Contacts of the strand formed by residues 341 - 353 (chain A) in PDB entry 2H4Q
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 ALA 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A ALA 3.8 6.5 - - - +
325A PHE 4.6 1.6 - - - +
326A THR 3.2 33.2 - - - +
327A THR* 4.8 3.6 - - + +
329A ALA* 4.1 1.6 - - - -
331A PHE* 4.3 2.5 - - - -
340A LEU* 1.3 75.7 - - - +
342A ILE* 1.3 66.7 + - - +
343A SER 3.4 0.3 + - - -
368A ILE* 3.4 5.9 - - - +
369A SER* 3.0 36.4 + - - +
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Residues in contact with ILE 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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39A LEU* 5.0 2.2 - - + -
42A THR* 4.0 14.1 - - + -
54A MET* 4.9 0.2 - - + -
313A ARG* 4.9 1.7 + - - -
321A MET* 3.6 30.5 - - + -
324A ALA* 2.9 23.8 + - + +
325A PHE* 3.3 47.9 - - + +
331A PHE* 3.7 22.0 - - + -
341A ALA* 1.3 71.8 - - - +
343A SER* 1.3 61.7 + - - +
344A LYS 3.6 20.6 - - - +
345A VAL* 3.9 6.1 - - + -
366A VAL* 4.2 9.0 - - + -
367A ILE 3.6 6.5 - - - +
368A ILE* 4.2 12.6 - - + -
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Residues in contact with SER 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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180A ASP 5.2 1.0 + - - -
313A ARG* 3.2 36.3 + - - +
341A ALA 3.4 1.6 + - - -
342A ILE* 1.3 73.5 - - - +
344A LYS* 1.3 69.6 + - - +
367A ILE* 2.8 38.7 + - - +
368A ILE 4.2 0.7 + - - -
369A SER* 4.3 20.0 + - - -
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Residues in contact with LYS 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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179A ASP* 3.1 31.4 + - - +
180A ASP* 2.8 40.4 + - - +
182A LYS* 5.5 4.0 - - - +
311A ASP* 3.2 27.5 + - - +
313A ARG* 4.8 2.0 - - - -
325A PHE* 5.1 0.2 - - - -
342A ILE* 3.6 2.6 - - - +
343A SER* 1.3 92.6 + - - +
345A VAL* 1.3 66.2 + - - +
346A ILE* 3.9 6.5 - - + +
365A ALA 4.3 0.2 - - - -
367A ILE* 2.8 44.3 + - + +
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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
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39A LEU* 4.2 18.2 - - + -
310A ILE 3.5 0.5 - - - +
311A ASP* 3.1 10.7 + - - -
312A LEU* 2.7 53.2 + - + +
313A ARG* 4.5 2.5 - - - +
316A LEU* 4.0 19.1 - - + -
325A PHE* 4.1 8.1 - - + -
342A ILE* 3.9 17.3 - - + -
344A LYS* 1.3 77.3 - - - +
346A ILE* 1.3 58.8 + - - +
347A HIS 3.7 0.5 + - - -
364A THR* 4.0 23.6 - - + -
365A ALA 3.4 3.4 - - - +
366A VAL* 4.4 11.7 - - + -
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Residues in contact with ILE 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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175A LEU* 3.9 22.7 - - + +
176A LEU* 4.3 7.9 - - + -
180A ASP* 3.9 23.3 - - - +
309A ARG* 3.6 32.8 - - + +
310A ILE 3.5 4.0 - - - +
311A ASP* 3.7 35.9 - - + +
344A LYS* 4.1 3.1 - - + -
345A VAL* 1.3 71.2 - - - +
347A HIS* 1.3 63.9 + - - +
363A ALA 3.9 0.3 - - - +
364A THR* 3.2 5.2 - - - +
365A ALA* 2.8 39.2 + - + +
367A ILE* 4.1 23.1 - - + -
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Residues in contact with HIS 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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29A PHE 4.9 1.0 + - - -
30A PHE* 3.5 21.1 - - + +
31A SER* 3.3 36.0 + - - -
34A SER* 4.3 0.4 - - - -
35A ILE* 3.5 14.6 - - + +
308A ASP* 4.1 0.8 + - - +
309A ARG* 3.3 3.6 - - - +
310A ILE* 2.9 45.6 + - + +
312A LEU* 4.0 20.0 - - + -
345A VAL 3.7 0.2 + - - -
346A ILE* 1.3 77.8 - - - +
348A GLN* 1.3 59.5 + - - +
349A SER* 4.0 15.5 + - - -
362A ALA* 3.7 13.1 - - + +
363A ALA 3.2 13.7 - - - -
364A THR* 3.0 27.3 + - + +
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Residues in contact with GLN 348 (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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171A LYS 4.8 2.2 + - - -
172A ILE* 3.6 40.0 - - + +
173A LYS 5.1 1.2 - - - +
174A ASN 3.9 6.8 + - - +
175A LEU* 3.6 34.0 - - + +
308A ASP 3.3 12.8 - - - +
309A ARG* 3.4 28.1 - - + -
347A HIS* 1.3 76.5 - - - +
349A SER* 1.3 65.3 + - - +
362A ALA* 3.1 4.6 - - - +
363A ALA 2.9 31.6 + - - -
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Residues in contact with SER 349 (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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29A PHE* 2.8 45.0 + - - -
30A PHE* 4.3 1.8 - - - -
172A ILE* 4.3 5.7 - - - +
307A GLU* 3.4 5.4 - - - +
308A ASP* 2.9 40.5 + - - +
347A HIS* 4.0 14.5 + - - -
348A GLN* 1.3 77.4 - - - +
350A PHE* 1.3 63.8 + - - +
361A VAL 3.5 5.6 - - - -
362A ALA* 4.1 6.1 - - - +
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Residues in contact with PHE 350 (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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29A PHE* 3.5 6.5 - - - -
171A LYS* 3.8 40.4 - - + +
172A ILE* 4.3 8.3 - - + -
305A SER* 3.7 14.8 - - - -
306A LEU 3.4 7.6 - - - -
307A GLU* 3.6 30.1 - - + -
349A SER* 1.3 76.6 - - - +
351A VAL* 1.3 72.3 + - - +
352A ALA* 3.7 22.0 - - + -
359A GLU* 3.8 20.0 - - + -
360A ALA* 3.3 1.9 - - - -
361A VAL* 2.7 58.9 + - + +
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Residues in contact with VAL 351 (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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29A PHE* 3.4 42.4 - - + -
304A PHE* 4.7 3.6 - - + -
305A SER* 2.8 21.1 + - - -
306A LEU* 3.0 35.8 + - + +
350A PHE* 1.3 78.0 - - - +
352A ALA* 1.3 62.2 + - - +
353A VAL* 4.2 12.1 - - + -
358A THR* 3.8 18.8 - - + -
359A GLU 3.2 12.1 - - - +
360A ALA* 4.2 4.3 - - + -
389B PHE* 4.5 12.3 - - + -
391B ILE* 4.8 2.2 - - + -
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Residues in contact with ALA 352 (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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304A PHE 3.6 4.9 - - - +
305A SER* 4.1 8.1 - - - +
350A PHE* 3.7 21.8 - - + -
351A VAL* 1.3 75.0 - - - +
353A VAL* 1.3 62.5 + - - +
354A ASP* 4.2 5.3 + - + +
357A GLY 4.1 0.3 - - - +
358A THR* 3.3 5.4 - - - +
359A GLU* 2.8 41.4 + - + +
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Residues in contact with VAL 353 (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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199A TRP* 3.9 24.5 - - + -
226A MET* 4.1 15.7 - - + -
256A MET* 3.9 16.6 - - + -
301A LEU* 4.2 7.4 - - + -
302A PRO 4.2 6.5 - - - +
303A LYS* 3.5 8.4 - - - +
304A PHE* 2.7 65.6 + - + +
351A VAL* 4.2 5.6 - - + -
352A ALA* 1.3 74.1 - - - +
354A ASP* 1.3 63.9 + - - +
357A GLY 3.8 2.9 - - - -
358A THR* 3.8 13.9 - - + +
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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