Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 5ZCJ
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 TYR 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE 4.4 0.9 + - - -
13A SER* 5.2 0.2 - - - -
14A ARG* 3.6 56.8 + - + +
74A LEU* 5.1 1.3 - - + -
93A GLU 3.1 17.2 + - - +
94A ALA 4.4 5.0 - - - +
95A ASP* 1.3 77.6 - - - +
97A LEU* 1.3 67.2 + - - +
98A SER* 3.5 21.4 - - - -
99A SER* 2.4 38.4 + - - -
111A HIS* 4.3 10.3 - - + -
112A LEU 4.2 1.8 - - - -
113A TYR* 3.4 33.9 - + + -
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Residues in contact with LEU 97 (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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95A ASP 3.4 4.4 + - - +
96A TYR* 1.3 84.9 - - - +
98A SER* 1.3 63.6 + - - +
112A LEU* 2.9 43.3 + - + +
113A TYR* 4.6 1.3 - - - -
114A ALA* 4.0 20.6 - - + +
175A PHE* 4.3 14.9 - - + -
176A ALA* 4.1 15.0 - - + -
179A VAL* 4.4 12.8 - - + -
180A LEU* 4.2 19.7 - - + -
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Residues in contact with SER 98 (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 GLN* 4.0 11.9 - - - -
96A TYR* 3.4 13.7 - - - -
97A LEU* 1.3 81.1 - - - +
99A SER* 1.3 62.4 + - - +
100A HIS* 3.1 25.5 + - - -
110A ALA 4.6 0.2 - - - -
111A HIS* 3.5 0.7 - - - -
112A LEU* 2.8 36.8 + - - +
175A PHE* 3.2 27.4 - - - -
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Residues in contact with SER 99 (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 GLN* 3.4 8.2 + - - +
12A ILE* 3.0 48.9 + - - +
13A SER 4.9 0.2 - - - -
14A ARG* 4.6 1.7 - - - -
17A ALA* 4.7 2.0 - - - -
96A TYR* 2.4 27.8 + - - -
98A SER* 1.3 72.2 + - - +
100A HIS* 1.3 63.7 + - - +
109A VAL* 4.2 0.7 - - - -
110A ALA 3.3 5.2 - - - -
111A HIS* 2.6 33.4 + - - -
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Residues in contact with HIS 100 (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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8A GLU* 5.3 2.4 - - - +
9A LEU* 3.5 50.1 + - + -
10A LYS 3.4 3.6 - - - -
11A GLN* 3.3 31.8 - - + +
98A SER* 3.1 32.4 + - - -
99A SER* 1.3 73.9 - - - +
101A LEU* 1.3 64.3 + - - +
102A THR 3.7 0.3 + - - -
109A VAL* 3.4 2.5 - - - -
110A ALA* 2.7 46.2 + - + +
112A LEU* 5.3 0.8 - - + +
171A CYS 6.4 0.2 - - - -
172A GLN* 4.9 15.3 + - + +
175A PHE* 4.0 28.8 - + + +
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Residues in contact with LEU 101 (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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9A LEU* 3.6 20.3 - - - +
10A LYS* 2.9 23.7 + - + +
12A ILE* 4.0 31.9 - - + -
20A LEU* 4.7 2.2 - - + -
24A TRP* 3.8 22.4 - - + -
100A HIS* 1.3 73.1 - - - +
102A THR* 1.3 64.8 + - - +
108A VAL 3.7 3.1 - - - +
109A VAL* 4.1 11.7 - - + -
1495C TRP* 3.7 35.7 - - + -
1523C TYR* 3.6 42.0 - - + +
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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