Contacts of the helix formed by residues 417 - 435 (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 PHE 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A PRO* 3.5 44.6 - - + -
158A PHE 3.5 11.7 - - - +
159A HIS* 3.9 4.7 - - + +
221A PHE* 4.5 18.2 - + - -
415A VAL* 3.8 31.4 - - + -
416A VAL* 1.3 76.8 - - - +
418A LEU* 1.3 66.4 + - - +
419A ASP* 4.5 6.5 - - + +
420A ASN* 3.1 17.4 + - + +
421A ILE* 3.0 23.0 + - - +
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Residues in contact with LEU 418 (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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158A PHE* 2.8 43.1 + - + +
159A HIS* 3.8 14.3 - - - +
160A ALA* 4.7 6.1 - - - -
163A LEU* 4.0 44.4 - - + -
280A THR* 5.2 9.9 - - + -
284A LEU* 4.8 11.2 - - + -
416A VAL 3.8 0.2 + - - -
417A PHE* 1.3 70.3 - - - +
419A ASP* 1.3 61.2 + - - +
421A ILE* 2.9 14.5 + - + +
422A LEU* 2.8 52.9 + - + +
458A VAL* 5.0 2.0 - - + -
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Residues in contact with ASP 419 (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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158A PHE* 4.6 8.6 + - - +
280A THR* 5.0 15.7 + - - +
283A ARG* 4.3 15.7 + - - +
417A PHE* 3.3 4.4 - - + +
418A LEU* 1.3 80.2 - - - +
420A ASN* 1.3 57.6 + - - +
422A LEU* 3.9 8.7 - - - +
423A GLU* 3.0 29.8 + - - +
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Residues in contact with ASN 420 (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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416A VAL* 4.0 9.7 - - - +
417A PHE* 3.1 19.8 + - + +
419A ASP* 1.3 76.0 - - - +
421A ILE* 1.3 59.8 + - - +
423A GLU* 3.9 5.4 - - - +
424A GLU* 2.9 34.1 + - - +
475A TRP* 3.8 21.8 - - - -
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Residues in contact with ILE 421 (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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160A ALA* 3.6 29.4 - - + -
416A VAL* 3.4 20.9 - - + +
417A PHE 3.0 18.9 + - - +
418A LEU* 2.9 12.9 + - + +
420A ASN* 1.3 75.3 - - - +
422A LEU* 1.3 61.9 + - + +
424A GLU* 3.4 1.4 + - - +
425A THR* 2.8 43.0 + - - +
458A VAL* 4.1 19.7 - - + -
473A PHE* 3.5 22.4 - - + -
475A TRP* 3.6 13.0 - - + -
478A MET* 4.1 17.9 - - + -
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Residues in contact with LEU 422 (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* 5.8 0.9 - - + -
280A THR* 6.5 1.3 - - + -
283A ARG* 3.8 43.7 - - - +
284A LEU* 4.8 14.6 - - + -
418A LEU* 2.8 41.7 + - + +
419A ASP* 3.9 5.4 - - - +
421A ILE* 1.3 77.7 - - + +
423A GLU* 1.3 57.4 + - - +
425A THR* 3.9 2.9 - - - -
426A LYS* 2.9 31.5 + - - +
451A ASP* 4.2 2.3 - - - +
454A GLY* 5.6 1.3 - - - -
455A ILE* 4.2 22.4 - - + -
458A VAL* 4.0 32.5 - - + -
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Residues in contact with GLU 423 (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* 4.4 8.9 + - - +
419A ASP 3.0 18.5 + - - +
420A ASN* 3.9 7.4 - - - +
422A LEU* 1.3 77.4 - - - +
424A GLU* 1.3 60.9 + - - +
426A LYS* 3.4 25.6 + - - +
427A GLU* 3.0 55.8 + - - +
447A GLU* 5.2 1.4 - - - +
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Residues in contact with GLU 424 (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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420A ASN* 2.9 24.6 + - - +
423A GLU* 1.3 74.8 - - - +
425A THR* 1.3 67.1 + - - +
427A GLU* 2.8 31.2 + - - +
428A LYS* 3.0 21.9 + - + +
475A TRP* 3.6 33.1 - - + -
479A LEU* 4.8 9.2 - - + -
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Residues in contact with THR 425 (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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421A ILE* 2.8 21.6 + - - +
422A LEU* 3.9 3.4 - - - -
424A GLU* 1.3 76.4 - - - +
426A LYS* 1.3 63.9 + - - +
428A LYS* 3.2 1.9 + - - +
429A MET* 2.9 37.3 + - + +
454A GLY* 3.4 34.8 - - - +
457A ALA* 4.3 0.4 - - + -
458A VAL* 3.8 8.8 - - + +
475A TRP* 4.6 1.0 - - - -
478A MET* 3.6 40.4 - - - +
479A LEU* 3.7 10.7 - - + +
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Residues in contact with LYS 426 (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* 4.5 6.5 - - - +
422A LEU 2.9 19.9 + - - +
423A GLU* 3.4 22.9 + - - +
425A THR* 1.3 77.3 - - - +
427A GLU* 1.3 57.6 + - - +
429A MET* 3.3 1.6 + - - +
430A HIS* 2.8 29.1 + - - +
447A GLU* 3.1 56.0 + - - +
448A GLU* 4.9 3.8 + - - +
450A ALA* 3.6 15.2 - - + +
451A ASP* 3.6 39.7 - - - +
454A GLY* 4.6 1.3 - - - -
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Residues in contact with GLU 427 (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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423A GLU* 3.0 39.5 + - - +
424A GLU* 2.8 31.7 - - - +
426A LYS* 1.3 76.4 - - + +
428A LYS* 1.3 63.0 + - - +
430A HIS* 3.3 8.6 + - - +
431A GLU* 3.0 34.6 + - - +
447A GLU* 5.4 5.4 - - - +
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Residues in contact with LYS 428 (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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424A GLU 3.0 13.4 + - - +
425A THR 3.2 8.5 + - - +
427A GLU* 1.3 78.4 - - - +
429A MET* 1.3 64.7 - - + +
431A GLU* 3.1 25.6 + - + +
432A VAL* 3.1 27.2 + - + +
479A LEU* 3.8 45.3 + - + +
481A PHE* 3.1 37.2 - - - -
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Residues in contact with MET 429 (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 THR* 2.9 27.5 + - + +
426A LYS 3.7 3.8 - - - +
428A LYS* 1.3 80.3 - - + +
430A HIS* 1.3 65.7 + - - +
432A VAL* 3.2 5.5 + - - +
433A MET* 2.9 26.4 + - + +
450A ALA* 3.8 14.8 - - - +
453A VAL* 3.8 16.4 - - + -
454A GLY* 3.7 20.6 - - - +
457A ALA* 4.3 6.3 - - + -
478A MET 3.8 18.2 - - - +
479A LEU* 3.4 28.3 - - - +
480A SER 4.2 8.1 - - - +
481A PHE* 4.5 5.2 - - + -
487A PRO* 4.1 2.9 - - + -
938B A 4.0 26.4 + - - +
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Residues in contact with HIS 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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426A LYS 2.8 17.7 + - - +
427A GLU* 3.5 10.3 - - - +
429A MET* 1.3 77.6 - - - +
431A GLU* 1.3 61.1 + - + +
433A MET* 3.2 8.7 - - - +
434A LYS* 3.1 37.0 + - - +
440A TYR* 2.9 36.8 + + - -
446A PRO* 3.8 11.7 - - + +
447A GLU* 3.2 39.9 + - + +
450A ALA* 3.8 13.4 - - + +
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Residues in contact with GLU 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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427A GLU* 3.0 27.2 + - - +
428A LYS* 3.3 22.4 + - + +
430A HIS* 1.3 74.5 - - + +
432A VAL* 1.3 65.4 + - + +
434A LYS* 3.2 24.1 + - + +
435A LYS* 3.5 24.0 + - - +
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Residues in contact with VAL 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 LYS* 3.1 22.8 + - + +
429A MET* 3.2 9.2 + - - +
431A GLU* 1.3 77.1 - - + +
433A MET* 1.3 63.5 + - - +
435A LYS* 3.3 36.7 + - + +
436A ASN* 4.4 1.4 + - - +
481A PHE* 3.7 40.6 - - + -
938B A 3.6 41.5 - - + +
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Residues in contact with MET 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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429A MET* 2.9 12.7 + - + +
430A HIS* 3.2 11.4 - - - +
432A VAL* 1.3 78.0 - - - +
434A LYS* 1.3 61.5 + - - +
435A LYS 3.4 0.9 + - - -
436A ASN* 3.6 11.6 + - - +
439A LYS* 5.9 0.2 - - - +
440A TYR* 3.5 34.5 + - + +
443A ILE* 3.9 20.9 - - + -
446A PRO* 3.6 18.2 - - - +
449A VAL* 4.0 11.9 - - + +
450A ALA* 3.5 39.9 - - + +
453A VAL* 5.1 3.1 - - + -
607A MET* 3.4 21.2 - - - +
936B G 6.0 0.2 + - - -
938B A 3.9 13.6 - - - +
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Residues in contact with LYS 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 HIS* 3.1 40.6 + - - +
431A GLU* 3.2 16.1 + - + +
433A MET* 1.3 75.1 - - - +
435A LYS* 1.3 64.9 + - - +
436A ASN 3.1 2.2 + - - -
437A GLU* 3.7 17.0 + - - +
440A TYR* 3.9 31.1 - - + +
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Residues in contact with LYS 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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431A GLU* 3.5 27.3 + - - +
432A VAL* 3.3 31.0 + - + +
434A LYS* 1.3 77.4 - - - +
436A ASN* 1.3 57.7 + - - +
437A GLU* 3.4 8.7 + - - +
481A PHE* 6.1 2.7 - - + -
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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