Contacts of the strand formed by residues 429 - 441 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321F ASP* 4.7 6.7 - - - +
323F THR* 3.2 5.6 + - - +
324F ILE* 4.0 28.9 - - + -
325F CYS 2.8 25.3 + - - -
383F ARG* 5.2 15.0 - - - +
423F ILE* 3.4 9.8 - - - +
424F TRP* 3.9 19.3 - - + -
427F GLY 5.4 0.9 - - - +
428F GLY* 1.3 79.3 - - - +
430F LEU* 1.3 60.3 + - - +
431F LEU* 4.1 18.3 - - + +
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Residues in contact with LEU 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325F CYS* 3.3 21.8 - - + +
327F VAL* 3.5 24.9 - - + -
383F ARG* 3.2 7.4 - - - +
384F SER* 3.1 44.5 + - - +
386F ALA* 3.6 31.6 - - - +
387F MET* 3.9 20.6 - - + +
420F SER* 4.8 5.2 - - - +
423F ILE* 4.9 8.7 - - + -
424F TRP* 3.3 25.5 - - + +
429F LYS* 1.3 74.9 - - - +
431F LEU* 1.3 59.5 + - - +
432F PHE* 4.5 3.1 - - + -
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Residues in contact with LEU 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F PRO* 4.2 10.8 - - + -
324F ILE* 3.8 32.5 - - + -
325F CYS 2.9 11.5 + - - +
326F THR* 3.4 7.7 - - - +
327F VAL* 2.8 27.8 + - - +
381F PRO* 3.9 21.8 - - + -
382F TYR* 3.0 13.9 - - - +
383F ARG* 3.4 31.0 - - + +
429F LYS* 4.5 18.8 - - + +
430F LEU* 1.3 76.5 - - - +
432F PHE* 1.3 65.3 + - - +
433F VAL* 3.8 1.4 + - + -
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Residues in contact with PHE 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327F VAL* 3.5 35.7 - - + -
328F PRO 5.6 1.1 - - - -
329F LEU* 4.2 13.9 - - + -
352F ALA* 3.4 28.0 - - + -
353F ARG 4.3 0.7 - - - -
354F GLY* 3.9 15.0 - - - -
362F TRP* 5.8 3.8 - + - -
364F ARG* 6.0 2.7 - - - -
381F PRO* 3.1 3.8 - - - +
382F TYR* 2.5 59.0 + + + +
384F SER* 3.4 28.9 - - - -
386F ALA 3.7 12.8 - - - -
387F MET* 4.5 4.5 - - - -
388F ALA 5.2 2.9 - - - -
430F LEU* 4.5 2.9 - - + -
431F LEU* 1.3 75.0 - - - +
433F VAL* 1.3 59.8 + - - +
434F PRO* 3.5 4.3 - - - +
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Residues in contact with VAL 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F PRO* 3.5 44.4 - - + +
317F PRO* 4.3 1.6 - - + -
326F THR* 3.3 34.5 - - + +
327F VAL 2.9 11.7 + - - +
329F LEU* 3.7 8.7 + - - +
379F THR 5.8 0.4 - - - +
381F PRO* 4.0 21.3 - - + -
431F LEU* 4.2 2.5 - - + +
432F PHE* 1.3 74.8 - - - +
434F PRO* 1.4 67.4 - - + +
435F CYS* 3.8 3.4 - - + +
436F SER* 3.1 29.8 - - - +
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Residues in contact with PRO 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F ARG* 4.8 1.2 - - - +
197F CYS* 4.3 1.4 - - - -
329F LEU* 3.7 11.3 - - + +
351F TYR* 3.4 41.9 + - + +
375F ARG* 4.5 1.3 - - - +
379F THR* 3.2 31.0 - - + +
380F GLU 3.7 9.9 - - - +
381F PRO* 3.8 2.7 - - + -
382F TYR* 3.8 17.7 - - + -
432F PHE 3.5 7.9 - - - +
433F VAL* 1.4 81.0 - - + +
435F CYS* 1.3 59.3 + - - +
436F SER 3.1 1.3 + - - +
437F ARG* 3.6 26.5 + - - +
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Residues in contact with CYS 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F ARG* 3.6 22.0 - - - -
197F CYS* 1.2 72.5 - - + +
200F TRP* 4.0 11.0 - - - -
202F TYR* 4.2 4.5 - - - +
308F VAL 4.9 0.2 - - - +
309F ASN* 3.8 13.4 + - - +
310F TRP* 4.7 0.2 - - - -
313F PRO* 3.8 21.9 - - + +
379F THR* 3.9 18.2 - - - +
433F VAL* 3.2 2.8 - - + +
434F PRO* 1.3 80.5 - - - +
436F SER* 1.3 58.2 + - - +
437F ARG 4.0 0.6 + - - -
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Residues in contact with SER 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F TRP* 2.4 43.6 + - - +
313F PRO* 4.2 0.4 - - - -
314F LEU* 3.5 28.8 - - - +
328F PRO* 3.2 5.6 - - - +
329F LEU 3.0 23.9 + - - -
433F VAL* 3.1 18.9 + - - +
434F PRO 3.1 0.4 - - - -
435F CYS* 1.3 80.4 - - - +
437F ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LEU* 3.7 21.4 + - - +
193F ARG* 3.9 33.5 - - + +
194F GLN* 5.0 4.4 - - - +
307F ALA* 3.1 40.1 + - + +
310F TRP* 4.0 5.5 - - - +
329F LEU* 3.4 35.3 - - + +
331F ASP* 2.9 41.8 + - - +
342F PRO* 3.7 19.8 - - - +
349F ASP* 3.8 17.8 + - - -
351F TYR* 4.9 6.7 + - - -
434F PRO 3.6 17.0 + - - +
435F CYS 4.0 1.2 + - - -
436F SER* 1.3 77.9 + - - +
438F VAL* 1.3 67.8 + - - +
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Residues in contact with VAL 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F LEU* 4.6 10.1 - - + -
304F CYS* 3.9 13.2 - - + -
305F GLU 3.7 9.4 - - - +
306F VAL* 3.5 24.7 - - + -
307F ALA 4.6 0.2 - - - +
310F TRP* 4.6 8.1 - - + -
328F PRO* 3.7 25.1 - - + -
329F LEU 3.1 5.8 + - - +
330F ILE* 3.3 7.1 - - - +
331F ASP* 2.7 32.2 + - - -
391F LEU* 3.9 23.3 - - + -
437F ARG* 1.3 83.3 - - - +
439F GLY* 1.3 68.1 + - - +
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Residues in contact with GLY 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304F CYS* 3.0 11.3 - - - +
305F GLU 2.7 39.1 + - - -
331F ASP* 3.2 15.2 - - - +
333F ILE* 3.6 18.4 - - - -
340F ILE* 4.8 5.4 - - - -
438F VAL* 1.3 72.5 - - - +
440F HIS* 1.3 61.3 + - - -
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Residues in contact with HIS 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F ASP* 2.3 44.1 + - + -
303F HIS* 3.0 17.0 + + - -
304F CYS* 4.0 5.4 - - - +
330F ILE* 3.9 23.1 - - + +
331F ASP 2.8 8.5 + - - +
332F VAL* 3.6 3.8 - - - +
333F ILE* 2.7 27.1 + - - +
390F GLY* 6.3 0.4 - - - -
391F LEU* 4.9 4.7 - - + -
439F GLY* 1.3 75.0 - - - +
441F ILE* 1.3 78.8 + - - +
442F TYR* 3.5 2.5 + - - -
701F MN 2.6 17.7 + - - -
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Residues in contact with ILE 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F PHE* 2.8 52.5 - - + -
222F THR* 4.2 18.4 - - + +
303F HIS* 3.2 34.3 + - + +
305F GLU* 5.1 6.3 - - - +
333F ILE* 3.3 28.0 - - + +
335F GLY* 3.7 14.4 - - - -
338F TYR* 4.0 20.2 - - + -
440F HIS* 1.3 91.2 + - - +
442F TYR* 1.3 67.4 + - - +
443F ARG* 3.9 0.7 + - - +
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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