Contacts of the helix formed by residues 443 - 458 (chain A) in PDB entry 4Y2P
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 THR 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A LEU* 3.8 6.7 - - - -
442A VAL* 1.3 76.9 - - - +
444A GLU* 1.3 64.3 + - - +
445A GLU* 3.3 18.1 + - - +
446A GLU* 2.9 43.3 + - - +
447A ILE* 3.0 22.7 + - - +
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Residues in contact with GLU 444 (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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402A SER* 4.5 0.2 + - - -
406A LYS* 2.8 36.9 + - - -
438A LEU* 3.9 18.7 - - + +
443A THR* 1.3 74.5 - - - +
445A GLU* 1.3 75.7 + - - +
447A ILE* 3.4 3.9 + - - +
448A GLN* 2.9 53.9 + - + +
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Residues in contact with GLU 445 (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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443A THR* 3.2 18.3 - - - +
444A GLU* 1.3 90.2 + - - +
446A GLU* 1.3 59.3 + - + +
448A GLN* 3.2 8.1 + - - +
449A PHE* 3.0 25.6 + - - +
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Residues in contact with GLU 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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231A SER* 4.4 5.2 + - - -
272A TYR* 3.3 31.3 + - + +
275A ARG* 3.2 33.5 + - - +
276A TYR* 3.9 12.0 + - - -
441A MET 4.2 1.9 - - - +
442A VAL* 3.5 12.7 - - + -
443A THR* 2.9 43.6 + - - +
445A GLU* 1.3 74.8 - - + +
447A ILE* 1.3 65.8 + - - +
449A PHE* 3.3 10.3 + - - +
450A TYR* 3.2 23.5 + - + -
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Residues in contact with ILE 447 (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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402A SER* 4.1 7.6 - - - +
405A PHE* 3.9 16.8 - - + +
406A LYS* 3.9 41.3 - - + +
409A PHE* 4.4 8.5 - - + -
438A LEU* 3.9 18.4 - - + -
442A VAL* 4.1 18.8 - - + +
443A THR 3.0 17.3 + - - +
444A GLU* 3.6 8.5 - - - +
446A GLU* 1.3 76.5 - - - +
448A GLN* 1.3 73.9 + - - +
450A TYR* 3.1 10.3 + - - +
451A VAL* 2.9 34.1 + - + +
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Residues in contact with GLN 448 (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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402A SER* 3.8 21.1 + - - -
444A GLU* 2.9 41.9 + - + +
445A GLU* 3.2 8.7 + - - +
447A ILE* 1.3 82.8 - - - +
449A PHE* 1.3 57.7 + - - +
451A VAL* 3.6 21.4 - - - +
452A GLN* 2.8 31.8 + - - +
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Residues in contact with PHE 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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234A PRO* 3.4 35.2 - - + -
270A SER* 3.7 6.7 - - - -
271A TRP* 3.9 18.2 - + - -
272A TYR* 3.4 47.3 - + + +
445A GLU 3.0 13.6 + - - +
446A GLU 3.5 9.0 - - - +
447A ILE 3.2 0.2 - - - -
448A GLN* 1.3 73.6 - - - +
450A TYR* 1.3 70.0 + + - +
452A GLN* 3.1 30.1 + - - +
453A GLN* 3.0 53.8 + - + +
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Residues in contact with TYR 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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269A GLU 4.2 4.5 - - - -
270A SER* 3.8 23.6 - - - -
272A TYR* 3.9 18.4 - + - -
273A SER* 2.7 32.3 + - - -
275A ARG* 3.0 28.9 + - - -
405A PHE* 3.9 19.3 - + + -
409A PHE* 3.7 37.9 - + - -
442A VAL* 5.5 2.0 - - + -
446A GLU* 3.2 26.8 + - + -
447A ILE* 3.1 9.4 + - - +
449A PHE* 1.3 79.7 - + - +
451A VAL* 1.3 65.0 + - - +
453A GLN* 3.3 4.1 + - - -
454A PHE* 3.0 41.4 + + - -
528A MET* 3.8 5.1 - - + +
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Residues in contact with VAL 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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401A LEU* 3.8 21.8 - - + +
402A SER* 3.6 34.5 - - - +
405A PHE* 4.2 8.7 - - + -
447A ILE* 2.9 22.9 + - + +
448A GLN* 3.6 27.6 - - - +
449A PHE 3.2 0.2 - - - -
450A TYR* 1.3 76.0 - - - +
452A GLN* 1.3 66.4 + - + +
454A PHE 3.2 0.2 + - - -
455A LYS* 3.1 43.2 + - - +
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Residues in contact with GLN 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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448A GLN 2.8 17.9 + - - +
449A PHE* 3.1 25.8 + - - +
451A VAL* 1.3 76.7 - - + +
453A GLN* 1.3 98.0 + - - +
455A LYS* 3.2 24.4 + - + +
456A LYS* 3.9 12.1 + - - +
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Residues in contact with GLN 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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270A SER* 4.6 7.6 + - - +
271A TRP* 4.9 2.9 + - - -
292A ASP* 4.2 6.1 - - - +
297A GLY* 3.4 33.1 + - - +
298A GLU* 4.0 11.7 + - - +
449A PHE* 3.0 49.2 + - + +
450A TYR* 3.7 7.4 - - - +
452A GLN* 1.3 102.6 - - - +
454A PHE* 1.3 70.9 + - + +
456A LYS* 3.0 44.5 + - - +
457A SER 4.3 1.2 + - - -
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Residues in contact with PHE 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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268A PRO* 3.4 24.2 - - + -
269A GLU 3.3 27.6 - - - -
296A TYR* 3.6 20.2 - + + -
297A GLY 6.0 0.4 - - - +
401A LEU* 4.2 21.8 - - + +
405A PHE* 3.3 18.2 - + + -
450A TYR* 3.0 34.8 + + - +
451A VAL 3.8 2.7 - - - +
453A GLN* 1.3 80.3 - - + +
455A LYS* 1.3 60.3 + - - +
456A LYS 3.1 1.8 - - - -
457A SER 4.9 0.4 - - - +
458A GLY* 2.9 43.1 + - - +
459A PHE* 3.6 32.8 - + + -
462A PRO* 4.1 8.3 - - + -
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Residues in contact with LYS 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 LEU* 3.7 15.7 - - + -
451A VAL* 3.1 35.6 + - + +
452A GLN* 3.2 16.3 + - + +
454A PHE* 1.3 79.1 - - - +
456A LYS* 1.3 63.4 + - + +
458A GLY 4.7 1.0 + - - -
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Residues in contact with LYS 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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297A GLY 3.1 25.8 - - - +
298A GLU* 4.1 16.2 - - - +
452A GLN* 4.0 10.1 - - - +
453A GLN* 3.0 50.1 - - - +
454A PHE 3.1 1.0 - - - -
455A LYS* 1.3 81.4 - - - +
457A SER* 1.3 68.7 + - - +
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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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295A GLY 4.3 10.5 - - - -
296A TYR 5.8 0.2 - - - -
297A GLY 4.6 9.0 + - - +
299A SER 4.8 3.3 + - - -
301A ALA* 3.6 31.9 + - - +
398A GLU* 4.8 0.5 - - - +
453A GLN 4.3 1.2 + - - -
454A PHE* 3.7 2.0 + - - +
456A LYS* 1.3 88.4 + - - +
458A GLY* 1.3 66.3 + - - +
459A PHE 3.7 0.7 + - - -
460A ARG* 4.3 9.9 + - - +
461A GLY 5.1 1.6 + - - -
462A PRO* 5.9 0.2 - - - -
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Residues in contact with GLY 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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295A GLY 4.4 2.1 - - - +
398A GLU* 3.5 16.6 - - - -
454A PHE* 2.9 30.7 + - - +
455A LYS 4.6 0.6 + - - -
456A LYS 3.8 0.4 - - - -
457A SER* 1.3 81.9 - - - +
459A PHE* 1.3 66.7 + - - -
462A PRO* 3.5 18.2 - - - +
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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
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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