Contacts of the helix formed by residues 429 - 437 (chain A) in PDB entry 3QFS
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 HIS 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A LEU* 4.8 10.2 - - + +
380A ILE 3.5 15.7 - - - +
381A THR* 3.4 29.2 + - + +
382A ASN 4.1 8.3 - - - -
384A PRO* 4.3 2.9 - - - -
427A ARG 3.4 2.6 + - - -
428A ARG* 1.3 74.8 - - - +
430A ILE* 1.3 67.3 + - - +
431A LEU* 3.5 22.1 - - + +
432A ALA* 3.1 49.6 + - + +
433A ILE* 3.1 12.0 + - - +
487A ARG* 4.5 11.2 + - + -
488A ILE 5.3 3.1 - - - -
489A ASN* 3.4 32.2 + - - -
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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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337A LEU* 4.0 15.3 - - + -
380A ILE* 3.7 34.5 + - + +
382A ASN 4.8 1.2 + - - -
384A PRO* 4.1 21.9 - - + +
388A VAL* 5.3 0.4 - - + -
392A LEU* 3.9 28.5 - - + -
429A HIS* 1.3 71.9 - - - +
431A LEU* 1.3 65.8 + - - +
433A ILE* 3.2 9.2 + - + +
434A LEU* 3.0 42.2 + - + +
447A LEU* 4.1 24.5 - - + -
451A LEU* 4.7 13.0 - - + -
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Residues in contact with LEU 431 (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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333A LEU* 3.4 28.7 - - + -
336A GLN* 3.7 37.2 - - + +
337A LEU* 3.8 24.9 - - + -
340A ILE* 4.1 19.5 - - + -
429A HIS* 3.3 14.6 - - + +
430A ILE* 1.3 82.2 - - + +
432A ALA* 1.3 58.8 + - - +
434A LEU* 3.1 2.3 + - - +
435A GLN* 2.9 60.4 + - + +
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Residues in contact with ALA 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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428A ARG* 4.0 13.0 - - + -
429A HIS* 3.1 33.8 + - + +
431A LEU* 1.3 75.8 - - - +
433A ILE* 1.3 58.8 + - - +
435A GLN* 3.3 1.4 + - - -
436A ASP* 2.9 35.9 + - - -
487A ARG* 3.5 41.3 + - - +
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Residues in contact with ILE 433 (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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384A PRO* 3.9 30.1 - - + -
389A LEU* 3.8 26.0 - - + -
392A LEU* 5.7 0.9 - - + -
405A LEU* 4.1 18.2 - - + -
422A TRP* 4.0 22.7 - - + -
423A VAL* 4.5 12.1 - - + -
428A ARG* 4.1 10.5 - - + +
429A HIS 3.1 8.8 + - - +
430A ILE* 3.6 12.1 - - + +
432A ALA* 1.3 76.5 - - - +
434A LEU* 1.3 58.2 + - - +
436A ASP 3.3 0.5 + - - -
437A CYS* 2.9 31.4 + - - +
440A LEU* 4.1 19.3 - - + -
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Residues in contact with LEU 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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337A LEU* 3.7 27.1 - - + -
340A ILE* 3.8 32.0 - - + +
341A LEU* 4.0 14.8 - - + -
392A LEU* 6.1 0.2 - - + -
430A ILE* 3.0 32.5 + - + +
431A LEU 3.5 6.1 - - - +
433A ILE* 1.3 75.8 - - - +
435A GLN* 1.3 62.3 + - - +
437A CYS 3.2 18.9 - - - +
438A PRO* 3.4 7.8 - - - +
440A LEU* 3.7 43.8 - - + +
442A PRO* 4.0 14.1 - - + -
447A LEU* 5.1 1.6 - - + -
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Residues in contact with GLN 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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336A GLN* 4.0 13.9 - - - +
340A ILE* 3.7 20.2 - - + +
431A LEU* 2.9 44.4 + - + +
432A ALA* 4.1 1.0 - - - -
434A LEU* 1.3 79.2 - - - +
436A ASP* 1.3 62.2 + - - +
438A PRO* 3.5 16.0 - - - +
487A ARG* 3.1 34.5 + - - +
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Residues in contact with ASP 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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401A GLU* 4.5 2.8 - - - +
404A LEU* 5.9 0.3 - - - +
422A TRP* 3.7 21.9 - - + -
428A ARG* 2.7 37.1 + - - -
432A ALA 2.9 17.2 + - - +
435A GLN* 1.3 77.5 - - - +
437A CYS* 1.3 62.2 - - - +
438A PRO* 3.3 7.7 - - - +
487A ARG* 2.9 27.8 + - - -
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Residues in contact with CYS 437 (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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401A GLU* 3.2 26.2 - - + +
404A LEU* 4.1 19.3 - - - -
405A LEU* 4.3 18.6 - - + -
422A TRP* 4.1 19.1 - - - -
433A ILE* 2.9 14.8 + - - +
434A LEU 3.2 7.6 - - - +
436A ASP* 1.3 80.3 - - - +
438A PRO* 1.3 59.0 - - - +
439A SER 3.1 5.6 - - - -
440A LEU* 3.0 36.1 + - + +
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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