Contacts of the strand formed by residues 449 - 457 (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 LYS 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A PHE* 4.3 25.6 - - + +
442A TYR 3.4 3.1 - - - -
443A PRO* 3.9 36.8 - - + -
447A GLY 3.3 7.2 + - - +
448A THR* 1.3 74.4 - - - +
450A ILE* 1.3 59.4 + - - +
451A PRO* 4.1 2.1 - - - +
510A TYR* 5.5 1.4 - - - -
514A TRP* 3.5 18.2 - - - -
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Residues in contact with ILE 450 (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* 3.2 4.5 - - - -
442A TYR* 2.7 73.7 + - + +
444A SER* 4.0 2.5 - - - -
448A THR* 3.7 20.9 - - + +
449A LYS* 1.3 76.5 - - - +
451A PRO* 1.3 73.2 - - - +
503A ASN 3.5 25.6 - - - +
504A ILE* 3.9 4.7 - - - -
505A ARG* 4.3 0.9 - - - +
514A TRP* 3.7 20.6 - - + -
529A ASP* 3.6 32.1 - - - +
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Residues in contact with PRO 451 (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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357A VAL* 4.1 10.1 - - + -
439A GLN* 4.1 7.0 - - - +
440A ILE 3.4 7.4 - - - +
441A PHE* 3.7 17.3 - - + -
449A LYS 4.1 2.2 - - - +
450A ILE* 1.3 94.5 - - + +
452A MET* 1.3 59.6 + - - +
502A ALA* 3.8 0.3 - - - -
503A ASN* 2.8 54.5 + - + +
510A TYR* 3.5 33.7 - - + +
514A TRP* 4.0 10.1 - - + -
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Residues in contact with MET 452 (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 3.8 0.5 - - - +
439A GLN* 3.4 4.3 - - - +
440A ILE* 2.9 42.3 + - + +
442A TYR* 3.9 22.0 - - + -
451A PRO* 1.3 77.2 - - - +
453A PHE* 1.3 73.4 + - - +
454A ILE* 4.1 4.9 - - + -
470A LEU* 3.9 28.0 - - - -
500A ALA* 3.9 8.3 - - - -
501A VAL 3.2 13.2 - - - +
502A ALA* 4.2 2.5 - - - -
503A ASN* 4.4 0.9 - - - -
533A ALA* 3.8 22.9 - - - +
536A TYR* 3.6 31.0 - - + -
537A LEU* 3.9 10.5 - - + -
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Residues in contact with PHE 453 (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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357A VAL* 3.5 49.8 - - + -
358A LYS* 4.5 9.6 - - + -
379A VAL* 5.2 4.9 - - + -
401A PHE* 3.6 35.7 - + + -
437A THR* 4.4 9.2 - - + -
438A VAL 3.4 4.9 - - - -
439A GLN* 3.7 31.6 - - + -
452A MET* 1.3 73.9 - - - +
454A ILE* 1.3 62.1 + - - +
455A VAL* 4.3 1.6 - - + -
480A ILE 4.2 4.9 - - - -
482A PRO* 3.7 23.1 - - + -
500A ALA* 3.2 5.2 - - - -
501A VAL* 2.9 40.3 + - + +
503A ASN* 3.8 11.9 - - - -
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Residues in contact with ILE 454 (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 3.6 1.6 - - - +
437A THR* 3.4 2.8 - - - -
438A VAL* 2.8 45.8 + - + +
440A ILE* 4.1 11.2 - - + -
452A MET* 4.1 13.0 - - + +
453A PHE* 1.3 79.7 - - - +
455A VAL* 1.3 62.7 + - - +
456A HIS* 4.0 7.4 - - + -
498A VAL* 3.6 27.8 - - + -
499A LEU 3.3 5.2 - - - +
500A ALA* 4.5 1.3 - - + -
536A TYR* 4.1 14.1 - - + -
537A LEU* 3.9 18.2 - - + -
542A TYR* 3.7 43.1 - - + +
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Residues in contact with VAL 455 (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 PHE* 3.7 31.4 - - + -
402A LEU* 4.0 26.5 - - + -
435A TYR* 4.8 4.3 - - + -
436A GLN 3.3 8.5 - - - +
437A THR* 3.6 17.9 - - + +
453A PHE 5.3 0.4 - - - -
454A ILE* 1.3 76.1 - - - +
456A HIS* 1.3 66.8 + - - +
489A LEU* 4.6 11.4 - - + -
492A VAL* 4.4 6.6 - - + +
498A VAL* 3.7 1.4 - - - -
499A LEU* 2.8 58.6 + - + +
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Residues in contact with HIS 456 (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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435A TYR* 3.5 7.4 - - - -
436A GLN* 2.8 68.1 + - + +
438A VAL* 4.7 5.8 - - + +
454A ILE* 4.0 24.7 - - + -
455A VAL* 1.3 76.8 - - - +
457A LYS* 1.3 85.8 + - - +
458A LYS* 4.9 2.7 - - - -
459A GLY 5.2 1.8 - - - -
460A ILE* 3.6 30.0 - - + +
462A LEU* 6.0 0.9 - - + -
492A VAL* 4.5 7.4 - - - -
497A GLY 4.7 0.9 - - - +
498A VAL* 4.1 13.5 - - + -
542A TYR* 4.0 16.6 + + - -
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Residues in contact with LYS 457 (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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434A ASP* 3.6 9.4 - - + +
435A TYR* 3.7 25.1 - - + -
456A HIS* 1.3 91.5 + - - +
458A LYS* 1.3 66.2 + - - +
459A GLY 3.6 0.2 + - - -
460A ILE* 3.3 28.0 - - + +
466A HIS* 6.1 1.1 + - - -
492A VAL* 3.8 24.6 + - + +
493A ARG* 4.9 8.6 + - - +
496A GLY* 3.7 26.8 + - - -
497A GLY 5.1 1.5 + - - -
709A ILE* 4.7 8.5 - - - +
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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