Contacts of the strand formed by residues 188 - 193 (chain J) in PDB entry 1ZUM
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 188 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66J ALA* 3.7 25.6 - - + +
69J ALA* 4.3 2.9 - - + -
70J PHE* 3.9 24.4 - - + +
76J TRP* 3.7 20.0 - - + -
160J GLY 3.0 15.3 + - - +
161J VAL* 3.6 19.7 - - + -
162J CYS* 2.9 26.6 + - - +
187J ASN* 1.3 76.8 - - - +
189J VAL* 1.3 66.6 + - - +
216J GLY 4.2 4.9 - - - +
217J VAL* 3.4 19.3 - - - +
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Residues in contact with VAL 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ALA* 4.9 0.4 - - - -
162J CYS* 3.4 10.3 - - + +
164J GLN* 3.0 31.6 - - - +
179J LEU* 4.2 17.5 - - + -
182J ALA* 3.9 23.8 - - + -
183J LEU* 4.4 7.4 - - + -
188J VAL* 1.3 81.1 - - - +
190J VAL* 1.3 77.0 + - - +
191J MET* 3.7 11.2 - - + +
217J VAL 2.7 16.0 + - - +
218J VAL* 4.6 4.3 - - + -
219J ASN* 2.9 34.5 + - - +
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Residues in contact with VAL 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J VAL* 4.6 2.9 - - + -
62J ALA* 3.8 47.1 - - + +
63J VAL* 3.9 14.8 - - + +
66J ALA* 3.9 12.6 - - + -
161J VAL* 4.1 10.1 - - + -
162J CYS 3.0 7.6 + - - +
163J GLY* 3.3 7.8 - - - -
164J GLN 3.0 21.0 + - - +
189J VAL* 1.3 79.7 - - - +
191J MET* 1.3 59.6 + - - +
219J ASN* 3.5 4.5 - - - +
221J VAL* 4.7 6.7 - - + -
232J ILE* 3.9 27.3 - - + +
238J VAL* 5.7 0.9 - - + -
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Residues in contact with MET 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J GLN* 3.2 34.5 - - + +
166J ILE* 3.6 23.6 - - + -
175J GLN* 3.7 30.7 - - + +
178J LYS* 4.2 6.7 - - + -
179J LEU* 3.6 27.4 - - + -
189J VAL* 4.0 6.5 - - + -
190J VAL* 1.3 74.2 - - - +
192J LYS* 1.3 66.7 + - - +
193J VAL* 4.2 6.3 - - + -
218J VAL* 5.5 0.2 - - + -
219J ASN 2.7 14.5 + - - +
220J ILE* 3.3 17.0 - - + +
221J VAL* 2.7 34.0 + - - +
232J ILE* 4.5 1.8 - - - -
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Residues in contact with LYS 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J GLN 2.8 11.6 + - - +
165J ILE* 3.5 19.1 - - + -
166J ILE* 3.1 27.2 + - - +
190J VAL 4.1 0.4 + - - -
191J MET* 1.3 72.7 - - - +
193J VAL* 1.3 85.1 + - - +
194J ALA* 4.4 5.3 - - - +
195J GLU* 4.5 1.8 + - - +
221J VAL* 3.3 20.2 - - + +
223J GLY 3.2 19.4 + - - +
224J PHE 3.7 17.5 - - - -
225J GLY* 3.9 6.0 - - - +
228J ALA* 3.7 24.7 - - + -
229J GLY* 3.9 12.8 - - - +
232J ILE* 3.6 22.9 - - + -
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Residues in contact with VAL 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J ILE* 3.9 21.1 - - + -
191J MET* 4.1 5.1 - - + -
192J LYS* 1.3 99.7 + - - +
194J ALA* 1.3 62.7 + - - +
195J GLU 3.5 0.5 + - - -
197J THR 4.7 2.2 - - - +
198J PRO* 3.8 25.1 - - + +
201J ALA* 3.5 28.0 - - + -
202J LEU* 5.1 0.7 - - + -
220J ILE* 3.9 19.5 - - + -
221J VAL 3.9 0.4 + - - -
222J PRO* 3.7 28.5 - - + -
223J GLY 4.1 4.7 + - - +
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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