Contacts of the strand formed by residues 114 - 119 (chain A) in PDB entry 1Z83
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 LEU 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ILE 3.3 2.6 + - - +
11A ILE* 3.4 24.5 - - + -
12A PHE* 3.0 25.2 + - - +
112A PRO* 3.5 4.2 - - - +
113A THR* 1.3 85.1 - - + +
115A LEU* 1.3 64.6 + - - +
116A LEU* 4.1 5.4 - - + +
169A ILE* 3.2 24.7 - - - +
171A ARG* 3.7 30.7 - - + +
189A HIS* 5.3 1.6 - - + +
190A LEU* 4.0 23.6 - - + -
193A LEU* 3.4 37.9 - - + -
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Residues in contact with LEU 115 (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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12A PHE* 3.3 17.0 - - + +
14A VAL* 3.9 20.9 - - + -
114A LEU* 1.3 76.8 - - - +
116A LEU* 1.3 71.3 + - - +
117A TYR* 3.9 6.7 - - + +
160A VAL* 4.5 4.0 - - + +
161A ILE* 3.7 28.9 - - + -
164A TYR* 3.7 37.9 - - + -
169A ILE* 2.9 19.1 + - + +
170A VAL* 3.4 16.1 - - + -
171A ARG* 2.9 28.9 + - - +
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Residues in contact with LEU 116 (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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11A ILE* 4.3 15.4 - - + +
12A PHE 2.8 11.5 + - - +
13A VAL* 3.5 19.9 - - + +
14A VAL 2.9 27.4 + - - +
24A GLN* 5.8 2.2 - - + -
28A ILE* 4.0 15.5 - - + -
114A LEU* 4.1 3.9 - - + -
115A LEU* 1.3 71.9 - - - +
117A TYR* 1.3 60.3 + - - +
118A VAL* 3.7 10.2 + - + -
171A ARG* 3.6 20.9 - - + +
173A VAL* 4.2 18.8 - - + -
186A VAL* 3.9 33.2 - - + +
189A HIS* 4.5 10.3 - - + -
190A LEU* 5.3 10.1 - - + -
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Residues in contact with TYR 117 (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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14A VAL 3.5 10.1 - - - -
115A LEU* 3.7 14.7 + - + -
116A LEU* 1.3 68.7 - - - +
118A VAL* 1.3 62.6 + - - +
119A ASP* 3.5 33.6 + - + -
153A TYR* 3.8 19.8 + - - -
158A GLU* 4.3 16.8 + - - +
161A ILE* 4.0 37.5 - - + -
170A VAL* 4.1 7.9 - - + -
171A ARG 2.9 14.3 + - - +
172A LYS* 3.4 32.2 - - + +
173A VAL* 2.8 31.8 + - - +
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Residues in contact with VAL 118 (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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13A VAL* 4.2 25.1 - - + -
14A VAL 2.9 10.0 + - - +
15A GLY* 3.5 18.5 - - - -
16A GLY 4.2 1.0 + - - -
19A SER* 3.5 40.7 - - - +
20A GLY 4.5 8.5 - - - -
21A LYS* 4.5 7.0 - - + -
24A GLN* 5.3 10.1 - - + -
116A LEU* 4.3 10.5 - - + +
117A TYR* 1.3 73.0 - - - +
119A ASP* 1.3 59.7 + - - +
120A ALA 3.6 2.6 + - - -
153A TYR* 5.2 0.2 + - - -
173A VAL* 3.8 16.6 - - + -
175A ALA* 3.6 10.5 - - + -
182A VAL* 5.2 4.7 - - + -
186A VAL* 5.8 0.2 - - + -
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Residues in contact with ASP 119 (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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117A TYR* 3.6 33.3 + - + -
118A VAL* 1.3 69.6 - - - +
120A ALA* 1.3 68.1 + - - +
172A LYS* 3.6 29.7 + - + +
173A VAL 3.1 15.2 + - - +
174A ASN* 4.0 7.1 - - - +
175A ALA* 3.0 22.0 + - - +
176A GLU* 4.7 0.7 - - - +
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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