Contacts of the strand formed by residues 150 - 156 (chain B) 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 VAL 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B ARG* 3.7 28.5 - - + +
129B VAL 3.3 10.5 - - - +
130B ARG* 3.2 50.9 - - + +
149B ARG* 1.3 72.8 - - - +
151B GLY* 1.3 68.1 + - - +
184B PHE* 3.3 15.2 - - - -
185B ALA 5.2 0.5 + - - -
188B GLU* 2.9 27.5 + - - +
211B ALA* 4.0 10.5 - - + -
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Residues in contact with GLY 151 (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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128B ARG* 3.4 8.2 - - - +
129B VAL* 2.9 31.5 + - - -
150B VAL* 1.3 76.9 - - - +
152B THR* 1.3 59.2 + - - -
182B VAL* 3.9 13.9 - - - +
183B LYS 3.2 14.8 - - - -
184B PHE* 3.8 6.9 - - - -
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Residues in contact with THR 152 (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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126B GLY* 3.7 18.9 + - - -
127B GLN 3.4 7.4 - - - -
128B ARG* 5.1 6.1 - - - -
151B GLY* 1.3 73.9 - - - -
153B ILE* 1.3 72.5 + - - +
154B SER* 3.4 2.8 + - - +
182B VAL* 3.5 4.1 - - - +
183B LYS* 2.8 60.3 + - + +
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Residues in contact with ILE 153 (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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123B PHE* 4.0 11.2 - - + +
124B GLU 3.3 27.1 - - - +
125B VAL* 3.6 9.7 - - + +
126B GLY* 2.8 25.6 + - - -
127B GLN 3.0 16.7 + - - +
129B VAL* 3.7 31.9 - - + -
152B THR* 1.3 74.5 + - - +
154B SER* 1.3 61.8 + - - +
155B HIS 3.7 24.5 - - - +
156B ARG* 5.1 0.4 - - + -
180B TYR* 3.8 36.1 - - + -
181B HIS 3.6 2.9 - - - +
182B VAL* 4.1 4.5 - - + -
208B LEU* 4.4 1.8 - - + -
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Residues in contact with SER 154 (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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160A TYR* 6.0 2.0 - - - -
125B VAL* 3.9 18.5 - - - +
152B THR* 3.8 1.6 + - - +
153B ILE* 1.3 73.7 - - - +
155B HIS* 1.3 63.0 + - - +
181B HIS* 2.8 21.2 + - - -
183B LYS* 3.7 30.7 + - - +
200B VAL* 5.1 4.5 - - - +
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Residues in contact with HIS 155 (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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75A THR 5.5 5.2 + - - -
93A TYR* 2.8 38.5 + + - -
95A VAL* 4.4 12.1 - - + +
125B VAL* 4.2 5.8 - - + -
153B ILE* 3.6 11.6 - - - +
154B SER* 1.3 83.1 - - - +
156B ARG* 1.3 75.1 + - - +
157B THR* 3.7 5.9 + - - +
158B THR* 5.6 2.8 - - - +
180B TYR* 3.2 6.1 - - - -
181B HIS* 3.0 60.3 + + + +
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Residues in contact with ARG 156 (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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122B THR* 3.8 14.6 - - - +
123B PHE 2.8 28.4 + - - +
124B GLU* 3.1 32.7 + - - +
125B VAL* 4.5 9.2 - - + +
153B ILE* 5.2 1.6 - - + -
155B HIS* 1.3 85.4 + - - +
157B THR* 1.3 75.8 + - - +
158B THR* 3.6 6.4 + - - +
178B PRO* 4.3 11.0 - - + -
179B THR 3.7 2.9 - - - -
180B TYR* 3.5 38.8 - - + -
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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