Contacts of the strand formed by residues 122 - 130 (chain B) in PDB entry 1ZN8
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 ARG 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ARG* 3.2 68.2 + - - +
59B ASP* 2.8 39.5 + - - +
60B TYR 3.3 3.6 + - - -
120B GLY 3.8 13.3 + - - +
121B GLN* 1.3 77.1 - - - +
123B VAL* 1.3 62.4 + - - +
149B GLU* 3.0 33.8 + - + +
151B LEU* 3.9 16.6 - - + -
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Residues in contact with VAL 123 (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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58B ILE* 4.8 0.7 - - - -
60B TYR* 3.3 14.8 - - + +
61B ILE 4.4 0.4 - - - -
62B ALA* 3.6 31.0 - - + +
84B VAL* 4.9 0.9 - - + -
117B LEU* 3.3 40.6 - - + -
121B GLN 4.5 3.8 - - - +
122B ARG* 1.3 84.0 - - - +
124B VAL* 1.3 69.4 + - - +
125B VAL* 4.3 0.4 - - + -
143B LEU* 4.4 15.3 - - + -
148B ALA* 4.5 3.1 - - + -
149B GLU 2.8 10.7 + - - +
150B VAL* 3.5 6.4 - - + +
151B LEU* 2.9 29.4 + - - +
152B GLU 4.0 0.3 + - - -
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Residues in contact with VAL 124 (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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50B LEU* 3.8 34.3 - - + -
54B HIS* 4.5 1.1 - - + -
58B ILE* 4.0 29.3 - - + +
60B TYR 3.2 5.3 + - - -
61B ILE* 3.4 19.2 - - + +
62B ALA 2.8 25.3 + - - +
75B LEU* 5.7 0.4 - - + -
123B VAL* 1.3 79.1 - - - +
125B VAL* 1.3 72.2 - - - +
126B VAL* 5.7 0.4 - - + -
151B LEU* 4.1 12.3 - - + -
152B GLU* 3.3 19.3 - - + +
154B VAL* 4.1 9.0 - - + -
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 3.4 10.8 - - + +
64B LEU* 3.8 36.3 - - + -
123B VAL* 4.7 1.1 - - + -
124B VAL* 1.3 74.0 - - - +
126B VAL* 1.3 59.1 + - - +
136B MET* 4.9 5.4 - - + -
139B ALA* 4.2 9.6 - - + -
140B CYS* 4.9 2.0 - - - -
143B LEU* 3.3 33.2 - - + -
150B VAL* 4.2 16.2 - - + -
152B GLU 3.1 5.1 + - - -
153B CYS* 3.3 19.1 - - - +
154B VAL* 2.8 35.0 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.8 7.4 - - + -
61B ILE* 3.8 9.0 - - + -
62B ALA 2.9 18.2 + - - +
63B GLY* 4.0 3.4 - - - -
64B LEU* 3.1 29.8 + - - +
68B GLY* 3.8 3.8 - - - +
71B PHE* 4.3 15.5 - - + -
72B GLY* 3.6 33.4 - - - +
75B LEU* 4.3 13.5 - - + -
124B VAL* 3.9 0.4 + - + -
125B VAL* 1.3 73.7 - - - +
127B ASP* 1.3 73.1 + - - +
136B MET* 4.5 0.9 - - - -
154B VAL* 3.5 25.1 - - + +
155B SER* 5.0 0.7 - - - -
156B LEU* 5.5 0.2 - - + -
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Residues in contact with ASP 127 (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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64B LEU* 3.6 28.3 - - + +
65B ASP 5.3 1.8 - - - +
67B ARG* 4.0 2.1 + - - +
68B GLY* 3.2 23.3 + - - -
71B PHE* 5.1 0.9 - - - -
126B VAL* 1.3 80.8 - - - +
128B ASP* 1.3 84.1 + - - +
129B LEU 3.4 6.4 - - - +
135B THR* 4.3 4.7 - - - +
136B MET* 3.4 21.3 - - + +
154B VAL 3.2 5.3 + - - +
155B SER* 3.1 19.3 - - - -
156B LEU* 3.8 2.8 + - - +
1032B AMP 3.4 25.6 + - - -
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Residues in contact with ASP 128 (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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27B ARG 4.8 5.9 - - - +
29B ILE* 3.6 30.8 - - + +
67B ARG* 3.1 37.0 + - + +
68B GLY* 4.3 3.4 - - - +
71B PHE* 4.0 12.3 - - + -
127B ASP* 1.3 88.0 + - - +
129B LEU* 1.3 76.5 + - - +
156B LEU* 3.0 32.9 + - - +
157B VAL* 3.1 8.3 + - - +
1032B AMP 2.7 26.2 + - - -
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Residues in contact with LEU 129 (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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27B ARG* 3.6 27.6 - - + +
29B ILE* 6.0 0.9 - - + -
127B ASP* 3.4 9.7 - - - +
128B ASP* 1.3 94.9 + - - +
130B LEU* 1.3 82.4 + - - +
131B ALA* 3.5 9.5 + - + +
136B MET* 4.9 2.0 - - - +
155B SER* 3.9 4.7 - - - -
157B VAL* 3.2 35.7 - - + +
159B LEU* 3.6 17.9 - - + -
1032B AMP 3.8 47.5 - - + +
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Residues in contact with LEU 130 (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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129B LEU* 1.3 76.7 - - - +
131B ALA* 1.3 65.7 + - - +
133B GLY* 3.6 27.8 - - - -
136B MET* 3.5 28.0 - - + -
155B SER* 3.9 0.6 + - - +
157B VAL 2.8 10.1 + - - +
158B GLU* 4.4 9.9 - - + -
159B LEU 2.9 26.9 + - - +
164B GLY* 3.7 3.4 - - - +
165B ARG* 3.6 26.2 - - - +
168B LEU* 4.0 9.2 - - + -
173B PHE* 3.7 43.5 - - + -
1032B AMP 4.3 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