Contacts of the helix formed by residues 431 - 443 (chain A) in PDB entry 2QFZ
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 PRO 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A VAL* 1.3 91.7 - - + +
432A LEU* 1.3 60.6 + - - +
433A ARG* 3.3 40.8 - - + +
434A CYS* 2.8 30.8 + - - +
435A THR* 3.1 8.9 + - - -
486A THR* 3.3 32.1 - - - +
487A ALA* 4.2 7.0 - - - +
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Residues in contact with LEU 432 (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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289A PRO* 3.9 24.2 - - + -
292A LEU* 5.3 0.4 - - + -
327A THR* 3.5 29.2 - - + -
328A PRO* 3.9 32.8 - - + -
331A VAL* 4.0 22.7 - - + -
427A MET* 4.2 12.3 - - + -
430A VAL 3.8 1.2 + - - -
431A PRO* 1.3 73.4 - - - +
433A ARG* 1.3 62.2 + - - +
435A THR* 3.1 7.5 + - - +
436A ILE* 3.0 29.4 + - + +
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Residues in contact with ARG 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PRO* 3.5 24.3 - - + +
432A LEU* 1.3 78.4 - - - +
434A CYS* 1.3 66.7 + - - +
436A ILE* 3.6 11.4 + - - +
437A ARG* 3.4 19.9 + - - +
487A ALA 2.9 28.3 + - - -
488A HIS* 3.9 2.6 - - - +
489A TRP 2.8 30.0 + - - +
490A ASP* 4.7 5.1 - - - +
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Residues in contact with CYS 434 (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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430A VAL* 3.9 12.8 - - + -
431A PRO* 2.8 25.7 + - - +
433A ARG* 1.3 81.2 - - - +
435A THR* 1.3 62.4 + - - +
437A ARG* 3.3 3.9 + - - +
438A LEU* 3.0 24.4 + - - +
489A TRP* 3.7 42.0 - - - -
490A ASP* 4.5 3.8 - - - -
494A ILE* 3.8 32.0 - - + +
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Residues in contact with THR 435 (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 PRO* 3.8 17.3 - - + -
425A LEU 5.2 1.4 + - - +
426A LEU 4.9 0.3 - - - -
427A MET* 3.6 34.6 + - + +
430A VAL* 3.6 20.9 + - - +
431A PRO 3.1 6.0 + - - -
432A LEU* 3.1 15.2 + - - -
434A CYS* 1.3 75.8 - - - +
436A ILE* 1.3 57.0 + - - +
438A LEU* 3.3 9.1 + - + +
439A TRP* 2.8 58.9 + - + +
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Residues in contact with ILE 436 (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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228A ARG* 3.4 42.8 - - - +
232A TRP* 3.5 9.8 - - + -
328A PRO* 4.3 15.5 - - + +
331A VAL* 4.0 25.1 - - + -
332A VAL* 3.8 23.6 - - + -
432A LEU* 3.0 32.0 + - + +
433A ARG* 3.9 9.4 - - - +
434A CYS 3.2 0.2 - - - -
435A THR* 1.3 77.4 - - - +
437A ARG* 1.3 62.3 + - - +
439A TRP 3.2 6.6 + - - -
440A ASP* 3.3 13.9 + - - +
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Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TRP* 3.6 9.9 + - - -
221A SER* 3.4 22.6 + - - +
222A GLY* 3.6 18.5 - - - -
228A ARG* 4.5 8.5 - - - +
433A ARG 3.4 10.2 + - - +
434A CYS* 3.3 9.3 + - - +
435A THR 3.3 0.4 - - - -
436A ILE* 1.3 79.7 - - - +
438A LEU* 1.3 60.3 + - - +
440A ASP* 3.1 28.1 + - - +
441A THR* 2.9 21.8 + - - -
491A ASP* 5.1 16.4 - - + +
494A ILE* 3.7 19.3 - - + -
495A SER* 4.1 22.0 + - - +
498A LEU* 3.5 16.6 - - - +
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Residues in contact with LEU 438 (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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425A LEU 4.8 4.7 - - - +
426A LEU* 4.7 18.8 - - + -
430A VAL* 5.1 8.3 - - + -
434A CYS 3.0 17.4 + - - +
435A THR* 3.4 11.9 - - - +
437A ARG* 1.3 75.4 - - - +
439A TRP* 1.3 62.9 + - + +
441A THR* 3.2 8.1 + - - -
442A TYR* 3.0 54.1 + - + +
456A VAL* 4.1 18.2 - - + -
494A ILE* 3.8 30.2 - - + +
497A LEU* 4.4 5.6 - - + -
498A LEU* 4.0 22.6 - - + +
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Residues in contact with TRP 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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232A TRP* 3.9 19.7 - + + -
325A LEU* 3.8 26.9 - - + -
328A PRO* 3.6 31.4 - - + -
329A PHE* 3.5 33.0 - + - -
370A LEU* 3.5 17.7 - - + -
425A LEU* 4.2 16.0 + - + +
427A MET* 3.9 17.9 - - - -
435A THR* 2.8 38.8 + - + +
436A ILE 3.2 0.2 + - - -
437A ARG 3.2 0.4 - - - -
438A LEU* 1.3 74.6 - - + +
440A ASP* 1.4 64.7 + - - +
442A TYR* 3.7 27.3 - + - +
443A GLN* 3.0 32.0 + - - +
449A PHE* 3.6 22.1 - + + -
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Residues in contact with ASP 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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219A SER* 3.7 19.2 - - - +
222A GLY* 3.5 4.5 - - - -
223A ILE* 2.9 36.5 + - + +
228A ARG* 3.0 30.4 + - - -
232A TRP* 2.9 25.7 + - - +
235A LEU* 4.8 0.3 - - - +
436A ILE 3.3 6.4 + - - +
437A ARG* 3.1 19.9 + - - +
439A TRP* 1.4 76.0 - - - +
441A THR* 1.3 60.7 + - - +
443A GLN* 3.5 3.9 + - - +
444A SER* 2.9 24.4 + - - -
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Residues in contact with THR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TRP* 2.7 59.7 + - + +
437A ARG* 2.9 14.9 + - - -
438A LEU 3.2 8.6 + - - -
440A ASP* 1.3 75.8 - - - +
442A TYR* 1.3 64.8 + - - +
444A SER* 3.0 15.7 + - - -
445A GLU* 3.1 12.7 + - + +
452A PHE* 4.1 8.7 - - + -
498A LEU* 3.2 26.1 - - + +
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Residues in contact with TYR 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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425A LEU* 5.2 3.8 - - + -
438A LEU* 3.0 32.6 + - + +
439A TRP* 3.4 24.4 + + - +
441A THR* 1.3 78.0 - - - +
443A GLN* 1.3 60.8 + - - +
444A SER 3.5 0.2 + - - -
445A GLU* 3.6 7.6 - - - +
448A GLY* 3.3 39.2 + - - -
449A PHE* 3.5 46.1 + + + -
452A PHE* 4.1 12.8 - + - -
453A HIS* 2.8 39.4 + + + -
456A VAL* 3.4 40.3 - - + +
498A LEU* 4.8 1.8 - - + -
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Residues in contact with GLN 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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216A ARG* 4.5 4.3 + - - +
232A TRP* 3.4 50.9 + - - +
235A LEU* 3.8 38.4 - - + +
236A SER* 4.1 14.8 - - - +
329A PHE* 3.8 27.5 - - - -
439A TRP* 3.0 21.7 + - - +
440A ASP* 4.0 3.8 - - - +
441A THR 3.2 0.2 - - - -
442A TYR* 1.3 76.9 - - - +
444A SER* 1.3 58.7 + - - +
445A GLU 3.4 3.4 - - - +
449A PHE* 3.9 22.4 - - + -
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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