Contacts of the strand formed by residues 417 - 427 (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 LEU 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A ALA 3.5 1.6 - - - +
396A GLN* 3.2 5.0 - - - -
397A LEU* 2.7 46.7 + - + +
399A MSE 3.6 34.1 - - + +
415A LYS* 3.5 43.1 - - + +
416A VAL* 1.3 73.6 - - - +
418A ARG* 1.3 59.1 + - - +
419A MSE 3.8 19.3 + - + +
447A SER* 6.1 3.8 - - - -
449A GLU* 5.3 2.0 - - - +
1001A 1PE 4.4 17.5 - - - +
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Residues in contact with ARG 418 (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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272A PHE* 3.6 38.0 - - - -
276A SER* 6.0 1.8 - - - -
394A GLN* 4.7 17.9 + - + +
395A ALA 3.6 4.9 - - - +
396A GLN* 3.4 44.9 + - + +
416A VAL* 3.9 3.3 + - + +
417A LEU* 1.3 71.2 - - - +
419A MSE 1.3 63.5 + - - +
447A SER* 3.4 7.1 - - - -
448A THR* 3.0 46.1 + - - +
449A GLU* 4.9 3.3 + - + +
451A ILE 5.6 4.9 + - - -
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Residues in contact with MSE 419 (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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394A GLN* 3.2 9.5 - - - +
395A ALA 2.8 37.5 + - - +
397A LEU* 4.4 11.2 - - + -
417A LEU* 4.4 23.8 - - + +
418A ARG* 1.3 77.0 - - - +
420A LEU* 1.3 59.8 + - - +
421A TYR* 3.7 34.5 - - + +
445A ALA* 3.9 24.0 - - + -
446A SER 3.6 9.9 - - - +
447A SER* 4.1 20.4 - - - +
448A THR* 4.3 3.8 - - - +
1001A 1PE 3.7 39.5 - - - +
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Residues in contact with LEU 420 (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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279A LEU* 4.6 10.5 - - + -
280A THR* 4.4 7.4 - - - +
283A VAL* 4.2 32.5 - - + -
392A THR* 4.6 5.6 - - - -
393A PHE 3.7 5.6 - - - +
394A GLN* 3.3 33.4 - - + +
419A MSE 1.3 73.4 - - - +
421A TYR* 1.3 77.3 + - - +
422A VAL* 4.3 11.2 - - + +
445A ALA* 3.2 4.7 - - - -
446A SER* 3.0 37.3 + - - +
448A THR* 3.8 12.3 - - + -
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Residues in contact with TYR 421 (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* 4.1 16.2 - - + +
331A MSE 5.4 3.6 - - + +
332A ILE* 5.7 0.3 - - - +
392A THR* 3.1 28.1 - - - -
393A PHE* 2.9 55.7 + + + +
395A ALA* 4.4 10.1 - - + -
397A LEU* 3.5 22.2 - - + +
419A MSE 3.7 30.0 - - + +
420A LEU* 1.3 74.6 - - - +
422A VAL* 1.3 62.4 + - - +
423A TRP* 3.6 15.7 - - - +
443A ILE* 3.7 20.9 - - + -
444A SER 3.6 2.5 - - - -
445A ALA* 3.5 22.0 - - + -
1001A 1PE 4.0 19.9 + - - -
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Residues in contact with VAL 422 (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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283A VAL* 4.6 9.4 - - + -
287A LEU* 4.2 17.5 - - + -
390A ILE* 3.6 29.2 - - + -
391A ILE 3.4 5.2 - - - +
392A THR* 4.0 10.8 - - + -
420A LEU* 4.3 10.8 - - + +
421A TYR* 1.3 78.1 - - - +
423A TRP* 1.3 61.4 + - - +
424A ALA 4.4 0.2 + - - -
443A ILE* 3.4 5.4 - - - -
444A SER* 3.0 46.9 + - - +
445A ALA* 5.9 0.4 - - - -
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Residues in contact with TRP 423 (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* 4.2 5.6 - - + -
324A ILE* 3.9 29.4 - - + -
327A VAL* 3.5 39.3 - - + -
328A LEU* 3.9 19.7 - - + -
331A MSE 4.3 13.5 - - - -
389A LEU 3.8 1.2 - - - +
390A ILE* 3.3 6.2 - - - -
391A ILE* 2.9 50.9 + - + +
392A THR* 5.0 0.2 - - - +
393A PHE* 3.6 25.4 - + - -
421A TYR* 3.6 18.9 - + + -
422A VAL* 1.3 82.4 - - - +
424A ALA* 1.3 61.0 + - - +
425A LEU* 3.8 12.9 + - + -
440A LEU* 3.8 20.6 - - + -
442A ASP 3.6 2.7 - - - -
443A ILE* 3.2 29.4 - - + +
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Residues in contact with ALA 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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381A LYS* 5.1 5.8 - - - +
388A VAL* 4.0 17.0 - - + -
389A LEU 3.9 4.0 - - - -
390A ILE* 4.1 13.9 - - + -
422A VAL 4.4 0.2 + - - -
423A TRP* 1.3 72.1 - - - +
425A LEU* 1.3 60.7 + - - +
440A LEU* 3.8 3.1 - - - +
441A LEU* 2.8 34.7 + - + +
442A ASP* 2.9 31.2 + - + +
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Residues in contact with LEU 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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315A PHE* 3.9 11.2 - - + -
319A CYS* 3.8 29.2 - - - -
323A ILE* 4.1 30.5 - - + -
388A VAL* 3.3 5.0 - - - -
389A LEU 3.0 37.3 + - - +
391A ILE* 4.0 17.9 - - + -
423A TRP* 4.5 10.1 - - + +
424A ALA* 1.3 75.4 - - - +
426A CYS* 1.3 59.6 + - - +
438A TRP* 3.4 18.9 - - + -
439A ARG* 3.4 17.0 - - - +
440A LEU* 4.0 22.2 - - + +
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Residues in contact with CYS 426 (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* 3.4 32.6 + - + -
383A VAL* 3.9 9.9 - - - -
385A GLN* 3.7 15.3 - - - -
386A GLY 3.7 29.2 - - - -
387A PRO 3.5 10.1 - - - -
388A VAL* 4.0 7.0 - - + -
424A ALA 4.2 0.6 + - - -
425A LEU* 1.3 74.1 - - - +
427A ARG* 1.3 62.0 + - - +
437A ALA 3.7 0.7 - - - +
438A TRP* 3.5 4.8 - - - -
439A ARG 3.0 29.2 + - - -
441A LEU* 4.2 11.2 - - + -
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Residues in contact with ARG 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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303A ILE* 4.2 20.2 - - - +
306A VAL* 3.7 22.1 - - - +
307A ASP* 3.8 24.3 + - - +
310A PHE* 5.7 1.0 - - - -
344A TYR* 3.9 2.5 - - - -
385A GLN 3.6 16.3 - - - +
386A GLY* 4.0 0.2 - - - -
387A PRO* 3.1 27.8 + - + +
426A CYS* 1.3 72.9 - - - +
428A ASP* 1.3 74.3 + - - +
429A GLN* 3.1 30.2 + - - +
431A GLU 4.6 5.5 + - - -
434A PRO* 3.9 26.1 + - - +
437A ALA* 3.5 22.2 - - + +
438A TRP* 3.7 40.9 - - + +
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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