Contacts of the strand formed by residues 103 - 108 (chain A) in PDB entry 2ZPB
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLU 3.6 19.3 - - - +
99A ASP* 3.4 7.6 - - - +
100A THR* 2.9 45.4 + - + +
102A THR* 1.3 81.5 - - - +
104A LYS* 1.3 61.2 + - - +
105A ASN* 3.9 12.8 - - - +
155A ILE* 3.6 3.7 - - - +
156A GLU* 3.3 26.9 - - - +
158A ARG* 3.6 55.6 - - + +
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Residues in contact with LYS 104 (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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99A ASP* 2.8 28.4 + - + +
103A LEU* 1.3 74.3 - - - +
105A ASN* 1.3 88.4 + - - +
106A VAL* 4.6 6.7 - - + -
144A LEU* 4.6 2.2 - - + -
149A THR* 5.5 0.2 - - - -
151A ILE* 3.8 33.4 - - + -
155A ILE* 3.5 14.9 - - + +
156A GLU 2.8 10.7 + - - +
157A ILE* 3.3 8.2 - - + +
158A ARG 2.8 26.0 + - - -
170A VAL* 3.9 3.4 - - - +
172A PRO* 5.6 1.1 - - - +
194A CYS 5.1 0.2 + - - -
197A GLY* 3.1 27.9 + - - +
198A VAL 5.4 0.2 - - - -
199A ALA 4.3 6.7 + - - +
200A ILE* 4.1 23.8 - - + -
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Residues in contact with ASN 105 (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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97A VAL* 3.6 27.2 - - + +
98A GLU 3.0 32.7 + - - +
99A ASP* 2.8 30.0 + - - +
103A LEU* 3.9 13.8 - - - +
104A LYS* 1.3 94.1 + - - +
106A VAL* 1.3 67.8 + - - +
158A ARG* 3.3 16.6 - - - +
160A TYR* 3.4 21.2 + - + -
170A VAL* 3.7 6.3 - - + +
197A GLY* 3.5 6.6 - - - -
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Residues in contact with VAL 106 (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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104A LYS* 4.6 3.1 - - + -
105A ASN* 1.3 80.7 - - - +
107A ILE* 1.3 60.8 + - - +
132A TYR* 3.3 25.1 - - - +
136A VAL* 4.1 14.6 - - + -
140A PRO* 5.3 0.4 - - + -
144A LEU* 4.0 20.6 - - + -
157A ILE* 4.1 19.5 - - + -
158A ARG 2.9 8.2 + - - +
159A VAL* 3.3 12.4 - - + +
160A TYR* 2.8 32.4 + - - +
196A ILE 3.7 6.1 - - - +
197A GLY* 3.7 11.2 - - - +
198A VAL* 4.0 16.2 - - + -
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Residues in contact with ILE 107 (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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97A VAL* 5.2 3.1 - - + -
106A VAL* 1.3 77.0 - - - +
108A VAL* 1.3 62.3 + - - +
114A CSO 5.2 0.4 - - - +
115A THR* 6.2 1.3 - - - -
120A LEU* 4.9 4.3 - - + -
127A TYR* 3.4 20.6 - - + +
132A TYR* 2.7 26.3 + - - -
159A VAL* 5.2 0.2 - - - -
160A TYR* 3.5 9.9 - - + +
162A THR* 3.5 22.0 - - - +
168A TYR* 3.5 46.0 - - + +
169A MET* 3.8 1.3 - - - +
170A VAL* 3.8 13.5 - - + -
195A LEU 3.6 23.8 - - - +
196A ILE* 2.9 20.4 + - + +
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Residues in contact with VAL 108 (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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107A ILE* 1.3 75.1 - - - +
109A CYS* 1.3 69.2 + - - +
110A SER* 3.9 5.4 - - - +
127A TYR* 3.3 13.2 - - - +
132A TYR* 3.6 28.0 - - + +
133A ARG* 4.2 8.7 - - + +
136A VAL* 3.6 20.6 - - + -
137A VAL* 5.2 4.3 - - + -
159A VAL* 3.8 24.5 - - + -
160A TYR 3.0 10.3 + - - +
161A ASP* 3.9 17.3 - - + +
162A THR* 2.8 36.2 + - - -
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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