67.0 + - + +
63B ASP 3.3 0.2 + - - -
64B THR* 3.7 17.5 + - - +
94B PHE* 3.6 35.4 - - + +
97B ARG* 3.4 57.9 - - + +
98B ILE* 3.5 28.9 - - + +
103B LYS* 4.4 8.5 + - - +
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Residues in contact with PHE 62 (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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365A LEU* 4.2 18.4 - - + -
368A VAL* 6.3 0.9 - - + -
43B PHE* 5.3 7.6 - + - -
58B VAL* 2.9 39.8 + - + +
59B ILE* 3.2 8.7 + - - +
61B ILE* 1.3 77.1 - - + +
63B ASP* 1.3 50.7 + - - +
64B THR* 2.7 19.5 + - - +
70B VAL* 3.9 25.4 - - + -
74B GLU* 3.3 30.6 - - - +
75B PHE* 4.1 14.4 - + - -
78B GLY* 3.4 46.4 - - - -
79B VAL* 3.8 10.8 - - + -
82B PHE* 4.6 0.7 - + - -
94B PHE* 3.9 19.3 - + - -
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Residues in contact with ASP 63 (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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59B ILE* 2.9 17.6 + - + +
60B ASP* 3.6 16.6 - - - +
61B ILE 3.2 1.0 - - - -
62B PHE* 1.3 70.6 - - - +
64B THR* 1.3 60.0 + - - +
65B ASP* 3.1 7.8 - - - +
66B GLY* 3.1 12.2 + - - -
67B ASN* 3.3 2.8 + - - +
68B GLY* 2.7 30.6 + - - -
69B GLU 3.5 14.8 - - - +
70B VAL* 4.5 1.3 - - + +
74B GLU* 3.7 6.7 - - - -
103B LYS* 3.0 15.4 + - - -
201B CA 2.3 29.4 - - - -
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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