Contacts of the strand formed by residues 411 - 430 (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 VAL 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLN* 5.4 9.9 - - - +
132A ILE* 5.8 3.8 - - + -
133A THR 5.4 1.8 - - - +
136A GLN* 3.7 30.3 - - + +
403A GLU* 4.2 15.7 - - + +
404A HIS 3.2 12.6 - - - +
405A ASN* 4.3 10.3 - - - +
406A PHE* 4.1 4.5 - - - -
409A GLY 4.2 7.2 - - - +
410A TRP* 1.3 76.8 - - - +
412A GLY* 1.3 69.3 + - - +
413A LYS* 5.3 1.3 - - + -
460A TYR* 4.2 2.0 - - + +
461A LEU* 3.8 1.9 - - - +
462A THR* 2.7 55.6 + - + +
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Residues in contact with GLY 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU 4.6 0.2 - - - -
403A GLU* 3.3 6.6 - - - +
404A HIS* 2.7 38.6 + - - +
406A PHE* 3.6 17.0 - - - -
411A VAL* 1.3 74.2 - - - +
413A LYS* 1.3 63.2 + - - +
460A TYR 3.6 7.4 - - - -
461A LEU* 4.7 4.3 - - - -
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Residues in contact with LYS 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLN* 4.1 13.8 - - + +
137A LEU* 4.6 19.4 - - - +
401A ASN* 4.5 12.3 - - + -
402A LEU 3.4 11.9 - - - +
403A GLU* 4.0 27.6 + - + +
411A VAL* 5.3 1.6 - - + -
412A GLY* 1.3 75.0 - - - +
414A VAL* 1.3 67.3 + - - +
415A GLN* 3.7 32.9 + - - +
458A ASP 3.6 1.4 - - - +
459A ILE* 3.4 4.8 - - - +
460A TYR* 3.1 70.6 + - + +
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Residues in contact with VAL 414 (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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400A ALA 4.0 0.2 - - - +
401A ASN* 3.1 8.3 - - - +
402A LEU* 2.9 49.2 + - + +
413A LYS* 1.3 76.6 - - - +
415A GLN* 1.3 65.8 + - - +
416A LEU* 4.3 10.8 - - + -
457A LEU* 3.9 24.9 - - + -
458A ASP 3.5 4.3 - - - +
459A ILE* 4.4 20.2 - - + -
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Residues in contact with GLN 415 (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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157A ARG* 4.9 3.5 + - - -
220A ASP* 3.6 22.5 + - - +
222A ILE* 3.3 43.8 - - + +
400A ALA 3.8 1.6 - - - -
401A ASN* 3.3 31.1 - - + +
413A LYS* 3.7 26.2 + - - +
414A VAL* 1.3 72.9 - - - +
416A LEU* 1.3 60.7 + - - +
417A ASP* 4.3 3.7 + - - +
456A SER* 3.6 1.9 - - - +
457A LEU* 3.4 6.2 - - - +
458A ASP* 2.8 43.3 + - + +
460A TYR* 4.0 18.4 - - - -
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Residues in contact with LEU 416 (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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399A PHE* 3.2 4.3 - - - +
400A ALA* 2.8 48.6 + - + +
414A VAL* 5.0 12.6 - - + -
415A GLN* 1.3 73.5 - - - +
417A ASP* 1.3 72.9 + - - +
455A ASN* 6.6 0.2 - - + -
456A SER 3.4 9.2 - - - +
457A LEU* 4.8 12.1 - - + -
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Residues in contact with ASP 417 (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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222A ILE* 4.5 27.7 - - + +
270A ARG* 4.8 6.8 + - - -
397A THR* 3.8 19.1 - - - +
398A VAL 3.7 1.8 - - - -
399A PHE* 3.8 11.2 - - - +
401A ASN* 4.9 2.1 + - - -
415A GLN* 4.3 4.7 - - - +
416A LEU* 1.3 89.3 + - - +
418A HIS* 1.3 61.8 + - - +
419A LYS* 3.9 4.2 - - + +
454A SER 3.6 0.2 - - - +
455A ASN* 3.1 11.0 + - - +
456A SER* 2.9 49.4 + - - +
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Residues in contact with HIS 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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396A ARG 3.9 0.3 - - - +
397A THR* 3.3 4.7 - - - +
398A VAL* 2.8 54.7 + - + +
417A ASP* 1.3 74.0 - - - +
419A LYS* 1.3 61.5 + - - +
420A ILE* 3.8 17.5 - - + +
453A LYS* 5.0 13.2 - - + +
454A SER 4.9 2.0 - - - -
455A ASN* 3.0 28.4 + - - +
1821A PO4 2.9 42.3 + - - -
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Residues in contact with LYS 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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219A TYR* 3.8 32.3 - - + -
224A SER* 5.0 13.4 - - - -
235A ASN* 3.9 16.0 + - - +
351A ASP* 5.6 0.2 - - - -
395A THR* 4.4 20.2 - - - +
396A ARG 3.5 6.7 - - - +
397A THR* 3.9 23.3 - - + +
417A ASP* 3.9 5.3 - - + +
418A HIS* 1.3 75.9 - - - +
420A ILE* 1.3 67.5 + - - +
421A ASN* 3.5 25.8 - - - +
452A THR 3.7 0.5 - - - +
453A LYS* 3.4 4.3 - - - +
454A SER* 2.8 49.7 + - - +
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Residues in contact with ILE 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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394A TYR* 3.6 25.4 - - + -
395A THR* 3.1 8.0 - - - -
396A ARG* 2.8 73.1 + - + +
418A HIS* 3.8 15.9 - - + +
419A LYS* 1.3 79.7 - - - +
421A ASN* 1.3 64.6 + - - +
451A GLU* 3.4 28.0 - - + +
452A THR 3.3 10.3 - - - +
453A LYS* 4.3 8.1 - - + -
1821A PO4 3.1 29.8 - - - +
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Residues in contact with ASN 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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224A SER* 5.7 2.1 - - - -
230A GLY 4.4 3.3 - - - +
231A TYR 3.2 31.4 + - - +
232A SER* 3.8 3.0 - - - +
233A ALA* 2.7 30.2 + - + +
235A ASN* 3.6 17.2 + - - +
394A TYR 3.7 4.0 - - - -
395A THR* 3.8 6.9 - - - +
419A LYS* 3.5 25.5 - - - +
420A ILE* 1.3 73.9 - - - +
422A GLY* 1.3 58.5 + - - +
423A TYR* 5.0 0.2 - - - -
451A GLU* 3.7 0.7 - - - -
452A THR* 2.9 39.2 + - - +
454A SER* 5.3 4.2 + - - -
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Residues in contact with GLY 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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233A ALA* 3.3 10.2 - - - +
394A TYR* 2.6 69.2 + - - +
420A ILE 4.1 0.8 - - - -
421A ASN* 1.3 74.4 - - - +
423A TYR* 1.3 57.9 + - - -
450A GLY 3.6 8.5 - - - -
451A GLU* 4.2 1.1 - - - -
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Residues in contact with TYR 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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229A VAL 5.0 2.2 - - - -
230A GLY* 4.0 22.7 - - - -
233A ALA* 4.1 12.6 - - + -
391A TRP* 4.2 14.6 - - - +
392A GLU* 3.3 15.9 - - - +
393A GLN* 4.3 0.7 - - + +
394A TYR* 3.8 4.7 - - - -
421A ASN 5.0 0.2 - - - -
422A GLY* 1.3 76.9 - - - +
424A HIS* 1.3 59.4 + - - +
425A ALA* 4.6 5.8 - - + -
448A TYR* 3.8 30.9 - - + +
449A THR* 3.5 20.7 + - - -
450A GLY* 2.9 53.8 + - - +
451A GLU* 4.3 0.9 - - - -
485A TRP* 2.9 39.6 + + - -
487A GLY* 4.5 2.8 - - - -
522A ILE* 5.1 1.6 - - - +
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Residues in contact with HIS 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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390A SER* 3.6 2.8 + - - +
392A GLU* 3.0 50.3 + - + +
394A TYR* 6.1 1.1 - - + -
423A TYR* 1.3 73.4 - - - +
425A ALA* 1.3 59.3 + - - +
426A PRO* 3.4 15.3 - - + +
447A LYS* 4.4 13.2 - - - -
448A TYR 3.9 2.5 - - - -
449A THR* 4.1 14.1 - - + +
1818A PO4 3.2 25.6 + - - -
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Residues in contact with ALA 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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390A SER 3.3 6.7 - - - +
391A TRP* 3.9 25.8 - - + +
423A TYR* 4.6 4.5 - - + -
424A HIS* 1.3 75.2 - - - +
426A PRO* 1.3 61.8 - - - +
427A LEU* 3.1 22.3 + - + +
446A GLN 3.6 0.9 - - - +
447A LYS* 3.3 2.7 - - - -
448A TYR* 2.6 48.2 + - + +
449A THR* 4.7 1.2 - - - +
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Residues in contact with PRO 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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388A TRP* 3.4 15.3 - - + +
389A SER* 3.5 0.2 - - - -
390A SER* 3.1 36.4 + - - +
424A HIS* 3.4 21.5 - - + +
425A ALA* 1.3 84.9 - - - +
427A LEU* 1.3 63.9 + - - +
446A GLN 4.0 1.6 - - - +
447A LYS* 4.0 16.8 - - + -
515A TRP* 3.9 14.8 - - + -
1818A PO4 3.5 33.0 - - - +
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Residues in contact with LEU 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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360A SER* 3.9 7.6 - - - -
361A GLY 4.1 11.9 - - - +
362A TRP* 4.1 35.7 - - + +
388A TRP* 3.8 2.2 - - - -
389A SER* 3.6 8.5 - - - +
390A SER 3.7 20.9 - - - +
391A TRP* 3.8 28.9 - - + -
425A ALA* 3.1 19.2 + - + +
426A PRO* 1.3 75.7 - - - +
428A GLY* 1.3 58.7 + - - +
444A VAL 4.8 0.4 - - - -
445A ALA* 3.3 4.4 - - - +
446A GLN 3.0 34.7 + - - +
448A TYR* 4.9 11.7 - - + -
515A TRP* 3.9 2.6 - - - -
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Residues in contact with GLY 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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362A TRP* 6.0 0.2 - - - -
385A GLY* 3.5 0.2 - - - -
386A ALA* 2.7 30.2 + - - +
388A TRP* 3.5 19.2 - - - -
389A SER* 3.1 15.2 + - - -
427A LEU* 1.3 75.0 - - - +
429A ALA* 1.3 63.5 + - - +
443A ILE* 4.2 4.5 - - - -
444A VAL 3.5 8.3 - - - -
445A ALA* 4.0 2.9 - - - -
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Residues in contact with ALA 429 (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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361A GLY* 4.2 0.7 - - - -
362A TRP* 4.1 28.2 - - + +
384A ASN* 3.3 24.9 - - - +
385A GLY* 3.8 8.5 - - - -
386A ALA* 4.3 0.7 - - - +
428A GLY* 1.3 76.9 - - - +
430A ILE* 1.3 66.7 + - - +
431A MET* 3.4 6.4 + - + +
443A ILE* 3.6 9.3 - - - +
444A VAL 3.0 27.0 + - - +
506A TRP* 5.5 0.9 - - - -
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Residues in contact with ILE 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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363A SER* 5.8 0.3 + - - -
367A PRO* 4.6 9.7 - - + +
382A PHE* 4.8 1.1 - - + -
384A ASN* 3.1 34.8 + - + -
429A ALA* 1.3 72.1 - - - +
431A MET* 1.3 63.4 + - - +
434A TRP* 4.2 15.3 - - + -
441A ALA* 4.2 15.3 - - + -
442A LYS 3.6 9.9 - - - +
443A ILE* 3.3 24.2 - - + +
500A THR* 4.4 0.7 - - + -
503A PHE* 4.2 31.9 - - + -
506A TRP* 3.4 47.5 - - + +
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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