Contacts of the helix formed by residues 1056 - 1063 (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 SER1056 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1050A LEU* 3.2 27.6 - - - -
1051A GLU 3.4 9.1 + - - -
1053A ASP* 3.2 10.3 - - - +
1054A PRO 2.9 0.6 + - - -
1055A TYR* 1.3 75.3 - - - +
1057A LYS* 1.3 69.2 + - - +
1058A TRP 2.9 2.9 - - - +
1059A ALA* 2.7 37.4 + - - +
1112A PRO 6.1 0.4 - - - -
1113A LEU* 5.0 5.6 - - - +
1117A GLN* 4.5 15.3 - - - -
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Residues in contact with LYS1057 (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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1011A THR 5.9 3.1 - - - +
1012A ARG 5.6 6.1 - - - +
1053A ASP* 3.0 10.8 - - + +
1054A PRO* 2.2 39.2 + - + +
1055A TYR 4.2 0.2 - - - -
1056A SER* 1.3 69.7 - - - +
1058A TRP* 1.3 60.2 + - - +
1059A ALA 2.8 6.9 + - - -
1060A ILE* 3.4 14.9 + - - +
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Residues in contact with TRP1058 (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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1049A LEU* 3.1 47.3 - - + +
1050A LEU* 5.1 0.2 - - - -
1053A ASP* 4.5 1.9 - - + +
1056A SER 2.9 0.2 - - - -
1057A LYS* 1.3 79.3 - - - +
1059A ALA* 1.3 54.0 + - - +
1060A ILE 2.9 0.4 - - - -
1061A LEU* 2.2 48.5 + - + +
1062A ASN 3.7 0.7 + - - -
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Residues in contact with ALA1059 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1050A LEU* 6.3 1.1 - - - +
1055A TYR 4.9 0.4 - - - +
1056A SER* 2.7 35.8 + - - +
1058A TRP* 1.3 75.7 - - - +
1060A ILE* 1.3 63.6 + - - +
1062A ASN* 2.9 25.2 + - - +
1117A GLN* 4.9 7.0 - - + -
1120A PHE* 4.6 19.5 - - + +
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Residues in contact with ILE1060 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1057A LYS 3.4 11.2 + - - +
1058A TRP 2.7 2.8 + - - -
1059A ALA* 1.3 76.7 - - - +
1061A LEU* 1.3 53.2 + - - +
1062A ASN* 2.6 13.2 + - - +
1063A VAL* 2.8 21.3 + - - +
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Residues in contact with LEU1061 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018A PHE* 3.8 28.7 - - + -
1046A LEU* 5.6 11.0 - - + +
1049A LEU* 5.7 1.6 - - + -
1058A TRP* 2.2 41.3 + - + +
1060A ILE* 1.3 69.6 - - - +
1062A ASN* 1.3 63.3 + - - +
1063A VAL* 2.9 1.8 + - - -
1064A MET* 3.6 9.8 + - - +
1065A GLY* 4.1 4.7 + - - -
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Residues in contact with ASN1062 (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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1058A TRP 3.7 1.0 + - - -
1059A ALA 2.9 16.7 + - - +
1060A ILE 2.6 4.8 + - - +
1061A LEU* 1.3 74.1 - - - +
1063A VAL* 1.3 54.3 + - - +
1065A GLY* 2.5 32.4 + - - -
1120A PHE* 4.8 17.9 - - + +
1121A GLU* 5.2 3.6 - - - -
1123A ALA* 6.2 0.7 - - + -
1124A TYR* 4.3 22.0 - - + +
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Residues in contact with VAL1063 (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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1060A ILE 2.8 19.5 + - - +
1061A LEU* 2.9 0.6 + - - -
1062A ASN* 1.3 73.2 - - - +
1064A MET* 1.3 64.6 + - - +
1065A GLY 2.9 2.1 + - - -
1066A LYS 4.5 0.9 + - - -
1067A ASP* 3.5 11.7 - - - +
1124A TYR* 5.0 11.4 - - - +
1127A ALA* 5.8 3.1 - - - +
1385A VAL* 6.4 3.4 - - + -
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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