Contacts of the helix formed by residues 56 - 62 (chain D) in PDB entry 5NVN
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 ARG 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C ARG* 3.5 20.8 - - - +
149C GLU* 3.8 13.9 + - - -
150C ASN* 2.8 33.2 + - - +
153C LEU* 4.2 15.8 - - + +
154C ALA* 6.2 0.4 - - - +
159C GLN* 5.0 2.8 - - - +
203C VAL 5.7 1.6 - - - -
305C FMT 3.4 23.5 - - - -
54D TYR 3.9 0.4 + - - -
55D ASP* 1.3 84.3 + - - +
57D LYS* 1.3 64.3 + - - +
59D LEU* 3.2 11.9 + - - +
60D MET* 3.0 57.8 + - + +
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Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ASP* 3.3 8.5 + - + -
56D ARG* 1.3 80.1 - - - +
58D PHE* 1.3 63.5 + - - +
60D MET* 3.3 8.2 + - - +
61D GLU* 3.2 21.6 + - + +
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Residues in contact with PHE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C HIS* 3.4 30.3 - + - -
91C VAL* 5.4 0.2 - - + -
54D TYR* 3.5 39.5 - + - -
55D ASP* 3.2 19.1 + - + +
57D LYS* 1.3 79.3 - - - +
59D LEU* 1.3 67.2 + - + +
61D GLU* 3.1 17.6 + - + +
62D CYS* 3.2 34.5 + - - -
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 5.5 1.8 - - + -
91C VAL* 3.5 37.2 - - + -
94C PHE* 6.5 0.4 - - + -
95C TRP* 2.8 28.1 + - - +
153C LEU* 3.3 53.4 - - + +
156C LEU* 4.9 4.5 - - + -
157C GLY* 4.1 7.9 - - - +
54D TYR* 3.5 32.8 - - + +
55D ASP 3.2 13.9 + - - +
56D ARG* 3.2 6.0 + - - +
58D PHE* 1.3 79.1 - - + +
60D MET* 1.3 61.7 + - - +
62D CYS* 3.3 7.6 + - - +
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Residues in contact with MET 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TRP* 3.7 24.9 - - - -
149C GLU* 4.0 10.8 - - - +
153C LEU* 3.3 21.8 - - + -
56D ARG* 3.0 57.0 + - + +
57D LYS* 3.6 11.2 - - - +
58D PHE 3.2 0.2 - - - -
59D LEU* 1.3 78.3 - - - +
61D GLU* 1.3 61.3 + - - +
63D ARG* 3.3 37.9 + - - +
64D ASN* 4.6 1.0 + - - -
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LYS* 3.2 9.4 + - + +
58D PHE* 3.1 11.6 + - + +
60D MET* 1.3 74.8 - - - +
62D CYS* 1.3 61.4 + - - +
63D ARG 3.1 5.9 + - - -
64D ASN* 2.5 43.2 + - - +
65D SER 4.7 0.7 + - - -
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Residues in contact with CYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C HIS* 4.0 18.8 - - - -
91C VAL* 3.7 21.5 - - + -
92C GLU* 4.1 11.7 - - - +
95C TRP* 4.2 3.7 - - + -
58D PHE* 3.2 51.4 + - - -
59D LEU 3.3 10.0 + - - +
61D GLU* 1.3 76.2 - - - +
63D ARG* 1.3 61.2 + - - +
64D ASN 3.1 1.5 + - - -
65D SER* 3.3 21.5 + - - +
68D THR* 4.0 1.7 + - - -
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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