Contacts of the strand formed by residues 438 - 447 (chain A) in PDB entry 2CW9
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 TRP 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ILE* 3.8 15.5 - - + -
310A PHE* 4.1 16.9 - + - -
315A PHE* 3.6 24.3 - + - -
318A GLN* 4.5 8.9 + - - -
323A ILE* 4.2 19.1 - - + +
342A TRP* 4.0 19.1 - - - -
387A PRO 3.9 5.6 - - - -
389A LEU* 3.5 37.2 - - + -
425A LEU* 3.4 35.0 - - + -
426A CYS 3.5 18.4 - - - -
427A ARG* 3.7 42.0 - - + +
434A PRO 4.1 17.3 + - - -
435A TYR 5.5 0.8 - - - -
436A ALA 3.5 3.5 - - - +
437A ALA* 1.3 80.4 - - + +
439A ARG* 1.3 66.3 + - - +
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Residues in contact with ARG 439 (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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323A ILE* 6.3 0.2 - - - -
341A ASP 3.4 21.6 + - - +
342A TRP* 3.3 22.2 - - + +
343A CYS* 4.4 10.1 - - - -
344A TYR* 3.6 26.5 + - + +
425A LEU* 3.4 8.8 - - - -
426A CYS 3.0 31.1 + - - +
428A ASP* 4.4 17.3 + - - +
431A GLU* 5.5 4.6 + - - +
436A ALA 3.7 22.4 + - - -
437A ALA 4.0 10.9 + - - -
438A TRP* 1.3 76.6 - - - +
440A LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 440 (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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323A ILE* 6.1 0.2 - - - +
327A VAL* 4.2 26.4 - - + +
331A MSE 4.8 4.5 - - - -
342A TRP* 2.8 17.4 + - - +
343A CYS* 3.6 10.3 - - - -
344A TYR* 3.2 25.6 + - - -
347A THR* 3.7 7.3 - - + +
351A LEU* 4.2 24.0 - - + -
423A TRP* 3.8 34.1 - - + -
424A ALA 3.8 8.1 - - - +
425A LEU* 4.0 7.5 - - + +
439A ARG* 1.3 70.1 - - - +
441A LEU* 1.3 58.2 + - - +
442A ASP 3.5 26.0 - - - +
443A ILE* 4.4 14.1 - - + -
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Residues in contact with LEU 441 (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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344A TYR* 4.0 16.2 - - + -
347A THR* 2.6 31.7 + - - +
381A LYS* 5.2 5.2 - - - +
383A VAL* 4.2 16.2 - - + -
385A GLN* 3.9 24.5 - - - +
388A VAL* 3.9 27.6 - - + -
424A ALA* 2.8 21.6 + - + +
426A CYS* 4.2 15.9 - - + -
439A ARG 3.5 0.4 + - - -
440A LEU* 1.3 72.8 - - - +
442A ASP* 1.3 66.9 + - + +
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Residues in contact with ASP 442 (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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347A THR* 4.6 3.4 - - - -
381A LYS* 6.2 1.6 - - - +
423A TRP* 3.6 0.7 - - - -
424A ALA* 2.9 38.4 + - + -
440A LEU* 3.5 9.3 - - - +
441A LEU* 1.3 85.7 - - + +
443A ILE* 1.3 91.7 + - - +
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Residues in contact with ILE 443 (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 MSE 3.9 22.4 - - + -
347A THR* 5.6 2.0 - - + -
351A LEU* 4.5 19.3 - - + -
421A TYR* 3.7 20.6 - - + -
422A VAL 3.4 6.3 - - - -
423A TRP* 3.2 35.9 - - + +
440A LEU* 4.4 15.3 - - + -
442A ASP* 1.3 95.7 + - - +
444A SER* 1.3 72.4 + - - +
1001A 1PE 4.5 18.7 - - - +
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Residues in contact with SER 444 (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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421A TYR* 3.6 1.0 - - - -
422A VAL* 3.0 50.8 + - - +
443A ILE* 1.3 80.8 - - - +
445A ALA* 1.3 66.3 + - - +
1001A 1PE 4.2 6.1 - - - -
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Residues in contact with ALA 445 (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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419A MSE 3.9 10.5 - - + -
420A LEU 3.2 10.8 - - - +
421A TYR* 3.5 30.7 - - + -
422A VAL* 5.9 0.7 - - - -
444A SER* 1.3 81.5 + - - +
446A SER* 1.3 66.4 + - - +
1001A 1PE 3.2 32.4 - - - +
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Residues in contact with SER 446 (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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419A MSE 3.6 8.0 - - - -
420A LEU* 3.0 35.1 + - - +
445A ALA* 1.3 80.3 - - - +
447A SER* 1.3 73.2 + - - +
448A THR* 6.2 0.2 - - - -
1001A 1PE 4.6 4.3 - - - -
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Residues in contact with SER 447 (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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417A LEU* 6.1 4.7 - - - -
418A ARG 3.4 11.7 - - - -
419A MSE 4.1 14.5 - - - +
446A SER* 1.3 86.9 + - - +
448A THR* 1.3 60.7 + - - +
449A GLU* 3.8 21.9 + - - +
451A ILE* 5.2 2.9 - - - +
1001A 1PE 5.5 2.9 - - - -
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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