Contacts of the helix formed by residues 421 - 437 (chain A) in PDB entry 2WJP
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 ASN 421 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A SER* 3.0 13.3 + - - -
416A LEU* 4.0 1.8 - - + -
419A PHE* 3.3 3.5 - - - +
420A LYS* 1.3 100.2 + - - +
422A PHE* 1.3 64.5 + - - +
423A GLU* 3.4 22.4 + - - +
424A GLN* 2.9 41.4 + - - +
425A ARG 3.2 8.5 + - - -
1441A D17 3.3 13.5 - - - +
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Residues in contact with PHE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 6.3 1.8 - - + -
301A HIS* 4.0 7.8 + - + -
302A ARG* 3.7 5.8 - - - -
318A SER* 2.7 39.3 + - - +
319A LYS* 2.9 63.9 - - + -
321A THR* 4.3 4.0 - - + -
415A SER* 3.2 8.5 + - - -
421A ASN* 1.3 72.6 - - - +
423A GLU* 1.3 75.9 + - + +
425A ARG* 3.4 5.5 + - - +
426A GLY* 2.9 14.6 + - - -
1441A D17 2.7 40.0 + - - +
1445A AZI 3.2 32.5 - - - -
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Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A HIS* 3.3 23.3 - - + +
421A ASN* 3.4 24.3 + - - +
422A PHE* 1.3 98.0 - - - +
424A GLN* 1.3 57.5 + - - +
426A GLY 3.2 0.7 + - - -
427A ASN* 2.8 40.9 + - - +
1445A AZI 2.8 32.2 + - - +
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Residues in contact with GLN 424 (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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418A GLN 4.7 0.7 - - - +
419A PHE* 3.4 17.7 - - + +
420A LYS* 2.9 45.0 + - + +
421A ASN* 2.9 24.7 + - - +
423A GLU* 1.3 76.0 - - - +
425A ARG* 1.3 57.7 + - - +
427A ASN* 3.3 10.0 + - + +
428A GLU* 2.9 31.8 + - + +
1443A AZI 5.1 1.6 + - - -
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Residues in contact with ARG 425 (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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318A SER* 2.8 39.5 + - - +
321A THR* 3.7 10.3 - - - +
344A GLY 3.8 9.5 + - - -
345A GLY* 5.1 0.6 - - - -
369A PHE* 4.8 5.6 - - - -
390A MET* 3.5 27.0 - - - +
409A LEU* 4.1 5.2 - - + -
411A PRO* 3.3 25.5 - - - +
413A CYS 3.1 28.7 + - - -
414A ALA 3.6 3.4 + - - -
415A SER* 3.5 28.3 - - - +
419A PHE* 3.6 37.5 - - + -
421A ASN 3.2 6.6 + - - +
422A PHE* 3.6 8.4 - - - +
424A GLN* 1.3 78.5 - - - +
426A GLY* 1.3 56.2 + - - +
428A GLU 3.4 0.2 + - - -
429A PHE* 3.0 24.7 + - - +
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Residues in contact with GLY 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A HIS* 3.7 6.3 - - - -
316A ASN* 3.6 37.6 + - - -
318A SER* 3.4 6.0 + - - -
422A PHE 2.9 11.7 + - - -
423A GLU 3.2 2.7 + - - -
425A ARG* 1.3 72.8 - - - +
427A ASN* 1.3 61.5 + - - +
429A PHE* 3.3 6.1 + - - +
430A ALA* 2.9 25.8 + - - +
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Residues in contact with ASN 427 (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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301A HIS* 3.4 15.9 + - - -
316A ASN* 5.5 0.2 + - - -
423A GLU* 2.8 31.4 + - - +
424A GLN* 3.7 7.9 - - + +
426A GLY* 1.3 73.5 - - - +
428A GLU* 1.3 58.7 + - - +
430A ALA* 3.3 7.7 + - - +
431A ARG* 3.0 28.4 + - - +
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Residues in contact with GLU 428 (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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389A THR* 6.0 0.2 - - - -
390A MET* 3.6 14.9 - - + +
391A GLU* 3.9 27.0 + - - +
419A PHE* 3.5 25.5 - - + -
424A GLN* 2.9 20.8 + - + +
425A ARG 3.7 3.8 - - - +
427A ASN* 1.3 72.1 - - - +
429A PHE* 1.3 66.5 + - - +
431A ARG* 3.3 21.4 + - - +
432A LEU* 3.0 31.9 + - + +
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Residues in contact with PHE 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A VAL* 3.8 15.5 - - + -
314A TRP* 4.3 9.2 - + + -
315A ILE 3.5 39.3 - - - -
316A ASN* 3.7 20.4 - - + -
342A LEU* 3.8 10.5 - - + -
390A MET* 3.5 12.9 - - + +
394A MET* 3.6 37.7 - - + +
407A VAL* 4.1 12.1 - - + -
409A LEU* 3.7 30.5 - - + -
425A ARG 3.0 14.6 + - - +
426A GLY 3.4 7.0 - - - +
428A GLU* 1.3 76.6 - - - +
430A ALA* 1.3 59.6 + - - +
432A LEU* 3.3 4.2 + - - -
433A ALA* 2.8 28.5 + - + +
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Residues in contact with ALA 430 (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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306A VAL* 4.0 37.4 - - + +
316A ASN* 5.2 0.9 - - - +
426A GLY 2.9 16.9 + - - +
427A ASN* 3.7 8.3 - - - +
428A GLU 3.2 0.2 - - - -
429A PHE* 1.3 74.4 - - - +
431A ARG* 1.3 66.6 + - - +
433A ALA* 3.3 1.7 + - - +
434A LYS* 3.0 40.0 + - - +
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Residues in contact with ARG 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLU* 4.0 15.0 + - - -
395A ARG* 4.8 2.2 - - - +
427A ASN 3.0 14.4 + - - +
428A GLU* 3.6 20.2 + - - +
430A ALA* 1.3 77.7 - - - +
432A LEU* 1.3 96.5 + - - +
434A LYS* 3.3 9.0 + - - +
435A GLU* 3.1 32.2 + - + +
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A MET* 4.6 2.5 - - + -
391A GLU* 3.8 37.0 - - + +
394A MET* 3.9 22.2 - - + -
395A ARG* 3.5 31.2 - - + +
428A GLU* 3.0 37.9 + - + +
429A PHE 3.9 2.9 - - - +
431A ARG* 1.3 97.3 - - - +
433A ALA* 1.3 59.2 + - - +
435A GLU* 3.3 6.8 + - - +
436A LEU* 2.8 43.1 + - + +
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Residues in contact with ALA 433 (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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306A VAL* 4.3 11.4 - - + -
307A LEU* 3.4 7.2 - - + +
314A TRP* 3.6 46.3 - - + -
394A MET* 3.7 3.1 - - + +
429A PHE* 2.8 22.9 + - + +
430A ALA 3.6 4.7 - - - +
432A LEU* 1.3 72.5 - - - +
434A LYS* 1.3 56.1 + - + +
437A GLY* 2.7 35.0 + - - -
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Residues in contact with LYS 434 (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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306A VAL* 4.1 23.2 + - + +
307A LEU* 4.2 18.1 - - + +
430A ALA* 3.0 32.7 + - - +
431A ARG* 3.7 7.9 - - - +
433A ALA* 1.3 78.4 - - - +
435A GLU* 1.3 61.7 + - - +
437A GLY 3.8 1.6 + - - -
438A SER* 3.2 21.8 + - - -
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Residues in contact with GLU 435 (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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395A ARG* 2.9 43.1 + - - -
431A ARG* 3.1 22.8 + - + +
432A LEU* 3.3 14.6 + - - +
434A LYS* 1.3 79.2 - - - +
436A LEU* 1.3 67.1 + - + +
437A GLY 3.5 0.3 + - - -
438A SER* 3.7 12.8 + - - +
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Residues in contact with LEU 436 (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 TRP* 4.2 12.4 - - + -
394A MET* 3.7 45.8 - - + +
395A ARG* 3.8 34.3 - - + +
398A ALA* 3.9 24.6 - - + +
432A LEU* 2.8 29.7 + - + +
435A GLU* 1.3 81.5 - - + +
437A GLY* 1.3 59.8 + - - +
438A SER 3.5 3.9 + - - +
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Residues in contact with GLY 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.8 13.7 - - - +
309A HIS* 3.2 22.9 - - - +
310A ASN* 4.2 5.2 + - - +
314A TRP* 3.7 18.9 + - - -
433A ALA 2.7 23.2 + - - -
435A GLU 3.3 0.4 - - - -
436A LEU* 1.3 74.7 - - - +
438A SER* 1.3 57.5 + - - +
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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