Contacts of the helix formed by residues 1043 - 1054 (chain B) in PDB entry 2NVU
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 LYS1043 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013B ASN* 5.3 3.2 + - - -
1041B PRO 3.6 0.6 + - - -
1042B ASP* 1.3 82.4 - - + +
1044B LEU* 1.3 51.6 + - - +
1045B GLU* 3.2 19.0 + - - +
1046B GLU* 2.8 23.6 + - + +
1047B LYS* 2.6 62.3 + - - +
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Residues in contact with LEU1044 (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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1011B TRP* 3.7 12.9 - - + -
1012B ILE 3.0 46.9 - - - +
1013B ASN* 4.4 2.3 + - - +
1041B PRO* 3.3 35.1 + - + +
1042B ASP 3.1 4.5 + - - -
1043B LYS* 1.3 77.3 - - - +
1045B GLU* 1.3 59.8 + - - +
1047B LYS* 3.9 9.2 - - - -
1048B PHE* 2.7 35.0 + - - +
1061B ILE* 3.4 26.0 - - + -
1062B PHE 4.5 1.1 - - - +
1063B TRP* 3.6 29.2 - - + -
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Residues in contact with GLU1045 (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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1013B ASN* 5.2 0.9 - - - +
1043B LYS* 3.8 16.8 + - - +
1044B LEU* 1.3 80.7 - - - +
1046B GLU* 1.3 66.3 + - - +
1048B PHE* 4.8 0.2 - - - -
1049B PRO* 3.3 13.8 - - - +
1063B TRP* 2.9 55.6 - - + -
1067B ARG* 2.6 48.3 + - - +
1071B TYR* 3.1 24.4 + - - +
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Residues in contact with GLU1046 (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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1043B LYS* 2.8 27.9 + - + +
1045B GLU* 1.3 91.5 + - - +
1047B LYS* 1.3 83.5 + - - +
1048B PHE 3.4 0.4 - - - -
1049B PRO* 3.4 10.7 - - - +
1050B GLN* 3.3 24.8 - - - +
1067B ARG* 5.5 2.9 + - - +
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Residues in contact with LYS1047 (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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1011B TRP* 4.2 13.5 - - + -
1041B PRO* 5.8 3.1 - - + -
1042B ASP 3.9 10.8 - - - +
1043B LYS* 2.6 47.1 + - - +
1044B LEU* 3.2 7.8 + - - -
1046B GLU* 1.3 101.7 + - - +
1048B PHE* 1.3 62.3 + - - +
1050B GLN* 3.4 26.3 + - - +
1051B VAL* 3.2 28.3 + - + +
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Residues in contact with PHE1048 (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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1011B TRP* 4.3 3.3 - + + -
1044B LEU 2.7 20.6 + - - +
1047B LYS* 1.3 70.5 - - - +
1049B PRO* 1.3 65.4 - - + +
1051B VAL* 3.0 6.6 + - + -
1052B ALA* 2.6 53.2 + - + +
1058B PRO* 3.1 46.2 - - + -
1060B ILE 5.4 0.2 - - - -
1061B ILE* 3.4 36.1 - - + -
1071B TYR* 3.9 26.5 - + + +
1076B LEU* 4.3 11.9 - - + -
1077B LEU* 4.6 6.7 - - + -
1268B ASN* 3.6 30.3 - - + -
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Residues in contact with PRO1049 (chain B).
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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1045B GLU 3.3 18.2 - - - +
1046B GLU* 3.4 13.0 - - - +
1048B PHE* 1.3 96.2 - - + +
1050B GLN* 1.3 64.1 + - + +
1053B ALA* 3.3 23.4 + - - +
1071B TYR* 3.1 23.8 - - + -
1076B LEU* 3.6 22.4 - - + +
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Residues in contact with GLN1050 (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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1046B GLU* 3.3 28.4 - - - +
1047B LYS* 3.4 30.9 + - - +
1049B PRO* 1.3 80.7 - - + +
1051B VAL* 1.3 64.8 - - + +
1053B ALA* 3.6 12.6 - - - +
1054B THR* 3.7 12.3 + - - +
2105B GLU* 5.5 2.3 - - - +
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Residues in contact with VAL1051 (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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1011B TRP* 4.2 16.2 - - + -
1047B LYS* 3.3 15.5 - - + +
1048B PHE* 3.2 14.6 - - - +
1050B GLN* 1.3 76.7 - - + +
1052B ALA* 1.3 64.3 + - + +
1053B ALA 3.0 6.6 + - - -
1054B THR* 3.3 17.5 + - - +
1055B GLY 3.3 5.7 + - - -
1056B ASP* 2.6 41.6 + - - +
1057B GLY* 3.9 13.0 - - - -
1058B PRO* 4.5 2.5 - - + -
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Residues in contact with ALA1052 (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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1048B PHE* 2.6 53.2 + - + +
1051B VAL* 1.3 73.1 - - - +
1053B ALA* 1.3 59.0 + - - +
1055B GLY* 3.8 8.2 + - - +
1056B ASP 3.7 7.6 - - - -
1076B LEU* 3.1 29.3 - - + +
1268B ASN* 3.5 17.0 + - - +
1270B ALA* 5.3 2.6 - - - +
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Residues in contact with ALA1053 (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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1049B PRO 3.3 18.4 + - - +
1050B GLN* 3.6 6.7 - - - +
1051B VAL 3.0 0.2 - - - -
1052B ALA* 1.3 77.0 - - - +
1054B THR* 1.3 61.3 + - + +
1055B GLY 3.0 8.6 + - - -
1076B LEU* 3.6 11.0 - - + +
2122B PRO* 4.8 27.7 - - + +
2123B HIS* 5.4 5.0 + - - -
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Residues in contact with THR1054 (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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1050B GLN 3.7 12.1 + - - +
1051B VAL* 3.3 14.2 + - - +
1053B ALA* 1.3 76.9 - - + +
1055B GLY* 1.3 55.3 + - - +
1056B ASP* 3.3 18.8 + - - +
2102B PRO* 6.2 0.4 - - + -
2105B GLU* 4.7 14.1 - - - +
2124B PHE* 5.0 23.1 - - + +
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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