Contacts of the strand formed by residues 435 - 443 (chain A) in PDB entry 1QFM
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 TYR 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A LEU* 3.7 32.5 - - + +
430A ILE* 3.9 23.6 - - + +
431A ASP 3.1 32.9 + - - -
432A ALA* 3.1 17.6 + - - +
434A ASP* 1.3 96.4 + - + +
436A GLN* 1.3 62.5 + - - +
455A VAL* 4.8 3.1 - - + -
456A HIS 3.5 6.5 - - - +
457A LYS* 3.7 22.0 - - + -
458A LYS* 3.3 17.7 - - - -
489A LEU* 5.2 8.3 - - + -
492A VAL* 3.6 32.8 - - + -
493A ARG* 3.2 36.2 - - + +
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Residues in contact with GLN 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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402A LEU* 4.6 2.2 - - - -
435A TYR* 1.3 77.7 - - - +
437A THR* 1.3 66.3 + - - +
438A VAL* 3.5 23.7 - - + +
454A ILE 3.6 1.4 - - - +
455A VAL* 3.3 5.2 - - - +
456A HIS* 2.8 66.4 + - + +
458A LYS* 4.0 21.5 - - + +
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Residues in contact with THR 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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379A VAL* 5.8 7.2 - - + -
401A PHE* 3.8 30.8 - - + +
402A LEU* 3.8 21.7 - - - +
436A GLN* 1.3 75.9 - - - +
438A VAL* 1.3 72.7 + - - +
453A PHE* 4.4 10.8 - - + -
454A ILE 3.4 4.3 - - - +
455A VAL* 3.6 17.9 - - + +
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Residues in contact with VAL 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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436A GLN* 3.5 30.7 - - + +
437A THR* 1.3 81.3 - - - +
439A GLN* 1.3 62.2 + - - +
440A ILE* 4.6 9.6 - - + -
452A MET 3.8 0.7 - - - +
453A PHE* 3.4 3.5 - - - +
454A ILE* 2.8 58.9 + - + +
456A HIS* 4.7 6.1 - - - +
542A TYR* 4.5 13.7 - - - +
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Residues in contact with GLN 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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356A ASP* 2.9 33.2 + - - +
357A VAL* 3.9 8.1 - - - +
358A LYS* 3.9 17.0 + - + -
438A VAL* 1.3 75.1 - - - +
440A ILE* 1.3 72.9 + - - +
441A PHE* 3.7 27.1 - - + -
451A PRO* 4.1 8.5 - - - +
452A MET 3.4 11.9 - - - +
453A PHE* 3.7 30.9 - - + +
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Residues in contact with ILE 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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438A VAL* 4.6 15.7 - - + -
439A GLN* 1.3 80.5 - - - +
441A PHE* 1.3 70.2 + - - +
442A TYR* 3.9 28.0 - - + +
451A PRO* 3.4 3.8 - - - +
452A MET* 2.9 45.9 + - + +
454A ILE* 4.1 11.0 - - + -
536A TYR* 3.6 47.3 - - + +
542A TYR* 5.3 2.7 - - - +
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Residues in contact with PHE 441 (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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356A ASP* 4.3 16.2 - - - -
439A GLN* 3.7 35.0 - - + -
440A ILE* 1.3 79.4 - - - +
442A TYR* 1.3 61.0 + - - +
443A PRO* 4.3 1.9 - - - +
449A LYS* 4.3 26.8 + - + +
450A ILE 3.2 6.5 - - - +
451A PRO* 3.7 28.0 - - + -
510A TYR* 3.6 22.0 - + - -
536A TYR* 5.1 3.1 - - - -
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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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440A ILE* 3.9 13.7 - - + -
441A PHE* 1.3 74.5 - - - +
443A PRO* 1.3 75.8 - - + +
444A SER 3.7 0.4 + - - -
448A THR 3.5 0.3 - - - +
449A LYS* 4.0 2.9 - - - -
450A ILE* 2.7 88.8 + - + +
451A PRO 4.1 0.4 - - - -
452A MET* 3.9 21.8 - - + -
502A ALA* 3.8 1.1 - - + +
504A ILE* 3.7 6.1 - - - +
529A ASP* 2.7 31.8 + - - -
532A CYS* 3.6 17.0 - - + -
533A ALA* 3.4 25.2 - - + +
536A TYR* 3.6 31.6 - - + -
539A LYS* 6.0 0.2 - - - -
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Residues in contact with PRO 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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441A PHE 4.3 1.8 - - - +
442A TYR* 1.3 94.9 - - + +
444A SER* 1.3 65.8 + - - +
447A GLY* 4.3 9.0 - - - +
448A THR 3.5 5.8 - - - +
449A LYS* 3.9 25.1 - - + -
532A CYS* 4.0 0.2 - - - +
536A TYR* 5.4 4.0 - - + -
539A LYS* 5.5 8.7 - - - +
784A SGM 3.5 32.3 - - + +
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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