Contacts of the strand formed by residues 429 - 442 (chain B) in PDB entry 6IWQ
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 LYS 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B ASP* 5.1 4.9 - - - +
323B THR* 3.6 6.3 + - - +
324B ILE* 4.1 29.6 - - + -
325B CYS 2.8 25.3 + - - -
383B ARG* 5.2 10.7 - - - +
423B ILE* 3.4 9.0 - - - +
424B TRP* 3.9 19.7 - - + -
427B GLY 5.4 0.7 - - - +
428B GLY* 1.3 79.2 - - - +
430B LEU* 1.3 59.8 + - - +
431B LEU* 4.1 17.6 - - + +
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B CYS* 3.3 21.3 - - + +
327B VAL* 3.5 25.4 - - + -
383B ARG* 3.2 6.8 - - - +
384B SER* 3.0 44.1 + - - +
386B ALA* 3.6 33.2 - - - +
387B MET* 3.9 21.5 - - + +
420B SER* 4.8 4.7 - - - +
423B ILE* 4.9 9.2 - - + -
424B TRP* 3.3 24.9 - - + +
429B LYS* 1.3 73.6 - - - +
431B LEU* 1.3 60.5 + - - +
432B PHE* 4.5 3.1 - - + -
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Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO* 4.4 7.4 - - + -
324B ILE* 3.8 34.8 - - + -
325B CYS 2.9 11.7 + - - +
326B THR* 3.4 7.3 - - - +
327B VAL* 2.8 27.4 + - - +
381B PRO* 3.6 26.7 - - + +
382B TYR* 3.2 5.8 - - - +
383B ARG* 3.3 36.8 - - + +
429B LYS* 4.5 17.5 - - + +
430B LEU* 1.3 77.6 - - - +
432B PHE* 1.3 64.1 + - - +
433B VAL* 3.8 0.8 + - + -
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Residues in contact with PHE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B VAL* 3.5 35.2 - - + -
328B PRO 5.7 0.9 - - - -
329B LEU* 4.2 14.6 - - + -
352B ALA 3.2 14.8 - - - -
353B ARG* 4.3 0.2 - - - -
354B GLY* 3.9 14.4 - - - -
362B TRP* 5.7 4.0 - + - -
364B ARG* 6.3 0.4 - - - -
381B PRO* 3.1 3.5 - - - +
382B TYR* 2.6 73.6 + + + -
384B SER* 3.5 26.2 - - - -
386B ALA 3.7 13.5 - - - -
387B MET* 4.5 4.9 - - - -
388B ALA 5.2 3.1 - - - -
430B LEU* 4.5 2.5 - - + -
431B LEU* 1.3 75.4 - - - +
433B VAL* 1.3 61.3 + - - +
434B PRO* 3.5 5.0 - - - +
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Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PRO* 3.5 43.7 - - + +
317B PRO* 4.4 0.7 - - + -
326B THR* 3.3 34.5 - - + +
327B VAL 2.9 10.7 + - - +
329B LEU* 3.7 7.9 + - - +
379B THR 5.6 0.4 - - - +
381B PRO* 3.8 22.4 - - + -
431B LEU 4.2 1.6 - - - +
432B PHE* 1.3 74.8 - - - +
434B PRO* 1.4 69.6 - - + +
435B CYS* 3.8 4.3 - - + +
436B SER* 3.1 29.7 - - - +
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Residues in contact with PRO 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ARG* 4.8 0.9 - - - +
194B GLN* 4.8 0.3 - - - +
197B CYS* 4.3 5.6 - - - -
329B LEU* 3.7 11.5 - - + +
351B TYR* 3.8 36.3 - - + +
375B ARG* 4.6 0.7 - - - +
379B THR* 3.1 32.8 - - - +
380B GLU 3.7 11.4 - - - +
381B PRO 4.0 0.2 - - - -
382B TYR* 4.0 23.3 - - + -
432B PHE 3.5 8.7 - - - +
433B VAL* 1.4 79.1 - - + +
435B CYS* 1.3 59.0 + - - +
436B SER 3.1 1.4 + - - -
437B ARG* 3.6 26.0 + - - +
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Residues in contact with CYS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ARG* 4.1 17.9 + - - +
197B CYS* 2.0 66.2 - - + +
200B TRP* 3.9 9.6 - - - -
202B TYR* 4.2 3.8 - - - +
308B VAL 4.9 0.3 - - - +
309B ASN* 3.8 14.5 - - - +
310B TRP* 4.7 0.2 - - - -
313B PRO* 3.8 23.1 - - + +
379B THR* 3.9 15.7 - - - +
433B VAL* 3.2 3.5 - - + +
434B PRO* 1.3 79.9 - - - +
436B SER* 1.3 57.5 + - - +
437B ARG* 4.0 3.3 + - - -
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Residues in contact with SER 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TRP* 2.4 43.4 + - - +
313B PRO* 4.2 0.7 - - - -
314B LEU* 3.5 29.0 - - - +
328B PRO* 3.2 5.7 - - - +
329B LEU 3.0 23.4 + - - -
433B VAL* 3.1 20.5 + - - +
434B PRO 3.1 0.4 - - - -
435B CYS* 1.3 79.7 - - - +
437B ARG* 1.3 60.4 + - - +
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Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LEU* 3.8 16.6 + - + +
193B ARG* 3.6 30.5 - - + +
194B GLN* 3.8 26.9 + - - +
307B ALA* 3.1 39.1 + - + +
310B TRP* 4.0 4.8 - - - +
329B LEU* 3.4 36.1 - - + +
331B ASP* 2.9 42.3 + - - +
342B PRO* 3.9 21.4 - - - +
350B GLY 5.4 3.6 + - - -
351B TYR* 4.3 1.0 - - - -
434B PRO 3.6 13.5 + - - +
435B CYS 4.0 1.6 + - - -
436B SER* 1.3 79.8 + - - +
438B VAL* 1.3 67.0 + - - +
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Residues in contact with VAL 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 4.5 9.4 - - + -
304B CYS* 4.5 2.5 - - + -
305B GLU 3.8 6.5 - - - +
306B VAL* 3.7 26.5 - - + -
307B ALA 4.5 0.2 - - - +
310B TRP* 4.6 8.1 - - + -
328B PRO* 3.8 22.7 - - + -
329B LEU 3.1 7.2 + - - +
330B ILE* 3.4 4.0 - - + +
331B ASP* 2.8 25.4 + - - +
391B LEU* 2.6 41.7 - - + -
437B ARG* 1.3 82.1 - - - +
439B GLY* 1.3 65.2 + - - +
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B CYS* 2.2 39.0 - - - +
305B GLU 2.8 16.3 + - - -
307B ALA* 6.1 0.2 - - - +
331B ASP* 3.3 14.7 - - - +
333B ILE* 3.7 19.5 - - - -
340B ILE* 4.8 5.1 - - - +
438B VAL* 1.3 72.9 - - - +
440B HIS* 1.3 52.6 + - - -
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Residues in contact with HIS 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ASP* 2.2 47.0 + - - +
303B HIS* 3.1 19.1 + + - -
304B CYS* 4.2 2.6 - - + -
330B ILE* 3.8 22.7 - - + -
331B ASP 2.8 5.5 + - - +
333B ILE* 2.8 23.0 + - - -
391B LEU* 4.8 5.0 - - + +
439B GLY* 1.3 74.5 - - - +
441B ILE* 1.3 63.9 + - - +
442B TYR* 3.2 47.1 - + + -
701B MN 3.1 16.3 + - - -
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Residues in contact with ILE 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B PHE* 3.0 44.9 - - + -
222B THR* 5.3 5.2 - - + -
303B HIS* 2.9 37.3 + - + +
305B GLU* 4.8 2.5 - - - +
333B ILE* 2.3 54.3 - - + +
334B ASN 4.3 0.2 - - - +
335B GLY* 3.6 13.9 - - - -
338B TYR* 3.7 21.8 - - + -
440B HIS* 1.3 87.7 + - - +
442B TYR* 1.3 61.9 + - - +
443B ARG* 4.1 1.0 + - - +
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Residues in contact with TYR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B PHE* 3.9 2.4 - - - -
330B ILE* 4.5 9.1 + - + +
331B ASP 4.4 1.8 - - - -
332B VAL* 3.5 34.1 - - + -
333B ILE 3.4 5.0 + - - +
334B ASN* 6.2 0.2 - - - -
335B GLY* 3.9 8.9 + - - +
343B GLN* 3.7 32.7 + - + -
440B HIS* 3.2 53.4 - + + -
441B ILE* 1.3 74.2 - - - +
443B ARG* 1.3 66.2 + - - +
444B LEU* 3.5 14.0 - - - +
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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