Contacts of the helix formed by residues 1080 - 1089 (chain A) in PDB entry 3ZW3
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 TRP1080 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892A GLN* 3.7 9.4 - - - -
902A PHE* 3.6 47.4 + + + -
903A LYS 3.6 20.2 - - - -
904A ASP* 2.8 22.9 + - - -
949A ASN* 4.3 13.7 - - - -
988A THR* 3.7 24.0 - - + -
989A PRO* 3.7 17.5 - - + +
990A ASP* 3.3 43.3 - - - -
1078A LYS 3.2 0.4 + - - -
1079A GLY* 1.3 70.5 - - - -
1081A THR* 1.3 62.6 + - - +
1082A VAL 3.4 2.2 - - - -
1083A GLN* 3.3 12.2 + - + +
1084A PHE* 3.0 24.4 + - + +
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Residues in contact with THR1081 (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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1078A LYS* 2.9 27.7 + - + -
1080A TRP* 1.3 75.9 - - - +
1082A VAL* 1.4 61.0 + - + +
1084A PHE* 3.4 8.0 + - - +
1085A ASN* 3.2 39.8 + - - +
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Residues in contact with VAL1082 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A ASP* 3.4 32.5 - - - +
982A ARG* 4.1 13.5 - - - +
983A VAL* 3.9 33.2 - - + +
1078A LYS* 3.9 19.4 + - + -
1079A GLY 4.9 3.2 + - - +
1080A TRP 3.4 0.4 - - - -
1081A THR* 1.4 74.7 - - + +
1083A GLN* 1.3 63.0 + - + +
1085A ASN* 3.2 9.1 + - + +
1086A TRP* 3.0 37.4 + - + +
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Residues in contact with GLN1083 (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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902A PHE* 4.0 18.8 - - + -
947A ARG 2.9 20.8 - - - +
948A HIS* 3.5 13.9 + - - +
949A ASN* 2.9 51.2 + - - +
986A VAL* 4.0 17.2 - - - +
988A THR* 3.7 25.7 - - + +
1079A GLY 5.5 0.4 + - - -
1080A TRP* 3.3 16.4 + - + +
1082A VAL* 1.3 78.9 - - - +
1084A PHE* 1.3 56.9 + - - +
1086A TRP* 3.3 7.7 + - - +
1087A PHE* 3.0 27.2 + - - +
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Residues in contact with PHE1084 (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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899A THR 5.8 0.9 - - - -
900A GLY* 4.3 24.5 - - - -
902A PHE* 4.1 9.1 - + + -
1080A TRP* 3.0 13.5 + - + +
1081A THR* 3.6 10.5 - - - +
1082A VAL 3.2 0.2 - - - -
1083A GLN* 1.3 77.3 - - - +
1085A ASN* 1.3 68.8 + - - +
1087A PHE* 3.3 10.7 + + + +
1088A LEU* 3.0 59.3 + - + +
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Residues in contact with ASN1085 (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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1081A THR* 3.2 26.9 + - - +
1082A VAL* 3.2 10.8 + - + +
1084A PHE* 1.3 85.3 - - - +
1086A TRP* 1.4 58.3 + - - +
1088A LEU* 3.5 13.8 + - - +
1089A HIS* 3.0 28.8 + - - +
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Residues in contact with TRP1086 (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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946A ASP* 2.8 47.5 + - + -
947A ARG* 3.8 18.7 - - - -
948A HIS* 3.7 38.8 + + + +
968A ILE* 5.7 7.9 - - + -
1082A VAL* 3.0 32.6 + - + +
1083A GLN* 3.3 11.9 + - - +
1085A ASN* 1.4 73.2 - - - +
1087A PHE* 1.3 63.9 + - - +
1089A HIS* 3.4 31.0 + - + +
1090A LEU* 4.9 0.3 - - - -
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Residues in contact with PHE1087 (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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898A ASN* 4.1 15.5 - - - -
899A THR* 4.1 13.0 - - - -
900A GLY* 3.6 38.4 - - - -
902A PHE* 4.5 13.5 - + + -
948A HIS* 4.4 16.3 - + + -
1083A GLN 3.0 13.2 + - - +
1084A PHE* 3.3 16.8 + + - +
1086A TRP* 1.3 74.1 - - - +
1088A LEU* 1.3 74.2 + - + +
1089A HIS 3.4 0.2 + - - -
1090A LEU* 3.4 19.2 - - - +
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Residues in contact with LEU1088 (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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1084A PHE* 3.0 54.5 + - + +
1085A ASN* 3.7 15.9 - - - +
1086A TRP 3.5 0.2 - - - -
1087A PHE* 1.3 76.7 - - + +
1089A HIS* 1.4 52.3 + - - +
1090A LEU* 2.6 22.9 + - - +
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Residues in contact with HIS1089 (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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1085A ASN 3.0 18.4 + - - +
1086A TRP* 3.6 27.6 - - + +
1087A PHE 3.3 0.4 - - - -
1088A LEU* 1.4 70.6 - - - +
1090A LEU* 1.4 57.9 + - - +
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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