Contacts of the helix formed by residues 1079 - 1092 (chain B) in PDB entry 2NUP
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 SER1079 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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904B LEU* 4.2 2.0 - - - -
1071B GLU 3.2 13.9 - - - -
1072B ASP* 3.7 2.2 - - - -
1073B ARG* 3.4 31.3 + - - +
1078B LEU* 1.3 75.5 - - - +
1080B TYR* 1.3 65.9 + - - +
1081B TYR* 3.5 8.6 + - - +
1082B GLU* 2.7 35.4 + - - +
1083B PHE* 2.9 21.3 + - - +
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Residues in contact with TYR1080 (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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353B LEU* 3.8 14.0 + - - +
357B ARG* 4.5 14.8 - - + -
359B MET* 3.5 37.9 - - + +
897B ARG 4.6 1.9 + - - -
900B PRO* 4.6 1.7 - - + +
901B LEU* 3.8 35.3 + - + +
904B LEU* 3.4 23.8 - - + +
1071B GLU* 2.7 55.7 + - + +
1079B SER* 1.3 72.0 - - - +
1081B TYR* 1.3 62.9 + - - +
1083B PHE* 3.5 3.1 + + - +
1084B LEU* 3.0 65.0 + - + +
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Residues in contact with TYR1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 4.0 27.6 + - + +
357B ARG* 3.1 56.5 - - - +
1079B SER* 3.1 8.6 + - - +
1080B TYR* 1.3 79.6 - - - +
1082B GLU* 1.3 67.6 + - + +
1084B LEU* 3.2 14.5 + - + +
1085B LEU* 2.9 52.7 + - + +
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Residues in contact with GLU1082 (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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1073B ARG* 3.5 39.9 + - - +
1077B ALA 4.0 0.5 - - - +
1078B LEU* 2.9 34.6 - - + +
1079B SER* 2.7 42.3 + - - +
1081B TYR* 1.3 78.3 - - + +
1083B PHE* 1.3 51.4 + - - +
1085B LEU* 2.8 16.4 + - + +
1086B HIS* 2.7 34.0 + - - +
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Residues in contact with PHE1083 (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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868B VAL* 4.1 22.4 - - + -
871B VAL* 5.0 1.6 - - + -
900B PRO* 3.4 28.0 - - + -
903B VAL* 4.4 10.8 - - + -
904B LEU* 3.8 34.1 - - + -
907B LEU* 3.8 30.7 - - + -
1078B LEU* 4.1 19.2 - - + +
1079B SER 2.9 16.9 + - - +
1080B TYR* 3.5 6.7 - + - +
1082B GLU* 1.3 77.2 - - - +
1084B LEU* 1.3 61.4 + - + +
1086B HIS* 3.3 7.4 + - + +
1087B ILE* 3.0 55.8 + - + +
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Residues in contact with LEU1084 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 3.4 51.6 - - + +
354B LEU* 4.1 16.2 - - + -
357B ARG* 5.3 1.6 - - + -
890B LEU* 3.7 10.6 - - + +
900B PRO* 4.1 11.9 - - + -
1080B TYR* 3.0 58.9 + - + +
1081B TYR* 3.4 16.8 - - + +
1082B GLU 3.1 0.2 - - - -
1083B PHE* 1.3 75.8 - - + +
1085B LEU* 1.3 65.5 + - - +
1087B ILE* 3.2 4.6 + - - +
1088B GLN* 3.0 24.9 + - - +
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Residues in contact with LEU1085 (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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354B LEU* 4.2 20.0 - - + -
1081B TYR* 2.9 43.8 + - + +
1082B GLU* 2.8 17.4 + - + +
1084B LEU* 1.3 79.5 - - - +
1086B HIS* 1.3 58.4 + - - +
1088B GLN* 3.7 16.0 + - - +
1089B GLN* 3.3 23.1 + - - +
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Residues in contact with HIS1086 (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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868B VAL* 4.1 23.9 - - + +
872B ILE* 4.4 1.8 - - + -
1078B LEU* 4.4 16.2 - - + -
1082B GLU 2.7 14.2 + - - +
1083B PHE* 3.6 15.8 - + + +
1084B LEU 3.2 0.2 - - - -
1085B LEU* 1.3 73.7 - - - +
1087B ILE* 1.3 71.6 + - - +
1089B GLN* 3.5 11.1 + - + +
1090B GLN* 3.3 41.1 + - + +
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Residues in contact with ILE1087 (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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868B VAL* 5.6 0.7 - - + -
871B VAL* 3.3 35.7 - - + -
872B ILE* 4.6 14.6 - - + -
875B LEU* 4.4 3.8 - - + -
890B LEU* 4.0 13.9 - - + -
900B PRO* 3.9 10.3 - - + -
1083B PHE* 3.0 52.3 + - + +
1084B LEU* 3.2 6.0 + - + +
1086B HIS* 1.3 82.3 - - - +
1088B GLN* 1.3 56.6 + - - +
1090B GLN* 2.8 8.5 + - - +
1091B VAL* 2.7 50.7 + - + -
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Residues in contact with GLN1088 (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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354B LEU* 3.5 18.1 - - + +
888B PRO 2.7 29.5 + - - -
889B GLY* 3.3 21.6 - - - +
890B LEU* 4.2 20.4 - - + +
1084B LEU 3.0 15.2 + - - +
1085B LEU* 4.1 16.2 - - - +
1087B ILE* 1.3 77.6 - - - +
1089B GLN* 1.3 62.6 + - - +
1090B GLN 3.3 0.3 + - - -
1091B VAL* 4.3 2.2 - - - -
1092B ASN* 3.0 43.7 + - - +
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Residues in contact with GLN1089 (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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1085B LEU 3.3 16.0 + - - +
1086B HIS* 3.7 12.7 - - - +
1087B ILE 3.1 0.6 - - - -
1088B GLN* 1.3 80.5 - - - +
1090B GLN* 1.3 75.4 + - - +
1092B ASN* 4.4 4.1 - - - +
1093B LYS* 3.8 18.4 + - - +
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Residues in contact with GLN1090 (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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872B ILE* 3.7 32.1 - - + +
876B SER* 5.0 0.7 + - - -
1086B HIS* 3.3 36.4 + - + +
1087B ILE 2.8 7.6 + - - +
1089B GLN* 1.3 98.5 + - - +
1091B VAL* 1.3 66.7 + - - +
1093B LYS* 3.2 51.0 + - - +
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Residues in contact with VAL1091 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872B ILE* 4.2 7.8 - - + +
875B LEU* 4.0 22.0 - - + +
876B SER* 3.2 41.9 + - - +
879B ARG* 3.7 30.8 - - + +
890B LEU* 4.2 11.7 - - + -
891B MET 6.2 0.2 - - - +
1087B ILE* 2.7 42.7 + - + +
1088B GLN* 4.0 7.2 - - - +
1090B GLN* 1.3 74.4 - - - +
1092B ASN* 1.3 57.8 + - - +
1093B LYS* 3.6 2.8 + - - +
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Residues in contact with ASN1092 (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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879B ARG* 2.4 55.0 - - - +
888B PRO 4.6 1.8 + - - -
1088B GLN* 3.0 41.1 + - - +
1089B GLN* 4.4 3.9 - - - +
1090B GLN 3.4 0.4 - - - -
1091B VAL* 1.3 76.6 - - - +
1093B LYS* 1.3 68.3 + - - +
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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