Contacts of the strand formed by residues 334 - 347 (chain A) in PDB entry 3HO5
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 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A TYR* 3.1 51.3 + - + +
266A LEU* 3.3 29.2 - - + -
299A LEU* 3.8 7.4 - - + -
324A TYR* 3.8 24.0 - - + -
325A THR 3.5 18.2 - - - +
326A VAL* 3.7 1.3 - - - +
327A SER* 3.6 2.9 - - - +
333A GLN* 1.3 87.5 + - - +
335A ASP* 1.3 64.2 + - - +
336A LEU* 3.7 8.8 + - + +
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Residues in contact with ASP 335 (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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325A THR 3.3 8.2 + - - +
326A VAL 4.3 5.7 - - - +
327A SER* 3.6 18.5 - - - +
328A ARG* 6.1 1.5 - - - +
334A VAL* 1.3 76.7 - - - +
336A LEU* 1.3 56.9 + - - +
337A ARG* 3.0 48.8 + - + +
338A THR* 2.6 53.3 + - - +
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.9 27.6 - - + -
267A ASP* 3.7 31.2 - - + +
268A ILE* 4.9 7.0 - - + -
271A LEU* 6.3 2.0 - - + -
324A TYR* 3.5 26.0 + - + +
334A VAL* 4.4 8.3 - - + +
335A ASP* 1.3 70.4 - - - +
337A ARG* 1.3 61.2 + - + +
338A THR 3.1 2.6 + - - -
339A ALA* 3.6 9.0 + - - +
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ASP* 3.0 31.2 + - + +
336A LEU* 1.3 79.7 - - + +
338A THR* 1.3 57.8 + - + +
339A ALA* 3.3 7.6 + - - +
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Residues in contact with THR 338 (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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298A LYS* 5.8 0.2 + - - -
323A GLU* 3.1 13.4 - - - +
324A TYR* 3.8 2.8 - - - -
325A THR* 3.1 43.4 + - + +
326A VAL 5.8 0.2 - - - +
335A ASP* 2.6 41.6 + - - +
336A LEU 3.1 0.4 - - - -
337A ARG* 1.3 77.4 - - + +
339A ALA* 1.3 65.7 + - - +
340A ARG* 3.2 10.0 + - - +
616A TYR* 5.8 0.9 - - - +
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Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 6.0 1.6 - - + -
303A TYR* 6.1 0.4 - - - +
322A VAL* 3.8 9.0 - - + -
323A GLU 3.5 6.5 - - - -
324A TYR* 3.6 30.4 - - + +
336A LEU 3.6 7.5 + - - +
337A ARG 3.3 4.5 - - - +
338A THR* 1.3 76.8 + - - +
340A ARG* 1.3 61.4 + - - +
341A VAL* 4.0 3.5 + - + +
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Residues in contact with ARG 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LYS* 4.1 7.1 - - - +
322A VAL* 3.5 3.5 - - - +
323A GLU* 2.6 81.8 + - + +
338A THR 4.0 7.4 - - - +
339A ALA* 1.3 75.0 - - - +
341A VAL* 1.3 66.9 + - - +
342A PHE* 3.2 26.5 + - + -
397A VAL 5.4 0.6 + - - -
405A PRO* 4.0 16.1 + - - +
616A TYR* 3.3 63.5 - - + +
617A CYS 4.3 6.5 + - - -
618A THR* 4.5 3.2 - - - +
619A PRO* 4.1 11.9 - - - +
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Residues in contact with VAL 341 (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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320A ARG* 3.8 32.3 - - + +
321A VAL 3.9 3.8 - - - -
322A VAL* 4.1 8.1 - - + -
339A ALA* 4.0 3.0 + - + -
340A ARG* 1.3 72.9 - - - +
342A PHE* 1.3 65.3 + - - +
343A LEU 4.1 8.5 - - - +
344A GLU* 3.6 35.9 - - + +
405A PRO* 4.1 12.0 - - - +
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Residues in contact with PHE 342 (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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300A TYR* 3.7 14.1 - + - -
321A VAL* 2.7 29.3 + - + +
323A GLU* 3.7 23.1 - - + -
340A ARG* 3.2 46.8 + - - -
341A VAL* 1.3 79.4 - - - +
343A LEU* 1.3 63.8 + - + +
365A LEU* 5.0 2.2 - - + -
395A LEU* 4.8 6.7 - - + -
397A VAL* 3.6 30.7 - - + -
405A PRO* 3.5 31.8 - - + +
406A TYR* 3.3 38.3 - + + -
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Residues in contact with LEU 343 (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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319A LEU 3.9 0.6 - - - +
320A ARG* 3.4 5.4 - - - +
321A VAL* 2.8 46.9 + - + +
341A VAL* 3.8 0.9 - - - -
342A PHE* 1.3 82.9 - - + +
344A GLU* 1.3 66.2 + - - +
345A VAL* 4.1 9.4 - - + -
367A ILE* 4.5 10.8 - - + -
369A LEU* 5.9 0.4 - - + -
388A PHE* 3.8 31.2 - - + -
393A LEU* 4.1 21.5 - - + -
395A LEU* 3.9 23.8 - - + -
406A TYR* 3.4 27.4 - - + +
423A GLU* 5.5 0.7 - - + -
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Residues in contact with GLU 344 (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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310A TRP* 4.0 31.3 - - + -
318A ILE* 3.9 13.6 - - + +
319A LEU 3.6 3.4 - - - -
320A ARG* 3.3 34.2 + - + +
341A VAL* 3.6 27.5 - - + +
343A LEU* 1.3 73.3 - - - +
345A VAL* 1.3 63.6 + - - +
346A ALA 3.9 2.4 + - - -
386A SER* 5.0 4.0 + - - -
388A PHE* 5.3 4.0 - - - -
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 4.1 2.0 - - - +
319A LEU* 2.7 51.1 + - + +
321A VAL* 6.1 0.9 - - + -
343A LEU* 4.8 10.5 - - + -
344A GLU* 1.3 76.5 - - - +
346A ALA* 1.3 64.2 + - - +
347A GLU* 3.3 17.1 + - - +
369A LEU* 4.0 30.5 - - + -
386A SER* 4.0 13.0 - - - +
388A PHE* 4.2 17.5 - - + -
389A THR* 3.8 22.4 - - + -
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Residues in contact with ALA 346 (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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310A TRP* 4.5 12.6 - - + -
314A PRO 4.1 12.8 - - - +
315A HIS* 4.7 0.9 - - + -
318A ILE* 3.5 20.4 - - + +
344A GLU 3.9 3.2 + - - -
345A VAL* 1.3 77.8 - - - +
347A GLU* 1.3 63.8 + - - +
348A LEU* 6.0 0.2 - - - -
374A ILE* 4.9 5.7 - - - +
384A GLY 3.5 25.1 - - - +
385A LEU* 4.7 8.2 - - - +
386A SER* 4.5 10.8 + - - +
389A THR* 4.6 5.5 - - - +
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Residues in contact with GLU 347 (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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314A PRO 5.4 0.2 - - - -
315A HIS* 3.5 3.3 - - - -
316A ASP* 2.8 23.9 + - - -
317A HIS* 2.7 39.6 + - + +
319A LEU* 4.0 11.1 - - - +
345A VAL* 3.3 24.4 + - - +
346A ALA* 1.3 81.6 - - - +
348A LEU* 1.3 65.1 + - - +
349A HIS 3.8 6.5 - - - +
353A LEU* 3.8 41.0 - - + +
370A GLY 4.7 0.7 - - - +
372A GLY* 3.4 27.1 + - - -
374A ILE* 5.1 2.2 - - + -
389A THR* 4.1 9.5 - - - +
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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