Contacts of the strand formed by residues 329 - 336 (chain B) in PDB entry 6HYI
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 GLU 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B THR* 6.4 0.7 - - - -
265B PHE 3.3 11.9 - - - +
266B LYS* 4.4 5.2 - - + +
287B SER 4.7 0.6 - - - -
288B GLY* 3.5 6.8 - - - -
325B VAL* 4.3 2.2 - - - -
327B THR* 2.7 23.3 + - - -
328B ASP* 1.3 98.2 - - - +
330B LEU* 1.3 62.6 + - - +
331B ILE* 5.6 5.8 - - + -
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Residues in contact with LEU 330 (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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264B THR* 3.3 5.9 - - - -
265B PHE* 2.9 47.1 + - + +
271B ILE* 4.1 9.6 - - + -
285B ILE* 4.2 17.5 - - + -
287B SER 3.3 14.1 - - - +
288B GLY* 3.9 6.5 - - - -
289B HIS 3.7 29.2 - - - +
290B ALA* 4.1 13.0 - - + -
325B VAL* 3.9 20.6 - - + -
329B GLU* 1.3 77.0 - - - +
331B ILE* 1.3 78.0 + - - +
332B ALA* 3.9 15.7 - - + -
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Residues in contact with ILE 331 (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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262B ARG* 4.0 26.2 - - + -
263B ALA 3.5 4.5 - - - +
264B THR* 4.2 13.5 - - + -
285B ILE* 3.7 1.7 - - - -
286B GLN* 2.8 58.0 + - + +
287B SER* 2.9 31.4 + - - +
329B GLU* 5.6 5.8 - - + -
330B LEU* 1.3 78.3 - - - +
332B ALA* 1.3 65.0 + - - +
333B TRP* 5.1 0.4 - - - +
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Residues in contact with ALA 332 (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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262B ARG* 3.5 7.4 - - - +
263B ALA 2.8 34.1 + - - +
265B PHE* 4.8 2.9 - - + -
283B TYR* 4.1 28.9 - - + -
284B ILE 3.3 17.5 - - - +
285B ILE* 4.3 1.1 - - + -
286B GLN 4.1 1.1 - - - +
330B LEU* 3.9 16.1 - - + +
331B ILE* 1.3 75.4 - - - +
333B TRP* 1.3 66.1 + - - +
334B VAL* 4.5 1.1 - - + -
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Residues in contact with TRP 333 (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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227B LYS* 3.8 13.2 - - + -
231B GLU* 4.0 19.7 - - + -
234B LEU* 3.7 11.2 - - + +
235B ILE* 3.6 36.8 - - + -
238B LEU* 3.9 22.4 - - + -
260B MET* 3.4 32.6 - - + +
261B GLN* 3.4 5.6 - - - -
262B ARG* 3.6 65.7 - - + +
283B TYR* 3.4 1.7 - - - -
284B ILE* 2.8 35.1 + - + +
286B GLN* 2.9 29.8 + - + -
331B ILE* 5.1 0.2 - - - +
332B ALA* 1.3 78.5 - - - +
334B VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 334 (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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259B ALA 4.0 1.7 - - - +
260B MET* 3.2 7.0 - - - -
261B GLN* 2.7 46.8 + - + +
262B ARG 4.9 0.2 - - - -
263B ALA* 3.6 20.0 - - + -
281B LYS* 3.8 35.9 - - + -
282B LEU 3.2 9.9 - - - +
283B TYR* 3.4 33.4 - - + -
332B ALA 4.4 0.7 - - - +
333B TRP* 1.3 78.2 - - - +
335B LEU* 1.3 63.9 + - - +
336B ASP 4.4 0.2 + - - -
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Residues in contact with LEU 335 (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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245B PHE* 4.7 1.6 - - + -
256B VAL* 3.9 22.2 - - + +
259B ALA* 3.7 21.5 - - + +
260B MET* 3.9 21.3 - - + -
281B LYS* 3.5 5.9 - - - +
282B LEU* 2.8 51.8 + - + +
333B TRP 4.2 0.4 + - - -
334B VAL* 1.3 75.5 - - - +
336B ASP* 1.3 70.5 + - - +
339B THR* 3.7 24.2 - - + -
340B TYR* 4.0 28.9 - - + +
344B VAL* 4.1 9.2 - - + -
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Residues in contact with ASP 336 (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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220B TYR* 3.5 6.0 + - - -
223B PRO* 3.8 17.1 - - - +
259B ALA* 4.6 3.2 + - - +
280B ASN 4.7 1.8 - - - -
281B LYS* 5.0 5.8 - - - -
313B LEU* 5.4 0.4 - - - -
334B VAL 4.4 0.8 + - - -
335B LEU* 1.3 80.6 - - - +
337B ARG* 1.3 64.3 + - - +
338B ASP* 3.2 11.3 + - - +
339B THR* 2.6 45.3 + - - -
340B TYR* 3.1 21.9 + - - +
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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