Contacts of the strand formed by residues 94 - 99 (chain B) in PDB entry 2ZOT
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 THR 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ILE* 5.7 0.2 - - + -
93B PHE* 1.3 80.5 + - - +
95B LEU* 1.3 70.7 + - - +
96B ILE* 4.5 2.5 - - + -
125B MET* 3.3 32.1 - - + +
132B VAL 3.3 9.6 - - - +
133B THR* 3.6 7.2 + - - +
160B LYS 3.8 0.5 - - - +
161B ALA* 3.2 4.5 - - - -
162B SER 2.7 38.7 + - - -
165B GLN* 4.7 4.5 + - - -
169B ILE* 4.1 27.1 - - + +
171B PHE* 3.8 17.8 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 4.4 8.7 - - + -
80B VAL* 5.1 10.3 - - + +
82B LEU* 3.8 13.5 - - + +
93B PHE* 3.8 19.1 - - + -
94B THR* 1.3 82.2 - - - +
96B ILE* 1.3 68.0 + - - +
114B PHE* 3.8 9.5 - - + -
131B ALA* 3.6 1.7 - - - +
132B VAL* 2.9 48.2 + - + +
143B ILE* 3.8 17.3 - - + -
145B VAL* 3.8 29.8 - - + -
160B LYS 3.2 6.5 - - - +
161B ALA* 3.6 21.5 - - + -
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.2 37.9 - - + -
94B THR* 4.5 1.6 - - + -
95B LEU* 1.3 79.9 - - - +
97B ALA* 1.3 61.6 + - - +
98B LEU* 3.6 29.4 - - + -
103B GLU 5.3 0.2 - - - +
110B HIS* 3.9 10.3 - - + +
114B PHE* 3.5 12.7 - - - -
130B VAL 5.0 1.1 - - - -
131B ALA* 3.7 16.8 - - + -
159B LEU* 3.5 3.6 - - - -
160B LYS* 2.9 48.2 + - + +
171B PHE* 3.9 28.5 - - + -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 1.3 76.2 - - - +
98B LEU* 1.3 62.2 + - - +
110B HIS* 3.3 12.7 - - + +
111B ALA 2.8 42.8 + - - +
112B GLY* 4.9 1.1 - - - -
114B PHE* 3.7 12.1 - - + -
130B VAL* 5.1 2.6 + - + +
147B TRP* 3.4 22.0 - - + +
157B VAL* 5.5 1.1 - - + -
158B ILE 3.7 5.2 - - - -
159B LEU* 3.8 11.2 - - + -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 3.6 20.4 - - + -
97B ALA* 1.3 74.6 - - - +
99B ARG* 1.3 65.3 + - - +
102B ARG* 3.4 26.0 - - + +
103B GLU 3.5 16.8 - - - +
104B GLY* 3.6 14.6 - - - +
109B ASP 3.7 7.6 - - - +
110B HIS* 3.3 41.5 - - + +
111B ALA 4.6 1.1 - - - -
157B VAL* 3.3 5.4 - - - +
158B ILE* 2.6 44.6 + - + +
160B LYS* 3.4 21.5 - - - +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA 4.1 0.6 + - - -
98B LEU* 1.3 77.5 - - - +
100B GLU* 1.3 67.5 + - - +
101B ASN 3.2 0.5 + - - -
102B ARG* 3.2 60.8 + - - +
108B GLU 5.0 3.2 + - - -
109B ASP* 3.3 27.7 + - - +
110B HIS 4.8 1.7 + - - -
111B ALA* 3.3 27.2 - - + +
153B GLY 5.4 1.4 + - - -
154B THR* 3.4 43.0 + - + +
156B CYS 3.8 7.4 - - - +
157B VAL* 4.4 1.8 - - + +
158B ILE* 4.7 1.8 - - - +
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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