Contacts of the strand formed by residues 157 - 163 (chain B) in PDB entry 1JZ3
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 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B TRP* 3.1 3.0 - - - -
154B CYS 2.8 35.4 + - - +
155B ASN* 4.0 10.1 - - - +
156B GLY* 1.3 81.3 - - - +
158B TRP* 1.3 65.1 + - - +
159B VAL* 3.5 3.1 + - - +
175B ALA* 3.2 30.3 + - - +
176B PHE* 3.6 39.3 - - + +
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Residues in contact with TRP 158 (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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24B LEU* 3.8 32.5 - - + -
25B ASN* 3.3 28.9 - - - -
151B HIS* 3.0 29.3 + + - -
152B LEU 3.6 13.9 - - - -
153B TRP* 3.4 36.4 - + - +
156B GLY 4.0 0.4 + - - -
157B ARG* 1.3 72.1 - - - +
159B VAL* 1.3 60.5 + - - +
160B GLY* 3.4 25.6 + - - -
176B PHE* 3.5 12.8 - - - -
13C ARG* 4.9 15.3 - - - -
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Residues in contact with VAL 159 (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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25B ASN* 2.9 29.3 + - + +
152B LEU* 2.8 26.9 + - + +
153B TRP 4.1 1.6 - - - -
154B CYS* 3.8 26.9 - - + +
157B ARG 3.7 13.7 - - - +
158B TRP* 1.3 76.9 - - - +
160B GLY* 1.3 59.0 + - - +
171B PHE* 3.8 29.8 - - + -
172B ASP 4.5 2.5 - - - +
173B LEU* 3.9 14.8 - - + -
176B PHE* 3.8 23.5 - - + -
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Residues in contact with GLY 160 (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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24B LEU 3.2 14.1 - - - -
151B HIS* 3.5 0.5 - - - -
152B LEU* 2.9 27.6 + - - +
158B TRP* 3.4 20.7 + - - -
159B VAL* 1.3 82.8 - - - +
161B TYR* 1.3 61.4 + - - -
171B PHE* 3.9 13.2 - - - -
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Residues in contact with TYR 161 (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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15B ASP* 4.0 15.5 - - + -
16B TRP* 3.3 26.1 - + + +
21B VAL* 3.9 17.7 - - + -
22B THR 4.3 1.3 - - - -
23B GLN* 3.2 19.0 - - - +
24B LEU* 3.0 39.5 + - + +
149B ALA* 3.6 5.1 - - + +
150B PHE* 3.0 37.7 - - - -
151B HIS* 3.5 38.6 - + + +
160B GLY* 1.3 75.8 - - - +
162B GLY* 1.3 59.3 + - - +
163B GLN* 2.6 45.2 + - + +
171B PHE* 3.6 12.0 - - - -
189B LEU* 5.1 1.6 - - + -
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Residues in contact with GLY 162 (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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22B THR 3.8 5.8 - - - -
26B ARG* 3.9 11.4 - - - -
149B ALA* 3.3 4.7 - - - +
150B PHE* 3.0 50.9 + - - -
161B TYR* 1.3 80.7 - - - +
163B GLN* 1.3 66.3 + - - +
169B SER* 4.3 1.8 - - - -
171B PHE* 4.7 1.8 - - - -
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Residues in contact with GLN 163 (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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16B TRP* 4.0 1.0 - - - -
21B VAL 3.3 6.1 - - - +
22B THR* 3.0 32.5 + - + +
26B ARG* 2.9 21.6 + - - +
146B VAL 5.7 0.4 - - - -
148B SER 3.9 9.0 - - - +
149B ALA* 3.9 6.7 - - + +
161B TYR* 2.6 27.8 + - + +
162B GLY* 1.3 76.5 - - - +
164B ASP* 1.3 74.1 + - - +
169B SER* 4.1 1.2 + - - -
192B SER* 4.5 3.4 - - - +
193B ASP* 2.8 27.5 + - - +
194B GLY* 3.7 16.5 - - - +
435B ALA* 6.1 0.2 - - - +
439B ARG* 4.6 5.6 - - - +
442B ARG* 4.5 0.2 + - - -
3002B MG 2.3 25.3 - - - -
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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