Contacts of the helix formed by residues 1103 - 1113 (chain A) in PDB entry 3NZ0
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 SER1103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1067A TRP* 5.9 0.4 - - - -
1092A TYR* 4.7 0.2 - - - -
1096A THR* 5.5 1.6 - - - -
1098A CYS 6.2 0.2 - - - -
1099A ASP 3.2 10.0 + - - -
1100A SER* 2.9 24.9 + - - -
1101A SER 3.5 0.2 - - - -
1102A GLN* 1.3 80.5 - - - +
1104A PRO* 1.3 76.7 - - - +
1105A PRO* 3.5 10.0 - - - +
1106A THR* 3.0 18.0 + - - -
1107A LYS* 2.9 20.6 + - - +
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Residues in contact with PRO1104 (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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1066A PHE* 4.0 13.9 - - + +
1067A TRP* 3.9 16.6 - - + -
1089A VAL* 3.5 32.1 - - + -
1092A TYR* 4.1 17.5 - - + -
1093A GLU* 4.2 12.3 - - + +
1102A GLN 3.8 0.4 - - - -
1103A SER* 1.3 82.7 - - - +
1105A PRO* 1.4 67.6 - - + +
1108A PHE* 2.8 38.8 + - + -
1134A LEU* 3.9 16.8 - - + -
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Residues in contact with PRO1105 (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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1066A PHE* 3.6 36.7 - - + -
1067A TRP* 3.8 19.5 - - + -
1103A SER* 3.5 12.3 - - - +
1104A PRO* 1.4 98.8 - - + +
1106A THR* 1.3 57.9 + - - +
1108A PHE* 3.9 0.3 - - - +
1109A LEU* 2.9 42.5 + - + +
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Residues in contact with THR1106 (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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1100A SER 3.1 11.4 + - - +
1101A SER* 3.3 27.1 - - - +
1103A SER* 3.0 21.8 + - - -
1105A PRO* 1.3 77.7 - - - +
1107A LYS* 1.3 62.2 + - + +
1109A LEU* 3.6 7.0 + - - +
1110A GLU* 3.2 25.2 + - - +
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Residues in contact with LYS1107 (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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1092A TYR* 3.5 18.2 - - - +
1101A SER 4.2 7.1 + - - +
1102A GLN* 3.0 44.1 + - - +
1103A SER 2.9 11.0 + - - +
1106A THR* 1.3 75.6 - - + +
1108A PHE* 1.3 60.4 + - - +
1110A GLU* 3.0 32.2 + - - +
1111A LEU* 3.0 33.1 + - + +
1134A LEU* 3.7 18.4 - - + -
1135A PRO* 4.1 23.4 - - + +
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Residues in contact with PHE1108 (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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1066A PHE* 3.6 50.9 - + + -
1085A TRP* 5.5 5.2 - + - -
1089A VAL* 5.6 2.7 - - + -
1104A PRO* 2.8 29.7 + - + +
1107A LYS* 1.3 73.1 - - - +
1109A LEU* 1.3 58.3 + - - +
1111A LEU* 3.1 10.7 + - + +
1112A ILE* 2.8 35.8 + - + +
1124A LEU* 3.8 18.8 - - + -
1127A LEU* 3.8 26.7 - - + -
1128A LEU* 3.8 20.2 - - + -
1133A ARG* 4.7 1.6 - - - -
1134A LEU* 3.7 43.3 - - + -
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Residues in contact with LEU1109 (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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1066A PHE* 4.3 21.8 - - + -
1105A PRO* 2.9 30.8 + - + +
1106A THR* 3.9 6.5 - - - +
1108A PHE* 1.3 74.8 - - - +
1110A GLU* 1.3 57.3 + - - +
1112A ILE* 3.6 18.3 + - + +
1113A GLY* 3.0 25.6 + - - -
1120A THR* 4.9 14.1 - - + -
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Residues in contact with GLU1110 (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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1106A THR* 3.2 15.3 + - + +
1107A LYS* 3.0 43.5 + - - +
1108A PHE 3.2 0.2 - - - -
1109A LEU* 1.3 75.3 - - - +
1111A LEU* 1.3 68.6 + - + +
1113A GLY* 3.4 12.3 + - - -
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Residues in contact with LEU1111 (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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1107A LYS* 3.0 20.3 + - + +
1108A PHE* 3.1 18.6 + - + +
1110A GLU* 1.3 77.9 - - + +
1112A ILE* 1.3 65.6 + - - +
1113A GLY* 3.4 0.9 + - - -
1123A ARG* 5.1 0.3 + - - -
1127A LEU* 3.4 23.4 - - + +
1130A ARG* 5.9 0.5 + - - -
1132A GLU* 3.9 28.0 - - + +
1133A ARG 3.7 27.8 - - - +
1134A LEU* 4.7 3.6 - - + +
1135A PRO* 5.4 4.9 - - + -
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Residues in contact with ILE1112 (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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1066A PHE* 4.9 5.4 - - + -
1108A PHE 2.8 28.4 + - - +
1109A LEU* 3.8 17.3 - - + +
1111A LEU* 1.3 71.9 - - - +
1113A GLY* 1.3 65.6 + - - +
1120A THR* 3.6 36.1 - - + +
1123A ARG* 2.8 54.9 + - + +
1124A LEU* 4.0 20.4 - - + +
1127A LEU* 3.7 16.4 - - + -
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Residues in contact with GLY1113 (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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1109A LEU 3.0 15.5 + - - -
1110A GLU* 3.4 11.4 + - - -
1111A LEU 3.2 2.7 - - - -
1112A ILE* 1.3 85.3 - - - +
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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