Contacts of the strand formed by residues 285 - 291 (chain A) in PDB entry 1JQE
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 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.7 27.8 - - + +
31A CYS* 4.1 16.8 - - + -
32A MET* 3.9 33.9 - - + -
143A GLN* 3.9 14.8 - - - +
171A ILE* 4.4 4.5 - - + -
172A VAL 3.8 4.0 - - - +
173A VAL* 4.1 14.8 - - + -
174A SER* 4.2 0.4 - - - -
218A TYR 3.8 0.7 - - - +
219A ASP* 3.2 3.8 - - - -
220A LEU 2.9 33.9 + - - +
222A SER* 4.3 5.6 - - - -
283A ASN* 3.4 18.8 - - - +
284A THR* 1.3 76.1 - - - +
286A SER* 1.3 62.2 + - - +
287A PHE* 3.9 17.2 - - + -
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ILE 3.6 1.2 - - - +
171A ILE* 3.3 25.3 - - - +
172A VAL* 2.8 15.6 + - - +
174A SER* 3.1 11.8 - - - +
201A SER* 3.0 37.9 + - - -
217A CYS* 4.0 7.6 - - - -
218A TYR 3.4 4.3 - - - -
219A ASP* 2.6 20.7 + - - -
285A LEU* 1.3 72.2 - - - +
287A PHE* 1.3 61.6 + - - +
288A ILE* 3.9 4.0 - - - +
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Residues in contact with PHE 287 (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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31A CYS* 4.1 15.7 - - - -
32A MET* 4.1 17.0 - - + -
35A PHE* 3.3 67.1 - + + -
36A MET* 4.6 0.2 - - + -
169A LEU* 4.3 3.1 - - + -
170A ILE 3.7 3.4 - - - -
171A ILE* 3.4 35.4 - - + -
217A CYS* 3.4 1.7 - - - -
218A TYR* 2.6 53.2 + - - +
220A LEU* 3.6 26.9 - - + -
285A LEU* 3.9 20.4 - - + -
286A SER* 1.3 73.7 - - - +
288A ILE* 1.3 62.0 + - - +
289A VAL* 4.0 0.4 - - - -
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Residues in contact with ILE 288 (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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168A MET 3.5 1.7 - - - +
169A LEU* 3.4 4.4 - - - +
170A ILE* 2.8 47.4 + - + +
172A VAL* 4.9 2.9 - - + -
201A SER* 4.4 9.6 - - - -
204A LEU* 4.0 36.1 - - + -
205A THR* 4.3 15.5 - - + -
208A LEU* 3.7 24.2 - - + -
215A TYR* 4.0 15.9 - - + -
216A GLU 3.4 8.1 - - - +
217A CYS* 3.7 21.3 - - + -
286A SER 4.7 1.6 - - - -
287A PHE* 1.3 75.9 - - - +
289A VAL* 1.3 63.3 + - - +
290A ILE* 3.9 8.1 + - + +
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Residues in contact with VAL 289 (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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35A PHE* 4.7 0.7 - - + -
43A ILE* 3.6 36.6 - - + -
167A LYS* 3.6 34.8 - - + -
168A MET 3.5 7.0 - - - +
169A LEU* 4.1 13.5 - - + -
215A TYR* 3.0 4.8 - - - -
216A GLU* 2.8 40.4 + - + +
218A TYR* 4.0 19.5 - - + -
287A PHE 4.8 0.2 - - - +
288A ILE* 1.3 74.6 - - - +
290A ILE* 1.3 63.4 + - - +
291A GLU* 4.1 10.6 + - - +
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Residues in contact with ILE 290 (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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155A LEU* 4.7 0.2 - - + -
159A HIS* 3.9 16.4 - - + -
162A LEU* 4.2 0.6 - - + +
167A LYS* 3.5 7.1 - - - +
168A MET* 2.7 66.4 + - + +
170A ILE* 3.5 26.2 - - + -
208A LEU* 3.6 23.8 - - + -
213A LEU* 4.3 12.6 - - + -
214A LYS 3.5 11.0 - - - +
215A TYR* 4.0 12.1 - - + -
288A ILE* 4.0 7.2 - - + +
289A VAL* 1.3 75.5 - - - +
291A GLU* 1.3 76.0 + - - +
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Residues in contact with GLU 291 (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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159A HIS* 3.2 19.9 + - - -
162A LEU* 4.1 1.3 - - - -
166A ALA 4.4 2.1 - - - +
167A LYS* 2.4 41.3 + - - +
214A LYS* 3.0 32.0 + - + +
215A TYR* 5.1 1.8 - - - +
216A GLU* 5.2 10.5 - - + +
289A VAL* 4.2 11.9 - - - +
290A ILE* 1.3 78.0 - - - +
292A ALA* 1.3 71.6 + - - +
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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