Contacts of the helix formed by residues 448 - 463 (chain A) in PDB entry 5FI2
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 SER 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A ASN* 2.9 22.9 + - - -
436A GLY 4.5 0.9 - - - -
445A ARG* 4.1 6.5 - - - +
447A LEU* 1.3 74.5 - - - +
449A PRO* 1.3 73.5 - - - +
450A GLU* 4.0 14.3 + - - +
451A ALA* 3.1 25.6 + - - +
452A VAL* 3.1 21.5 + - - +
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Residues in contact with PRO 449 (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 GLY* 4.0 14.8 - - - +
445A ARG* 3.4 31.2 - - - +
447A LEU 4.1 0.9 - - - +
448A SER* 1.3 85.2 - - - +
450A GLU* 1.3 56.4 + - - +
452A VAL* 3.4 3.3 + - + +
453A ARG* 2.9 41.3 + - - +
531D ASN* 6.3 0.2 - - + -
534D HIS 4.4 14.1 - - - +
535D PHE* 4.8 3.1 - - - -
536D ALA* 4.1 31.6 - - + +
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Residues in contact with GLU 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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296A VAL* 4.1 7.7 - - + +
300A GLY* 4.1 11.6 - - - -
301A THR* 3.1 42.5 + - - +
448A SER* 3.2 11.7 + - - +
449A PRO* 1.3 76.5 - - - +
451A ALA* 1.3 65.0 + - - +
453A ARG* 3.6 26.5 - - - +
454A ASN* 3.1 32.4 + - - +
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TYR* 4.7 0.5 - - - -
293A ALA* 3.5 26.8 - - - +
296A VAL* 3.6 11.9 - - - +
297A ASN* 3.7 13.9 - - + +
447A LEU* 4.3 6.7 - - + -
448A SER* 3.1 26.1 + - - +
450A GLU* 1.3 79.7 - - - +
452A VAL* 1.3 52.9 + - - +
454A ASN* 3.9 2.3 - - - +
455A THR* 2.8 35.7 + - - -
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Residues in contact with VAL 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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293A ALA* 5.5 0.2 - - - -
433A LEU* 3.1 39.9 - - + +
436A GLY* 4.1 14.6 - - - -
437A GLY* 3.7 26.5 - - - +
447A LEU* 3.7 21.8 - - + -
448A SER 3.1 15.8 + - - +
449A PRO 3.9 2.9 - - - +
451A ALA* 1.3 73.2 - - - +
453A ARG* 1.3 60.2 + - - +
455A THR* 3.3 6.2 + - - -
456A LEU* 2.9 37.8 + - + +
529D TYR 5.4 1.3 - - - +
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Residues in contact with ARG 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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449A PRO* 2.9 28.3 + - - +
450A GLU* 3.6 33.0 + - - +
452A VAL* 1.3 74.4 - - - +
454A ASN* 1.3 69.7 + - - +
456A LEU* 3.2 2.1 + - - +
457A SER* 2.8 33.1 + - - +
473D PHE 5.5 1.8 + - - +
527D HIS* 3.6 39.9 + - + +
529D TYR* 3.3 26.1 + - - +
530D ASP* 3.3 27.7 + - - +
538D LYS* 3.8 18.3 - - - +
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Residues in contact with ASN 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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292A TYR* 3.1 26.0 + - + +
296A VAL* 3.4 13.5 - - + +
301A THR* 2.5 33.7 + - - -
450A GLU 3.1 18.1 + - - +
451A ALA 3.9 2.2 - - - +
453A ARG* 1.3 88.9 + - - +
455A THR* 1.3 62.9 + - - +
457A SER* 3.4 4.1 + - - -
458A LEU* 3.2 28.9 + - - +
473D PHE* 3.3 28.6 - - + +
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Residues in contact with THR 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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289A PRO* 3.6 26.5 - - + +
292A TYR* 3.3 19.1 - - + -
293A ALA* 3.3 19.9 - - + +
332A MET* 4.1 1.2 - - + +
433A LEU* 4.5 11.9 - - + -
451A ALA 2.8 20.1 + - - -
452A VAL* 3.6 7.0 - - - -
453A ARG 3.2 0.4 - - - -
454A ASN* 1.3 78.8 - - - +
456A LEU* 1.3 57.3 + - + +
458A LEU* 3.2 2.9 + - - +
459A MET* 3.1 53.2 + - - +
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Residues in contact with LEU 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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433A LEU* 3.5 28.7 - - + +
434A ALA 5.7 0.2 - - - -
452A VAL* 2.9 26.9 + - + +
453A ARG 3.7 1.3 - - - +
455A THR* 1.3 73.6 - - + +
457A SER* 1.3 66.2 + - - +
459A MET* 4.3 7.6 - - - -
460A HIS* 3.2 20.6 + - - +
478A PRO* 3.5 22.8 - - + +
490A VAL* 3.6 37.9 - - + -
492A PRO* 4.4 8.7 - - + -
529D TYR* 3.5 39.1 - - + +
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Residues in contact with SER 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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453A ARG* 2.8 23.6 + - - +
454A ASN* 3.5 7.6 - - - -
455A THR 3.3 0.2 - - - -
456A LEU* 1.3 78.0 - - - +
458A LEU* 1.3 58.7 + - - +
460A HIS* 3.2 19.2 - - - +
461A SER* 3.4 11.1 + - - -
460D HIS* 5.5 3.3 + - - -
472D ALA 5.0 2.2 - - - -
473D PHE* 4.2 26.3 + - - -
527D HIS* 3.4 26.9 + - - -
529D TYR* 3.6 11.7 - - - -
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Residues in contact with LEU 458 (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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292A TYR* 3.9 19.3 - - + +
305A HIS* 4.2 5.8 - - + -
310A LYS* 3.4 28.9 - - - +
330A ASN* 5.2 0.2 - - + -
331A PRO* 3.5 35.4 - - + -
332A MET* 3.8 21.6 - - + +
454A ASN 3.2 13.5 + - - +
456A LEU 3.2 0.2 - - - -
457A SER* 1.3 78.7 - - - +
459A MET* 1.3 58.6 + - - +
460A HIS 3.3 0.2 - - - -
461A SER* 3.9 10.1 - - - +
462A CYS* 2.7 42.0 + - - +
463A GLY 3.6 0.5 + - - -
473D PHE* 3.9 19.3 - - + -
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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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289A PRO* 3.6 11.9 - - + -
332A MET* 3.8 15.9 - - + -
433A LEU* 4.5 4.3 - - + -
455A THR* 3.1 37.1 + - - +
456A LEU* 4.3 8.1 - - - -
457A SER 3.4 0.2 - - - -
458A LEU* 1.3 74.3 - - - +
460A HIS* 1.3 68.6 + - - +
463A GLY* 3.2 18.9 + - - +
464A MET* 4.8 3.1 + - - +
471A PHE* 5.8 0.7 - - - -
477A LEU 4.7 0.5 - - - +
478A PRO* 3.9 10.8 - - + +
479A ALA* 3.3 51.8 + - - +
480A LYS* 4.0 9.2 - - + +
488A LEU* 4.1 16.2 - - + +
490A VAL* 4.3 15.7 - - + -
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Residues in contact with HIS 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 LEU 3.2 8.3 + - - +
457A SER 3.2 11.7 - - - +
459A MET* 1.3 80.4 - - - +
461A SER* 1.3 68.7 + - - +
463A GLY 4.9 0.2 + - - -
464A MET* 6.1 0.2 - - - +
468A SER* 4.1 4.7 - - - +
471A PHE* 5.4 2.6 - - - -
472A ALA* 3.6 42.3 + - + +
476A GLY* 4.8 7.3 - - - -
477A LEU 4.4 4.3 - - - +
478A PRO* 3.7 10.1 - - + +
527A HIS* 6.2 0.2 - + - -
528A ASN* 4.2 19.0 - - + -
529A TYR* 4.9 5.8 - + - -
457D SER* 5.7 2.1 + - - -
460D HIS* 3.6 37.0 + + - -
461D SER* 5.9 1.7 - - - -
529D TYR* 2.6 34.0 + + + +
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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
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310A LYS 5.1 0.2 + - - -
312A PRO* 3.7 32.3 - - - +
457A SER 3.4 13.4 + - - -
458A LEU* 3.8 7.8 + - - +
460A HIS* 1.3 88.6 - - - +
462A CYS* 1.3 75.3 + - - +
463A GLY 3.8 0.2 - - - -
468A SER* 3.2 20.2 - - - -
469A GLY* 5.0 0.5 + - - -
472A ALA* 5.2 2.9 - - - -
460D HIS* 5.7 2.7 - - - -
461D SER* 6.3 2.7 - - - -
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Residues in contact with CYS 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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311A GLU 3.8 2.5 - - - -
312A PRO* 3.5 32.3 - - + -
330A ASN* 3.4 31.6 - - - +
332A MET* 3.3 18.5 - - + +
333A VAL* 5.7 2.4 - - + +
458A LEU* 2.7 25.2 + - - +
461A SER* 1.3 93.2 - - - +
463A GLY* 1.3 61.1 + - - +
464A MET 3.6 0.7 + - - -
465A TYR* 4.3 4.5 + - - -
468A SER* 3.3 9.7 + - - -
480A LYS* 5.0 0.3 + - - -
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Residues in contact with GLY 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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332A MET* 4.6 0.7 - - - -
458A LEU 3.6 0.4 + - - -
459A MET* 3.2 13.2 + - - -
461A SER 3.8 0.2 - - - -
462A CYS* 1.3 78.8 - - - +
464A MET* 1.3 63.1 + - - +
465A TYR 3.5 1.8 - - - -
468A SER* 3.4 1.2 + - - -
479A ALA 3.3 17.3 - - - -
480A LYS* 3.2 34.6 + - - -
481A SER 3.2 15.4 + - - -
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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