Contacts of the helix formed by residues 1030 - 1038 (chain F) in PDB entry 1AWV
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 PRO1030 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1026F ALA* 2.6 26.4 - - + +
1027F ASP* 3.3 12.8 - - - +
1028F LYS 3.6 3.4 - - - +
1029F VAL* 1.3 83.4 - - - +
1031F LYS* 1.3 57.2 + - - +
1033F ALA* 3.9 0.7 - - - +
1034F GLU* 2.9 38.2 + - - +
1086F GLU* 3.2 17.0 - - - +
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Residues in contact with LYS1031 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029F VAL 3.5 0.6 - - - -
1030F PRO* 1.3 78.0 - - + +
1032F THR* 1.3 61.1 + - - +
1034F GLU* 3.7 1.7 + - - -
1035F ASN* 3.2 14.2 + - - +
1079F TYR* 3.0 59.1 + - + +
1083F PHE* 4.0 16.2 - - + -
1084F GLU* 3.7 23.6 - - - +
1086F GLU* 3.5 18.1 + - + +
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Residues in contact with THR1032 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029F VAL* 3.2 17.7 + - - +
1031F LYS* 1.3 75.5 - - - +
1033F ALA* 1.3 66.2 + - - +
1035F ASN* 3.0 18.9 - - - +
1036F PHE 3.4 3.8 + - - -
1083F PHE* 3.8 25.5 - - + -
1086F GLU* 3.3 22.9 + - - +
1100F MET* 3.5 32.5 - - + -
1108F ASN* 5.5 1.5 + - - +
1127F VAL* 4.7 8.2 - - + +
1129F PHE* 3.9 20.6 - - + -
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Residues in contact with ALA1033 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024F LEU* 3.3 26.6 - - + +
1025F PHE 4.3 2.0 - - - +
1026F ALA* 3.5 33.2 - - + +
1029F VAL* 2.7 25.6 + - + +
1030F PRO 3.9 0.7 - - - +
1032F THR* 1.3 71.5 - - - +
1034F GLU* 1.3 63.3 + - - +
1035F ASN 3.2 0.5 + - - -
1036F PHE* 3.3 3.8 + - - +
1037F ARG 3.1 17.2 + - - -
1129F PHE* 4.0 13.4 - - + -
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Residues in contact with GLU1034 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004F PRO* 6.0 1.3 - - - +
1026F ALA* 4.8 11.3 - - - +
1030F PRO* 2.9 24.6 + - - +
1031F LYS* 3.8 6.3 - - - +
1033F ALA* 1.3 76.3 - - - +
1035F ASN* 1.3 54.7 + - - +
1037F ARG* 3.1 36.3 + - - +
1038F ALA* 2.8 38.8 + - + +
1078F ILE* 4.3 9.2 - - + -
1079F TYR* 4.2 7.0 - - - +
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Residues in contact with ASN1035 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031F LYS 3.2 12.0 + - - +
1032F THR 3.0 13.8 + - - +
1034F GLU* 1.3 77.5 - - - +
1036F PHE* 1.3 58.3 + - - +
1038F ALA* 3.9 0.3 - - - +
1039F LEU* 3.0 58.4 + - - +
1048F TYR* 4.8 1.8 + - - -
1077F SER* 3.3 15.6 - - - -
1078F ILE* 3.5 18.0 + - - +
1079F TYR* 4.0 2.0 - - + -
1083F PHE* 3.3 19.5 - - + -
1100F MET* 3.9 10.1 - - - +
1109F GLY 2.8 26.4 + - - -
1110F SER* 4.1 2.4 - - - +
1129F PHE* 6.3 0.2 - - - -
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Residues in contact with PHE1036 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006F VAL* 3.9 7.6 - - + -
1008F PHE* 3.3 37.0 - + - -
1022F PHE* 3.9 17.9 - + - -
1024F LEU* 3.8 17.5 - - + -
1032F THR 3.4 1.0 + - - -
1033F ALA 3.3 7.5 + - - +
1035F ASN* 1.3 79.3 - - - +
1037F ARG* 1.3 58.7 + - - +
1040F SER* 3.0 30.8 + - - -
1048F TYR* 3.7 19.9 - - - -
1098F LEU* 3.5 35.7 - - + -
1100F MET* 5.8 0.2 - - - -
1112F PHE* 3.5 23.8 - + + -
1129F PHE* 3.4 35.4 - + + -
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Residues in contact with ARG1037 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004F PRO* 4.3 12.8 - - - -
1006F VAL* 3.5 26.0 - - + -
1024F LEU* 3.4 17.0 - - + +
1033F ALA 3.1 7.2 + - - +
1034F GLU* 3.1 35.8 + - - +
1036F PHE* 1.3 73.1 - - - +
1038F ALA* 1.3 66.3 + - - +
1039F LEU 3.1 4.0 - - - -
1040F SER* 3.0 18.9 + - - -
1041F THR* 3.0 25.3 + - - +
1043F GLU* 2.8 44.0 + - - -
1163F GLN* 3.2 37.7 + - + +
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Residues in contact with ALA1038 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034F GLU* 2.8 20.9 + - + +
1037F ARG* 1.3 78.9 - - - +
1039F LEU* 1.3 60.5 + - - +
1041F THR* 3.7 10.5 - - - -
1042F GLY* 3.4 2.9 + - - -
1043F GLU* 3.4 46.9 + - + +
1044F LYS* 4.6 9.2 + - - +
1046F PHE 5.0 0.2 - - - +
1078F ILE* 4.2 22.9 - - + -
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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