Contacts of the helix formed by residues 1096 - 1107 (chain A) in PDB entry 3RZD
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 SER1096 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1081A LEU 4.6 2.9 + - - -
1082A ASN 2.9 13.5 + - - +
1083A THR 3.0 17.8 + - - -
1084A PHE* 3.5 14.6 - - - +
1085A HIS 4.9 0.2 + - - -
1086A PHE* 4.5 14.5 - - - -
1094A VAL* 3.1 9.1 + - - -
1095A THR* 1.3 72.0 - - - +
1097A GLY* 1.3 70.0 + - - +
1099A PRO* 3.3 12.3 - - - +
1100A ARG* 3.4 10.4 + - - -
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Residues in contact with GLY1097 (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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1079A MET* 3.9 22.1 - - - +
1081A LEU 5.0 2.2 - - - -
1082A ASN* 3.8 12.3 - - - -
1096A SER* 1.3 80.9 + - - +
1098A VAL* 1.3 58.2 + - - -
1100A ARG* 3.6 2.0 - - - +
1101A LEU* 3.1 26.3 + - - +
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Residues in contact with VAL1098 (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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830A LYS* 3.8 31.0 - - + -
833A GLU* 3.5 24.2 - - + +
834A THR* 3.9 23.8 - - + -
837A ILE* 3.9 14.1 - - + +
1079A MET* 3.9 26.5 - - + -
1082A ASN* 3.9 13.2 - - + +
1097A GLY* 1.3 66.6 - - - -
1099A PRO* 1.4 74.0 - - + +
1101A LEU* 3.2 5.9 + - + +
1102A LYS* 2.9 21.9 + - - +
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Residues in contact with PRO1099 (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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833A GLU* 4.8 4.2 - - - +
1082A ASN* 3.4 30.7 - - + +
1083A THR* 5.3 2.7 - - - -
1095A THR* 5.3 10.3 - - + -
1096A SER 3.3 15.7 - - - +
1098A VAL* 1.4 92.3 - - + +
1100A ARG* 1.4 54.0 + - - +
1102A LYS* 3.3 10.8 + - + +
1103A GLU* 3.0 34.2 + - + +
1112A LYS* 5.1 15.3 - - - +
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Residues in contact with ARG1100 (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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1095A THR* 3.2 31.7 + - - +
1096A SER* 3.4 17.1 + - - +
1097A GLY 3.6 4.5 - - - +
1098A VAL 3.2 0.6 - - - -
1099A PRO* 1.4 74.4 - - - +
1101A LEU* 1.3 66.7 + - - +
1103A GLU* 3.0 40.5 + - - +
1104A ILE* 3.0 57.0 + - + +
1111A MET* 3.5 33.4 - - - +
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Residues in contact with LEU1101 (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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837A ILE* 4.1 22.7 - - + -
841A LEU* 5.8 0.2 - - + -
1072A ILE* 5.0 16.8 - - + -
1076A ALA* 3.8 28.7 - - + -
1079A MET* 4.3 10.8 - - + -
1097A GLY 3.1 14.1 + - - +
1098A VAL* 3.6 9.0 - - + +
1100A ARG* 1.3 75.5 - - - +
1102A LYS* 1.4 56.7 + - - +
1104A ILE* 3.3 15.7 + - + +
1105A LEU* 3.0 53.0 + - + +
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Residues in contact with LYS1102 (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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833A GLU* 3.7 38.4 + - + +
836A TYR* 6.1 3.6 - - - -
837A ILE* 4.5 14.3 - - + +
840A ARG* 4.6 11.4 - - - +
1098A VAL 2.9 12.4 + - - +
1099A PRO* 3.4 13.0 - - + +
1100A ARG 3.1 0.2 - - - -
1101A LEU* 1.4 73.3 - - - +
1103A GLU* 1.4 63.2 + - + +
1105A LEU* 3.7 3.3 + - - -
1106A ASN* 2.7 52.0 + - - +
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Residues in contact with GLU1103 (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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1095A THR* 3.7 18.6 + - - -
1099A PRO* 3.0 21.1 + - - +
1100A ARG* 3.0 33.0 + - - +
1102A LYS* 1.4 74.5 - - - +
1104A ILE* 1.4 61.5 + - - +
1106A ASN* 3.9 1.0 - - - +
1107A VAL 3.2 3.1 + - - -
1108A ALA* 3.0 44.4 + - + +
1110A ASN 4.2 2.6 - - - +
1111A MET* 3.6 13.0 - - - +
1112A LYS* 2.9 47.1 + - - +
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Residues in contact with ILE1104 (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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1100A ARG* 3.0 59.3 + - + +
1101A LEU* 3.6 17.0 - - + +
1103A GLU* 1.4 71.8 - - - +
1105A LEU* 1.3 63.4 + - + +
1107A VAL* 2.9 32.9 + - - +
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Residues in contact with LEU1105 (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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837A ILE* 3.5 32.8 - - + +
840A ARG* 3.9 18.4 + - + +
841A LEU* 4.1 28.0 - - + +
1072A ILE* 6.0 0.9 - - + -
1101A LEU* 3.0 35.7 + - + +
1102A LYS* 4.3 1.3 - - - +
1104A ILE* 1.3 81.2 - - + +
1106A ASN* 1.3 59.3 - - - +
1107A VAL* 3.6 5.9 + - - +
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Residues in contact with ASN1106 (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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840A ARG* 2.6 31.3 + - - +
1102A LYS* 2.7 51.7 + - - +
1103A GLU* 4.3 3.3 - - - +
1105A LEU* 1.3 75.1 - - - +
1107A VAL* 1.4 70.0 + - - +
1108A ALA* 4.6 3.8 - - + +
1109A LYS* 4.1 6.8 + - - -
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Residues in contact with VAL1107 (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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1103A GLU 3.2 1.2 + - - -
1104A ILE 2.9 20.8 + - - +
1105A LEU 4.4 5.8 - - - +
1106A ASN* 1.4 78.0 - - - +
1108A ALA* 1.3 57.3 + - - +
1109A LYS* 2.9 28.1 + - - +
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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