Contacts of the strand formed by residues 302 - 306 (chain K) in PDB entry 1J0B
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 LYS 302 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37K ASP* 3.4 19.1 - - + +
39K TYR* 5.2 0.7 - - + -
180K VAL* 4.3 14.4 - - + -
181K LYS* 2.9 64.7 - - - +
182K PHE* 3.5 7.0 - - - -
183K ASP* 2.6 53.0 + - - +
301K GLU* 1.3 91.4 - - + +
303K ILE* 1.3 57.9 + - - +
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Residues in contact with ILE 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K ILE* 4.9 2.0 - - + -
36K ALA* 4.7 8.1 - - + -
37K ASP 2.7 14.3 + - - +
38K VAL* 3.5 6.2 - - + -
39K TYR* 2.7 35.9 + - - +
182K PHE* 3.6 2.9 - - - -
184K SER* 3.4 19.7 - - - +
186K VAL* 4.3 12.1 - - + -
290K LEU* 3.4 37.0 - - + -
294K ALA* 4.3 9.4 - - + -
299K LEU* 3.2 39.7 - - + +
300K GLY 3.5 15.9 - - - +
301K GLU 4.7 0.9 - - - +
302K LYS* 1.3 74.5 - - - +
304K LEU* 1.3 60.2 + - - +
305K PHE 4.2 0.2 - - - -
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Residues in contact with LEU 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ILE* 4.2 4.0 - - + -
39K TYR* 3.7 12.8 - - + -
40K ILE 3.8 1.6 - - - +
41K LYS* 3.5 28.3 - - + +
174K ILE* 4.1 16.2 - - + -
182K PHE* 3.2 45.9 - - + -
184K SER 2.9 12.3 + - - +
185K ILE* 2.9 34.7 - - + +
186K VAL 2.8 25.8 + - - -
303K ILE* 1.3 73.8 - - - +
305K PHE* 1.3 66.1 + - - +
306K ILE* 3.7 17.0 - - + +
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Residues in contact with PHE 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K TYR 3.1 15.3 + - - +
40K ILE* 3.2 25.9 - - + +
41K LYS 3.0 22.1 + - - -
186K VAL* 2.9 30.5 - - + +
187K VAL* 4.7 2.7 - - - -
188K ALA 4.7 1.1 - - - -
278K LEU* 4.7 7.9 - - + -
283K THR* 4.1 23.6 - - + -
286K ALA* 4.3 21.3 - - + -
287K PHE* 4.0 31.6 - + + -
290K LEU* 4.0 17.5 - - + -
303K ILE 4.2 0.2 - - - -
304K LEU* 1.3 73.1 - - - +
306K ILE* 1.3 73.3 + - - +
307K HIS* 3.8 20.9 - + + -
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Residues in contact with ILE 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K LYS* 3.8 13.7 - - + +
43K ASP* 3.0 32.8 - - + +
167K TYR* 3.9 32.8 - - + +
170K ALA* 5.7 1.6 - - + -
174K ILE* 4.5 12.1 - - + -
185K ILE* 3.6 27.6 - - + -
186K VAL 3.6 5.9 + - - -
187K VAL* 4.3 15.9 - - + +
198K LEU* 4.3 12.1 - - + -
304K LEU* 3.7 9.8 + - + -
305K PHE* 1.3 85.8 - - - +
307K HIS* 1.3 61.5 + - - +
308K THR* 3.2 17.3 + - + +
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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