Contacts of the strand formed by residues 285 - 293 (chain A) in PDB entry 1V8K
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 HIS 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A PHE 3.9 0.2 - - - +
217A GLU* 3.0 8.1 - - - -
218A ILE* 2.9 53.3 + - + +
270A ARG* 4.1 0.2 - - - -
284A SER* 1.4 73.7 - - - +
286A ALA* 1.3 61.9 + - - +
287A CYS* 3.9 1.6 + - + +
305A VAL* 5.1 0.9 - - + -
306A ASP 3.7 2.2 - - - +
307A LEU* 3.8 18.6 - - + +
308A ALA* 3.2 34.7 + - + +
329A GLU 5.3 0.4 - - - -
330A ILE* 4.7 12.6 - - + +
333A SER* 3.1 35.0 + - - -
334A LEU* 4.7 4.0 - - + +
358A LEU* 3.9 32.4 - - + +
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Residues in contact with ALA 286 (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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188A TYR* 4.1 7.2 - - - +
215A PHE* 4.4 10.1 - - + -
216A PHE 3.9 3.1 - - - -
217A GLU* 4.5 1.6 - - + +
226A LEU* 5.4 0.4 - - + -
270A ARG* 3.3 37.7 - - + +
285A HIS* 1.3 73.0 - - - +
287A CYS* 1.3 60.6 + - - +
288A PHE 4.2 0.9 - - - -
305A VAL* 3.2 7.7 - - - +
306A ASP* 2.6 52.8 + - + -
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Residues in contact with CYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PHE* 3.5 5.8 - - - -
216A PHE* 2.9 77.3 + - + -
218A ILE* 6.1 0.4 - - + -
285A HIS* 5.2 1.3 - - + +
286A ALA* 1.3 76.6 - - - +
288A PHE* 1.3 61.9 + - - +
289A GLN* 3.9 15.0 + - - -
303A SER* 4.2 9.4 - - - -
304A LEU 3.3 4.5 - - - -
305A VAL* 3.9 23.8 - - + -
358A LEU* 5.8 3.6 - - + -
362A LEU* 4.2 7.2 - - - -
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Residues in contact with PHE 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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188A TYR* 3.5 45.7 - + + -
192A SER* 4.2 6.1 - - - -
213A VAL* 3.3 40.2 - - + -
214A THR 3.4 9.9 - - - -
215A PHE* 3.7 28.4 - + + -
259A VAL* 3.7 16.4 - - + -
262A MET* 5.0 0.7 - - + -
263A ILE* 3.7 22.0 - - + -
286A ALA 4.2 0.2 - - - -
287A CYS* 1.3 73.7 - - - +
289A GLN* 1.3 62.1 + - - +
290A ILE* 3.7 26.2 - - + -
304A LEU* 2.8 37.9 + - + +
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Residues in contact with GLN 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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213A VAL* 3.2 12.1 - - - +
214A THR* 2.8 62.1 + - - +
216A PHE* 3.8 19.5 - - + -
248A LEU* 4.1 7.7 - - - +
287A CYS* 3.9 11.0 - - - -
288A PHE* 1.3 77.2 - - - +
290A ILE* 1.3 62.7 + - - +
291A LEU* 3.7 17.6 - - + +
301A LYS* 3.6 22.1 + - + +
302A PHE 3.3 4.5 - - - +
303A SER* 2.9 27.9 + - - +
361A VAL* 5.6 2.4 - - - +
362A LEU* 4.5 6.9 - - - +
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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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150A ILE* 4.7 7.6 - - + +
188A TYR 4.4 1.1 - - - +
191A ALA* 4.2 15.0 - - + -
192A SER* 3.5 37.0 - - - +
195A VAL* 4.2 22.4 - - + -
211A VAL* 4.1 23.1 - - + -
212A TYR 3.5 3.8 - - - +
213A VAL* 4.3 4.3 - - + -
288A PHE* 3.7 17.9 - - + -
289A GLN* 1.3 75.7 - - - +
291A LEU* 1.3 65.3 + - - +
292A LEU* 5.1 0.4 - - + -
300A GLY 4.2 0.2 - - - +
301A LYS* 3.5 2.3 - - - -
302A PHE* 2.8 46.5 + - + +
304A LEU* 4.5 9.9 - - + -
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Residues in contact with LEU 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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210A GLU 3.7 0.5 - - - +
211A VAL* 3.6 6.1 - - - +
212A TYR* 2.8 50.7 + - + +
214A THR* 3.9 18.6 - - + -
250A GLU* 3.7 15.9 - - + +
289A GLN* 3.7 29.6 - - + +
290A ILE* 1.3 77.4 - - - +
292A LEU* 1.3 64.0 + - - +
293A ARG* 3.6 29.6 - - - +
298A LEU* 4.0 14.6 - - + -
300A GLY 3.6 3.8 - - - -
301A LYS* 3.9 20.9 - - + +
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Residues in contact with LEU 292 (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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150A ILE* 3.6 49.6 - - + +
151A PHE* 3.9 22.9 - - + -
195A VAL* 4.2 14.1 - - + -
199A LYS* 5.8 0.2 - - - -
209A LEU* 4.1 20.6 - - + -
210A GLU 3.6 2.7 - - - +
211A VAL* 3.8 28.9 - - + -
290A ILE* 5.1 0.7 - - + -
291A LEU* 1.3 76.5 - - - +
293A ARG* 1.3 58.8 + - - +
298A LEU* 3.6 2.1 - - - +
299A HIS* 2.6 38.1 + - + -
300A GLY 2.8 20.5 + - - +
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Residues in contact with ARG 293 (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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209A LEU* 3.2 5.4 - - - +
210A GLU* 2.6 41.4 + - + +
212A TYR* 3.6 33.0 - - + -
250A GLU* 2.7 38.8 + - - -
291A LEU* 3.6 17.7 - - + +
292A LEU* 1.3 80.2 - - - +
294A THR* 1.3 60.7 + - - +
295A LYS 5.3 0.4 - - - +
296A GLY 4.4 10.9 + - - +
297A ARG 3.5 12.4 - - - +
298A LEU* 4.1 28.4 - - + +
299A HIS 4.2 0.7 - - - +
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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