Contacts of the helix formed by residues 113 - 118 (chain L) in PDB entry 4ZZ7
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 GLY 113 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109J GLU 5.9 2.9 - - - -
113J GLY* 5.5 11.2 - - - -
109L GLU 3.8 2.6 + - - -
110L TYR 3.4 9.0 + - - -
111L ALA 3.1 1.6 - - - -
112L CYS* 1.3 76.3 - - - +
114L ALA* 1.3 61.7 + - - -
115L PRO* 3.1 7.4 - - - -
116L GLU* 3.3 16.6 + - - +
117L LEU* 3.4 19.2 + - - +
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Residues in contact with ALA 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L PRO* 4.7 3.8 - - + +
65L ALA* 4.6 2.5 - - + -
111L ALA 3.0 16.5 + - - +
112L CYS 3.3 0.6 - - - -
113L GLY* 1.3 75.9 - - - +
115L PRO* 1.4 64.1 - - + +
117L LEU* 3.7 11.2 - - - -
118L LEU* 2.9 47.7 + - + +
161L MET* 5.8 0.9 - - - -
164L VAL* 3.6 32.3 - - + +
165L CYS* 5.9 0.2 - - - -
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Residues in contact with PRO 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446J TYR* 3.4 47.9 - - + +
123K SER* 4.8 1.7 + - - -
61L PRO* 4.1 11.2 - - + -
62L LEU* 4.1 32.1 - - + +
65L ALA* 4.4 3.8 - - + -
112L CYS 4.1 6.5 - - - +
113L GLY* 3.2 8.5 - - - -
114L ALA* 1.4 95.1 - - + +
116L GLU* 1.3 60.0 + - - +
118L LEU* 3.6 8.1 + - + +
119L LYS* 3.5 17.3 + - - +
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Residues in contact with GLU 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J TYR* 2.9 26.0 + - + -
116J GLU* 4.3 20.2 - - + +
117J LEU* 3.6 28.3 - - + +
446J TYR* 4.7 1.4 - - - +
465J PRO* 4.8 0.6 - - - +
121K GLU* 4.8 4.2 - - - +
113L GLY* 3.3 10.0 + - - +
115L PRO* 1.3 79.0 - - - +
117L LEU* 1.3 64.5 + - + +
119L LYS* 2.7 60.1 + - - +
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Residues in contact with LEU 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J GLU* 3.7 26.7 - - + +
110L TYR* 3.2 67.8 - - + +
113L GLY 3.4 15.5 - - - +
114L ALA* 3.3 11.4 + - - +
115L PRO 3.3 0.6 - - - -
116L GLU* 1.3 78.4 - - + +
118L LEU* 1.3 58.6 - - + +
119L LYS 3.3 4.9 + - - +
136L PHE* 5.4 2.3 - - - -
161L MET* 3.9 14.1 - - + -
468L VAL* 3.6 27.9 - - + +
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Residues in contact with LEU 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122K HIS 4.3 1.9 - - - +
123K SER* 6.0 1.1 - - - -
124K ARG* 5.5 3.2 + - - +
61L PRO* 4.1 18.6 - - + -
64L ARG* 3.6 26.7 - - - +
114L ALA* 2.9 24.9 + - + +
115L PRO* 3.6 6.5 + - + +
116L GLU 3.3 0.6 - - - -
117L LEU* 1.3 75.3 - - + +
119L LYS* 1.3 66.1 + - - +
120L GLY 3.2 2.9 + - - -
135L GLU* 5.8 0.2 - - - -
136L PHE* 4.2 27.2 + - + +
164L VAL 4.2 8.7 - - - +
165L CYS* 4.0 28.0 - - + +
468L VAL* 4.0 9.4 - - + -
472L THR* 4.0 17.9 - - + -
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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