Contacts of the strand formed by residues 323 - 336 (chain A) in PDB entry 2P0H
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 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A GLU* 1.3 75.4 - - + +
324A GLU* 1.3 65.8 + - - +
325A LYS* 3.6 26.9 - - - +
326A SER* 4.2 1.1 - - - +
351A VAL* 3.9 13.9 - - + -
352A LEU 3.5 6.7 - - - +
353A THR* 4.5 0.2 - - - +
369A SER 5.7 1.6 - - - +
370A SER 4.1 11.9 - - - +
371A GLY* 4.2 12.3 - - - -
372A TRP* 3.3 41.3 - - + +
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Residues in contact with GLU 324 (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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322A GLU 3.5 3.3 + - - +
323A VAL* 1.3 77.9 - - - +
325A LYS* 1.3 61.0 + - + +
352A LEU* 2.7 30.6 + - + +
353A THR 4.1 12.6 - - - -
354A GLY* 4.3 5.2 - - - +
429A ALA* 5.9 2.4 - - + +
432A THR* 5.9 2.4 - - - +
433A VAL* 4.1 18.8 - - + +
436A ARG* 5.5 5.0 + - - -
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL* 3.6 6.4 - - - +
324A GLU* 1.3 80.8 - - - +
326A SER* 1.3 65.0 + - - +
352A LEU* 2.7 47.4 + - + +
422A GLU* 4.4 8.7 + - - -
425A ALA* 3.6 18.6 - - - +
426A TRP* 3.5 57.3 - - + +
429A ALA* 3.9 22.4 - - + -
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL* 4.2 3.9 - - - +
325A LYS* 1.3 81.9 + - - +
327A GLY* 1.3 58.3 + - - +
349A TRP* 3.4 17.8 - - - -
350A VAL 3.1 13.5 - - - -
351A VAL* 4.3 3.1 - - - -
368A PRO 3.6 5.4 + - - -
369A SER* 4.2 6.6 + - - -
371A GLY* 3.5 30.0 + - - -
426A TRP* 3.7 7.5 + - - -
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Residues in contact with GLY 327 (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 SER* 1.3 75.3 - - - +
328A LEU* 1.3 60.0 + - - -
349A TRP* 3.4 19.4 - - - -
350A VAL* 2.6 43.8 + - - +
426A TRP* 3.6 12.6 - - - -
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Residues in contact with LEU 328 (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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327A GLY* 1.3 73.1 - - - -
329A LEU* 1.3 74.7 + - - +
330A ASN* 5.4 1.3 - - - +
347A PRO* 4.2 20.4 - - + -
348A SER 3.3 26.2 - - - +
349A TRP* 3.6 14.8 - - + +
362A GLU* 5.5 0.7 - - - -
363A PRO* 4.3 26.9 - - + -
417A SER* 5.4 2.4 + - - -
426A TRP* 5.1 1.0 + - - -
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Residues in contact with LEU 329 (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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327A GLY 3.8 0.2 + - - -
328A LEU* 1.3 82.8 - - - +
330A ASN* 1.3 71.8 + - - +
347A PRO* 3.5 2.4 - - - +
348A SER* 2.8 33.0 + - - +
350A VAL* 4.0 18.8 - - + -
415A LEU* 3.6 34.8 - - + -
416A GLN 3.9 7.9 - - - +
417A SER* 4.1 13.0 - - - +
422A GLU* 5.4 2.0 - - + -
423A LEU* 4.0 18.4 - - + +
426A TRP* 3.6 47.8 - - + +
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Residues in contact with ASN 330 (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 LEU* 5.4 1.9 - - - +
329A LEU* 1.3 75.4 - - - +
331A MET* 1.3 60.4 + - - +
345A TRP* 3.7 11.5 - - + -
346A GLY* 3.4 6.5 - - - +
347A PRO* 3.5 27.8 - - - +
399A ARG* 3.9 9.4 - - - +
415A LEU* 3.3 3.8 - - - -
416A GLN* 2.9 67.6 + - - +
417A SER* 5.5 1.6 - - - +
418A ASP* 4.9 8.5 + - - -
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Residues in contact with MET 331 (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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329A LEU 4.9 0.4 - - - +
330A ASN* 1.3 77.1 - - - +
332A THR* 1.3 79.9 + - - +
333A LYS* 3.7 20.9 - - + +
344A ASN 3.7 1.9 - - - +
345A TRP* 3.5 6.3 - - - -
346A GLY 2.9 31.2 + - - +
348A SER* 4.3 15.3 - - - +
359A PHE* 3.8 43.5 - - + -
380A GLU* 4.0 23.1 - - - +
381A SER* 4.7 2.5 - - - +
413A PHE* 4.5 6.7 - - + -
414A LEU 3.2 12.8 - - - +
415A LEU* 3.8 8.5 - - + -
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Residues in contact with THR 332 (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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331A MET* 1.3 81.3 - - - +
333A LYS* 1.3 69.4 + - - +
334A ILE* 4.3 0.2 - - + -
343A LYS* 3.3 8.8 - - + -
344A ASN 2.8 36.0 + - - -
345A TRP* 3.6 35.4 - - + +
413A PHE* 3.1 3.6 - - - +
414A LEU* 2.7 57.8 + - + -
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Residues in contact with LYS 333 (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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331A MET* 3.7 21.4 - - + +
332A THR* 1.3 88.3 + - - +
334A ILE* 1.3 62.9 + - - +
335A ALA 5.1 3.0 + - - +
336A GLN* 3.0 43.6 + - - +
341A LEU* 3.9 23.9 - - + +
342A ARG 4.5 2.9 - - - +
343A LYS* 4.1 8.8 - - - -
344A ASN* 4.8 2.0 + - - +
380A GLU* 5.6 2.9 - - - +
381A SER* 5.4 8.5 + - - -
411A HIS* 5.9 1.6 - - - +
412A GLU 3.7 7.0 - - - +
413A PHE* 3.9 4.3 - - + -
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Residues in contact with ILE 334 (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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332A THR* 4.3 0.4 - - + -
333A LYS* 1.3 77.0 - - - +
335A ALA* 1.3 63.0 + - + +
340A LYS* 3.7 4.0 - - - +
341A LEU* 2.9 31.4 + - - +
343A LYS* 3.7 30.1 - - + -
396A LEU* 4.2 25.4 - - + +
404A HIS* 4.6 0.7 - - + +
412A GLU* 2.8 32.3 + - + +
413A PHE* 4.0 6.3 - - - -
414A LEU* 3.6 42.4 - - + -
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Residues in contact with ALA 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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333A LYS* 3.8 3.3 + - - +
334A ILE* 1.3 83.0 + - + +
336A GLN* 1.3 63.3 + - - +
338A GLY* 4.5 3.6 - - - -
339A ARG 3.1 21.5 - - - +
340A LYS* 4.2 2.7 - - - -
341A LEU* 3.7 7.0 - - - +
410A GLY 3.8 14.1 - - - +
411A HIS* 3.4 3.5 - - - +
412A GLU* 3.0 43.2 + - + +
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Residues in contact with GLN 336 (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 LYS* 3.0 36.0 + - - +
335A ALA* 1.3 74.6 - - - +
337A GLY* 1.3 67.9 + - - +
338A GLY 3.1 0.7 - - - -
339A ARG* 2.8 26.7 + - + +
341A LEU* 3.7 17.6 - - + +
411A HIS* 3.6 27.4 + - + +
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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