Contacts of the helix formed by residues 445 - 464 (chain A) in PDB entry 1F7U
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 445 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A ILE* 3.9 5.8 - - - +
444A GLU* 1.3 98.4 + - + +
446A PRO* 1.3 66.0 - - - +
447A GLU 3.3 3.4 - - - -
448A GLU* 3.0 34.0 + - + +
449A VAL* 2.9 24.6 + - + +
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Residues in contact with PRO 446 (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 HIS* 3.8 5.4 - - + +
433A MET* 3.6 14.2 - - - +
440A TYR* 3.2 48.0 - - + +
443A ILE* 3.6 24.0 - - + +
444A GLU 3.2 9.0 - - - +
445A HIS* 1.3 87.1 - - - +
447A GLU* 1.3 57.2 + - + +
449A VAL* 3.3 0.7 + - + -
450A ALA* 2.9 31.0 + - - +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU* 5.2 2.1 - - - +
426A LYS* 3.1 56.0 - - - +
427A GLU* 5.4 5.5 - - - +
430A HIS* 3.2 32.2 + - - +
445A HIS 3.3 0.2 - - - -
446A PRO* 1.3 79.9 - - + +
448A GLU* 1.3 78.3 + - - +
450A ALA* 3.4 4.5 + - - +
451A ASP 3.2 9.4 + - - -
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LYS* 4.9 4.0 + - - +
445A HIS* 3.0 43.9 + - + +
447A GLU* 1.3 90.0 - - - +
449A VAL* 1.3 66.5 + - + +
451A ASP* 3.2 15.8 + - - +
452A LEU* 3.2 21.1 + - + +
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Residues in contact with VAL 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A MET* 4.0 14.6 - - + -
443A ILE* 3.6 21.5 - - + -
445A HIS* 2.9 20.7 + - + +
446A PRO 3.7 6.1 - - - +
448A GLU* 1.3 76.8 - - + +
450A ALA* 1.3 63.5 + - - +
452A LEU* 3.1 12.4 + - + +
453A VAL* 3.0 22.8 + - + +
604A VAL* 4.2 14.8 - - + -
606A ARG 3.3 24.0 - - - +
607A MET* 4.2 9.0 - - + -
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LYS* 3.6 26.2 - - + +
429A MET* 3.8 9.6 - - - +
430A HIS* 3.8 16.6 - - + +
433A MET* 3.5 18.4 - - + +
446A PRO 2.9 18.2 + - - +
447A GLU 3.4 7.2 - - - +
449A VAL* 1.3 77.8 - - - +
451A ASP* 1.3 57.2 + - - +
453A VAL* 4.5 1.1 - - - -
454A GLY* 2.9 26.0 + - - -
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Residues in contact with ASP 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 2.6 48.9 + - - +
422A LEU 4.2 2.6 - - - +
426A LYS* 3.6 30.6 - - + +
447A GLU 3.2 7.7 + - - +
448A GLU* 3.2 12.2 + - - +
449A VAL 3.2 0.4 - - - -
450A ALA* 1.3 74.3 - - - +
452A LEU* 1.3 64.2 + - + +
455A ILE* 2.9 49.2 + - - +
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Residues in contact with LEU 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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283A ARG 5.8 2.0 - - - +
448A GLU* 3.2 14.6 + - + +
449A VAL* 3.1 12.4 + - + +
451A ASP* 1.3 80.5 - - + +
453A VAL* 1.3 61.9 + - - +
455A ILE* 3.7 13.1 + - + +
456A SER* 3.2 22.9 + - - -
490A GLN* 3.7 5.2 + - - -
602A THR* 3.7 46.4 + - + +
603A PRO 5.3 0.7 - - - +
604A VAL* 3.8 23.6 - - + -
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Residues in contact with VAL 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A MET* 3.8 20.9 - - + -
433A MET* 5.1 3.1 - - + -
449A VAL* 3.0 31.2 + - + +
450A ALA* 3.8 5.2 - - - +
452A LEU* 1.3 74.5 - - - +
454A GLY* 1.3 64.9 + - - +
456A SER* 2.6 22.9 + - - +
457A ALA* 3.2 9.2 + - - +
487A PRO* 3.9 23.3 - - + +
490A GLN* 4.4 7.4 - - + +
604A VAL* 4.4 10.5 - - + -
607A MET* 4.3 22.4 - - + -
938B A 4.0 13.0 - - - +
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Residues in contact with GLY 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 5.6 2.0 - - - -
425A THR* 3.4 34.3 - - - +
426A LYS* 4.6 1.3 - - - -
429A MET* 3.7 7.4 - - - +
450A ALA 2.9 18.2 + - - -
451A ASP* 3.8 1.3 - - - -
452A LEU 3.3 0.2 - - - -
453A VAL* 1.3 78.3 - - - +
455A ILE* 1.3 60.8 + - - +
457A ALA* 3.0 14.1 + - - +
458A VAL* 3.1 12.9 + - - +
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Residues in contact with ILE 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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283A ARG* 3.7 33.7 - - + +
284A LEU* 3.9 17.5 - - + -
422A LEU* 4.2 17.5 - - + -
451A ASP* 2.9 47.0 + - - +
452A LEU* 4.0 12.6 - - + +
453A VAL 3.3 0.2 - - - -
454A GLY* 1.3 72.2 - - - +
456A SER* 1.3 61.0 + - - +
458A VAL* 3.2 8.1 + - + +
459A MET* 2.9 52.2 + - + +
600A GLY 5.7 0.7 - - - +
601A LEU* 5.4 2.0 - - + -
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Residues in contact with SER 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU 3.2 14.3 + - - -
453A VAL 2.6 22.9 + - - -
455A ILE* 1.3 77.3 - - - +
457A ALA* 1.3 57.5 + - - +
460A ILE* 3.0 35.2 + - - +
486A GLY* 3.5 11.8 - - - -
490A GLN* 3.5 28.6 - - - +
601A LEU* 3.8 30.5 - - - -
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Residues in contact with ALA 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A THR* 4.3 3.1 - - + -
429A MET* 4.3 2.5 - - + -
453A VAL 3.2 5.6 + - - +
454A GLY 3.0 11.3 + - - +
456A SER* 1.3 82.3 + - - +
458A VAL* 1.3 62.0 + - - +
460A ILE* 4.3 0.3 - - - +
461A GLN* 3.2 27.3 + - - +
477A ARG 4.4 3.1 - - - +
478A MET 3.4 24.0 - - - +
480A SER 4.6 2.7 - - - +
485A THR* 5.8 0.7 - - - -
486A GLY* 4.2 2.9 + - - +
487A PRO* 3.7 28.5 - - + -
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.5 31.0 - - + +
418A LEU* 5.0 2.0 - - + -
421A ILE* 4.1 13.7 - - + -
422A LEU* 4.0 25.4 - - + -
425A THR* 3.8 21.8 - - + +
454A GLY 3.1 12.5 + - - +
455A ILE* 3.2 7.6 + - + +
457A ALA* 1.3 75.0 - - - +
459A MET* 1.3 63.4 + - + +
461A GLN* 2.8 34.0 + - - +
462A ASP* 3.6 2.6 + - - +
478A MET* 4.2 16.2 - - + -
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Residues in contact with MET 459 (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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163A LEU* 4.9 6.1 - - + -
167A ILE* 3.9 41.7 - - + -
284A LEU* 4.7 11.4 - - + +
455A ILE* 2.9 37.5 + - + +
458A VAL* 1.3 76.6 - - + +
460A ILE* 1.3 59.4 + - - +
462A ASP* 3.1 4.3 + - - +
463A MET* 3.0 37.2 + - + +
599A LEU 3.3 27.4 - - - +
600A GLY* 3.6 22.9 - - - +
601A LEU* 3.4 25.1 - - + -
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Residues in contact with ILE 460 (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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456A SER 3.0 22.6 + - - +
457A ALA 4.3 0.2 - - - +
459A MET* 1.3 73.9 - - - +
461A GLN* 1.3 66.6 + - - +
463A MET* 3.7 4.0 - - - +
464A GLN* 2.9 50.9 + - + +
485A THR* 4.0 2.9 - - - -
486A GLY* 3.6 28.7 - - - +
489A LEU* 3.9 18.8 - - + -
551A VAL* 4.1 23.1 - - + -
555A PHE* 4.0 13.5 - - + -
599A LEU* 4.1 12.1 - - + -
601A LEU* 4.1 15.9 - - + -
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Residues in contact with GLN 461 (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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163A LEU* 4.2 5.7 - - - +
457A ALA 3.2 16.3 + - - +
458A VAL* 2.8 26.5 + - - +
460A ILE* 1.3 77.9 - - - +
462A ASP* 1.3 70.0 + - - +
464A GLN* 3.8 20.6 + - - +
465A GLY 5.3 0.9 + - - -
471A TYR* 3.2 23.0 + - - -
477A ARG* 2.9 70.7 + - + +
478A MET* 3.2 33.0 - - + +
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Residues in contact with ASP 462 (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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163A LEU* 4.1 6.0 - - + +
164A ARG* 3.0 52.8 + - - +
167A ILE* 3.7 24.3 - - + +
168A ILE* 5.0 4.3 - - - +
458A VAL 3.7 3.6 - - - +
459A MET 3.1 9.4 + - - +
460A ILE 3.0 0.2 - - - -
461A GLN* 1.3 99.9 - - - +
463A MET* 1.3 61.5 + - - +
464A GLN 3.4 0.6 + - - -
465A GLY 4.4 5.9 + - - +
471A TYR* 2.6 25.5 + - - -
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Residues in contact with MET 463 (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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167A ILE* 3.8 40.4 - - + +
168A ILE* 6.0 0.9 - - + -
171A PHE* 4.0 8.3 - - + -
459A MET* 3.0 27.4 + - - +
460A ILE* 3.2 4.9 + - - +
462A ASP* 1.3 78.7 - - - +
464A GLN* 1.3 63.0 + - - +
465A GLY 3.4 5.9 + - - +
547A PRO* 3.6 34.5 - - + +
548A THR* 3.3 24.8 + - - -
551A VAL* 3.9 11.6 - - + +
599A LEU* 3.5 44.9 - - + +
601A LEU* 5.5 0.2 - - - -
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Residues in contact with GLN 464 (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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460A ILE* 2.9 32.3 + - + +
461A GLN* 3.8 21.0 + - - +
462A ASP 3.4 2.2 - - - -
463A MET* 1.3 77.7 - - - +
465A GLY* 1.3 55.6 + - - +
484A ASP* 2.8 42.2 + - - +
485A THR* 5.3 0.3 - - - -
548A THR* 2.6 20.3 + - - -
551A VAL* 4.1 13.5 - - + +
552A THR* 4.8 1.2 + - - -
555A PHE* 3.7 11.1 - - - -
913B C 4.0 7.3 + - - +
914B A 4.0 6.6 - - - +
923B G 6.1 1.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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