Contacts of the helix formed by residues 454 - 470 (chain A) in PDB entry 5FMH
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 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A ASP* 4.0 1.7 + - - +
450A ARG* 4.2 10.9 + - - -
452A VAL* 3.6 28.6 + - + +
453A GLU* 1.3 89.0 + - + +
455A HIS* 1.3 64.3 + - - +
457A HIS* 3.3 6.3 + - + +
458A ALA* 3.1 18.4 + - - +
480A SER* 2.9 41.9 + - - +
481A MET 3.4 17.0 + - - +
482A PHE* 3.7 29.6 - + + +
494A ALA 5.5 1.6 - - - -
495A ILE* 6.2 0.9 - - - -
496A GLY 6.0 0.4 - - - -
1000A FAD 3.1 13.0 + - - +
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Residues in contact with HIS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A THR* 3.9 28.3 - - + +
171A MET* 4.2 16.8 - - + +
173A PRO* 4.1 18.4 - - + +
205A PHE* 4.4 6.0 - + - -
454A HIS* 1.3 70.7 - - - +
456A ASP* 1.3 63.5 + - - +
458A ALA* 3.2 5.1 + - - +
459A VAL* 3.0 43.1 + - + +
483A TRP* 3.8 13.8 - + + -
528A ILE* 3.7 24.4 - - + +
530A SER* 3.5 15.4 + - - -
531A GLU* 5.1 3.8 - - + -
1000A FAD 3.1 41.6 + - + +
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Residues in contact with ASP 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A HIS* 4.1 0.4 - - - +
455A HIS* 1.3 77.8 + - - +
457A HIS* 1.3 58.0 + - - +
459A VAL* 3.2 6.3 + - - +
460A VAL* 2.9 41.1 + - - +
478A HIS* 2.7 30.3 + - - -
480A SER* 3.4 0.9 - - - +
481A MET* 2.9 44.2 + - - +
483A TRP* 4.9 0.4 - - + -
530A SER* 3.7 27.6 + - - +
535A GLU* 4.0 11.8 - - - +
589A ARG* 3.1 6.6 + - - -
1000A FAD 4.5 0.8 + - - -
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Residues in contact with HIS 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 5.6 0.8 - - - +
437A GLY* 3.1 43.2 + - - -
438A ASP* 5.5 0.2 + - - -
440A ALA* 4.7 4.0 - - + +
442A PHE* 3.3 36.9 - + - -
452A VAL* 3.3 24.0 + - + +
454A HIS 3.3 6.9 + - - +
456A ASP* 1.3 79.4 - - - +
458A ALA* 1.3 53.1 + - - +
460A VAL* 4.9 0.4 - - - -
461A SER* 2.5 49.3 + - - -
476A TYR* 2.8 38.9 + + - -
480A SER* 3.2 21.2 + - - +
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Residues in contact with ALA 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A THR* 3.6 17.0 - - + -
142A ALA* 3.4 19.6 - - - +
437A GLY* 3.9 13.5 - - - -
454A HIS 3.1 6.7 + - - +
455A HIS 3.2 4.5 + - - +
457A HIS* 1.3 78.7 + - - +
459A VAL* 1.3 63.2 + - - +
461A SER* 3.9 4.5 - - - -
462A GLY* 3.0 17.0 + - - -
1000A FAD 3.4 35.0 - - - +
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Residues in contact with VAL 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A THR* 3.8 11.9 - - + -
145A ALA* 3.4 17.0 - - + +
205A PHE* 5.7 3.1 - - + -
455A HIS* 3.0 39.5 + - + +
456A ASP* 3.6 8.5 - - - +
458A ALA* 1.3 77.1 - - - +
460A VAL* 1.3 59.2 + - + +
463A ARG* 2.9 50.0 + - - +
530A SER* 5.5 0.7 - - - +
535A GLU* 4.2 6.5 - - - +
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Residues in contact with VAL 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ASP* 2.9 29.7 + - - +
459A VAL* 1.3 71.3 - - + +
461A SER* 1.3 61.8 + - - +
463A ARG* 3.4 17.9 + - - +
464A LEU* 2.9 29.7 + - + +
476A TYR* 3.9 7.2 - - + +
478A HIS* 3.7 40.6 - - + +
535A GLU* 3.5 32.1 - - - +
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Residues in contact with SER 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 3.6 21.4 - - - +
436A ALA* 3.8 6.1 - - - -
437A GLY 3.1 21.3 + - - -
457A HIS* 2.5 47.7 + - - -
458A ALA 3.7 0.7 + - - -
460A VAL* 1.3 70.6 - - - +
462A GLY* 1.3 61.5 + - - +
464A LEU* 4.4 0.4 - - - -
465A ALA* 2.8 31.5 + - - +
476A TYR* 3.8 12.0 - - - -
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Residues in contact with GLY 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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142A ALA* 3.6 17.7 - - - -
145A ALA* 4.3 0.2 - - - -
146A ALA* 3.2 20.4 - - - +
436A ALA* 3.8 11.0 - - - +
458A ALA 3.0 20.1 + - - -
459A VAL 3.8 0.4 - - - -
461A SER* 1.3 79.0 + - - +
463A ARG* 1.3 61.3 + - - +
465A ALA* 3.4 1.0 + - - +
466A GLY 3.0 18.5 + - - -
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Residues in contact with ARG 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA* 3.8 16.8 - - + +
148A ARG* 4.6 19.7 - - - +
149A SER* 2.7 38.4 + - - +
459A VAL* 2.9 33.5 + - - +
460A VAL* 3.7 18.0 - - - +
462A GLY* 1.3 74.4 - - - +
464A LEU* 1.3 63.3 + - - +
466A GLY 3.2 1.4 + - - -
467A GLU* 3.1 24.8 + - - +
535A GLU* 2.8 43.6 + - - -
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Residues in contact with LEU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 4.2 8.1 - - + -
460A VAL* 2.9 19.2 + - + +
461A SER* 3.8 4.9 - - - +
462A GLY 3.2 0.2 - - - -
463A ARG* 1.3 74.7 - - - +
465A ALA* 1.3 60.8 + - - +
467A GLU* 3.0 16.1 + - + +
468A ASN* 2.9 36.1 + - - +
474A LYS* 3.5 37.0 - - + +
475A PRO 3.6 5.4 - - - +
476A TYR* 3.4 51.8 - - + +
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Residues in contact with ALA 465 (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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257A LEU* 3.7 29.8 - - + -
427A LEU* 4.3 8.0 - - + +
434A TRP* 4.2 16.1 - - + -
436A ALA* 4.4 4.0 - - + -
461A SER 2.8 21.4 + - - +
462A GLY 3.7 4.5 - - - +
464A LEU* 1.3 74.5 - - - +
466A GLY* 1.3 56.4 + - - +
468A ASN* 3.3 7.1 + - - +
469A MET* 2.9 37.5 + - - +
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Residues in contact with GLY 466 (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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146A ALA* 3.9 10.9 - - - +
149A SER* 3.9 4.5 - - - -
150A ILE* 3.4 37.1 - - - +
462A GLY 3.0 12.4 + - - -
463A ARG 3.2 4.2 + - - -
464A LEU 3.2 0.2 - - - -
465A ALA* 1.3 75.4 - - - +
467A GLU* 1.3 60.3 + - - +
469A MET* 3.5 2.8 + - - -
470A THR* 3.0 22.3 + - - +
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Residues in contact with GLU 467 (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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149A SER* 3.1 19.1 + - - +
153A ARG* 3.6 18.1 - - - +
463A ARG* 3.1 27.3 - - - +
464A LEU* 3.0 12.6 + - + +
466A GLY* 1.3 75.7 - - - +
468A ASN* 1.3 59.2 + - - +
470A THR* 2.7 24.4 + - - -
472A ALA* 3.0 31.4 + - + +
474A LYS* 2.7 35.8 + - - +
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Residues in contact with ASN 468 (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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255A LYS* 5.0 1.2 + - - -
426A GLU* 3.1 28.5 + - + +
434A TRP* 3.4 30.9 - - + +
464A LEU* 2.9 26.3 + - - +
465A ALA 3.8 1.8 - - - +
467A GLU* 1.3 72.7 - - - +
469A MET* 1.3 60.1 + - - +
470A THR 3.1 1.8 - - - -
471A GLY* 3.0 17.5 + - - -
472A ALA* 3.5 9.2 + - - +
473A ALA* 3.2 9.7 + - - +
474A LYS 2.9 43.7 + - - +
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Residues in contact with MET 469 (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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134A PHE* 3.6 21.9 - - + -
136A LEU* 3.8 18.6 - - + -
146A ALA* 5.1 0.2 - - - -
150A ILE* 4.0 14.8 - - + -
255A LYS* 2.7 50.2 + - + +
256A CYS 3.6 6.1 - - - -
257A LEU* 3.6 41.3 - - - +
434A TRP* 3.5 29.4 - - + -
465A ALA* 2.9 29.0 + - - +
466A GLY* 3.7 7.2 - - - +
468A ASN* 1.3 75.2 - - - +
470A THR* 1.3 55.0 + - - +
471A GLY 3.5 0.4 - - - -
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Residues in contact with THR 470 (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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134A PHE* 3.9 24.2 - - + -
150A ILE* 4.0 22.9 - - + +
153A ARG* 2.8 37.3 + - + -
154A ASP* 4.4 10.8 - - + +
255A LYS* 4.8 2.0 - - - +
466A GLY 3.0 14.4 + - - +
467A GLU 2.7 18.5 + - - -
468A ASN 3.1 0.2 - - - -
469A MET* 1.3 77.0 - - - +
471A GLY* 1.3 55.7 + - - +
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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
------------------------------------------------------------
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