Contacts of the strand formed by residues 344 - 358 (chain A) in PDB entry 2W77
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 THR 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ARG* 4.0 1.7 - - - +
339A ASP* 3.7 1.2 - - - -
340A LEU* 2.9 37.4 + - + +
341A ASN* 2.9 32.9 + - - +
342A PRO 3.7 0.8 + - - -
343A ASP* 1.3 82.1 + - - +
345A MET* 1.3 60.8 + - - +
402A LEU* 4.3 20.6 - - + -
403A GLU 3.3 7.9 - - - +
404A HIS* 3.0 30.1 + - + +
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Residues in contact with MET 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 3.9 31.6 - - - +
272A LYS* 5.6 2.0 - - - +
308A ARG* 4.0 8.7 - - - -
337A GLU* 3.4 34.1 - - + +
338A PHE 3.3 16.4 - - - +
339A ASP* 3.4 17.3 - - - +
344A THR* 1.3 73.8 - - - +
346A LEU* 1.3 61.7 + - - +
347A THR* 3.2 27.0 + - + +
401A ASN 4.0 0.5 - - - +
402A LEU* 3.4 7.6 - - - +
403A GLU* 2.8 54.0 + - + +
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Residues in contact with LEU 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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337A GLU* 3.5 1.0 - - - -
338A PHE* 2.6 70.2 + - + +
340A LEU* 4.4 18.7 - - + +
344A THR 4.2 0.6 + - - -
345A MET* 1.3 72.2 - - - +
347A THR* 1.3 63.3 + - - +
348A VAL* 4.1 20.4 - - + -
400A ALA* 5.1 6.3 - - + -
401A ASN 3.6 17.5 - - - +
402A LEU* 4.2 17.7 - - + -
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Residues in contact with THR 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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335A ILE* 3.6 35.4 - - + -
336A LEU 3.5 6.1 - - - +
337A GLU* 3.9 11.9 - - + +
345A MET* 3.2 27.3 + - + +
346A LEU* 1.3 73.1 - - - +
348A VAL* 1.3 68.1 + - - +
399A PHE* 4.7 3.1 - - + -
400A ALA* 3.2 4.2 - - - +
401A ASN* 2.9 56.6 + - - +
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Residues in contact with VAL 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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335A ILE* 3.4 2.2 - - - +
336A LEU* 3.0 43.3 + - + +
338A PHE* 4.6 10.3 - - + -
346A LEU* 4.1 26.5 - - + -
347A THR* 1.3 80.8 - - - +
349A GLY* 1.3 59.9 + - - +
399A PHE* 3.3 11.7 - - - +
400A ALA* 4.4 7.9 - - + -
1816A N8E 4.3 26.3 - - + +
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Residues in contact with GLY 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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334A GLY 3.2 11.9 - - - -
335A ILE* 4.0 1.6 - - - -
348A VAL* 1.3 77.5 - - - +
350A ALA* 1.3 60.0 + - - +
398A VAL* 3.5 5.3 - - - +
399A PHE* 2.8 58.2 + - - +
1816A N8E 4.5 6.3 - - - +
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Residues in contact with ALA 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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333A TYR* 3.3 5.9 - - - -
334A GLY 2.7 39.9 + - - +
349A GLY* 1.3 74.6 - - - +
351A ASP* 1.3 63.0 + - - +
397A THR 3.1 12.8 - - - +
398A VAL* 4.3 11.2 - - + -
399A PHE* 4.0 2.4 - - - -
1816A N8E 4.3 23.9 - - + +
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Residues in contact with ASP 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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242A ILE* 4.2 15.8 - - + +
243A TYR* 5.0 1.3 + - - -
270A ARG* 2.6 34.7 + - - -
332A TYR 3.3 9.2 - - - +
333A TYR* 3.7 16.8 - - + -
350A ALA* 1.3 77.0 - - - +
352A TYR* 1.3 66.0 + - - +
395A THR* 4.8 2.3 + - - +
396A ARG* 3.2 10.4 + - - +
397A THR* 2.8 44.8 + - - +
399A PHE* 4.9 0.6 - - - -
419A LYS* 5.6 0.2 - - - -
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Residues in contact with TYR 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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330A SER* 4.1 7.0 - - - -
331A VAL* 3.1 25.8 - - - +
332A TYR* 2.9 46.7 + + + +
351A ASP* 1.3 81.2 + - - +
353A GLN* 1.3 64.9 + - - +
354A ASP* 3.5 36.8 + - + +
394A TYR* 5.6 8.2 - + + +
395A THR* 3.4 9.4 - - - -
396A ARG* 4.1 30.3 - - + -
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Residues in contact with GLN 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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234A GLY 5.8 0.7 - - - -
237A LEU 2.8 29.3 + - - -
238A SER* 3.5 7.7 - - - -
239A ASP* 2.8 36.5 + - - +
242A ILE* 6.2 0.3 - - - +
243A TYR* 6.0 0.2 - - - -
329A THR* 4.8 6.8 + - - +
330A SER 3.1 10.5 - - - +
331A VAL* 4.3 6.7 - - + +
352A TYR* 1.3 80.3 - - - +
354A ASP* 1.3 64.3 + - - +
355A ASN* 3.0 24.8 + - - +
394A TYR* 3.3 6.6 - - - +
395A THR* 2.8 47.7 + - - +
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Residues in contact with ASP 354 (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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328A LYS 3.3 3.1 - - - +
329A THR* 3.1 8.3 - - - -
330A SER* 2.9 39.3 + - - +
352A TYR* 3.5 26.8 + - + +
353A GLN* 1.3 74.9 - - - +
355A ASN* 1.3 66.1 + - - +
356A ASP* 4.1 12.1 - - - +
392A GLU* 2.6 32.6 - - - +
393A GLN 4.1 0.2 - - - -
394A TYR* 3.4 12.8 - - + +
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Residues in contact with ASN 355 (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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234A GLY* 4.4 8.3 + - - -
237A LEU* 3.4 39.3 - - + +
327A ARG* 4.7 7.2 - - - -
328A LYS 4.0 2.5 - - - -
329A THR* 4.0 12.6 - - - +
353A GLN* 3.0 40.4 + - - +
354A ASP* 1.3 75.2 + - - +
356A ASP* 1.3 58.2 + - - +
357A PRO* 4.1 3.1 - - + -
391A TRP 5.8 0.4 - - - +
392A GLU* 3.3 6.4 - - - +
393A GLN* 2.8 57.5 + - - +
394A TYR* 4.6 1.2 - - - +
395A THR* 5.2 1.4 + - - -
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Residues in contact with ASP 356 (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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326A GLU* 4.3 2.4 - - - +
327A ARG* 3.7 5.3 - - - +
328A LYS* 3.2 48.9 + - + +
354A ASP* 4.1 11.4 - - - +
355A ASN* 1.3 73.7 - - - +
357A PRO* 1.3 69.6 - - - +
358A LYS* 5.1 8.2 + - - +
390A SER* 4.5 1.2 + - - -
392A GLU* 3.9 21.1 - - - +
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Residues in contact with PRO 357 (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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203A ASP* 3.5 24.7 - - - +
325A TYR* 3.7 9.0 - - + +
326A GLU* 3.2 14.4 - - - +
327A ARG* 4.1 7.2 - - - -
355A ASN 4.0 0.9 - - - +
356A ASP* 1.3 91.7 - - - +
358A LYS* 1.3 70.4 + - - +
360A SER* 3.1 24.2 - - - +
390A SER* 3.0 24.4 + - - +
391A TRP 3.6 10.3 - - - +
392A GLU* 3.5 23.6 - - - +
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Residues in contact with LYS 358 (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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324A HIS 3.4 2.6 - - - +
325A TYR* 3.3 6.4 - - - -
326A GLU* 3.0 48.8 + - + +
356A ASP* 5.1 7.4 + - - +
357A PRO* 1.3 81.7 + - - +
359A GLY* 1.3 60.5 + - - +
360A SER 3.4 0.2 - - - -
387A LYS 3.7 13.7 - - - +
388A TRP* 4.6 15.5 + - - +
389A SER 3.3 4.7 - - - -
390A SER* 4.5 11.0 + - - -
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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