Contacts of the helix formed by residues 440 - 452 (chain A) in PDB entry 1A4Y
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 GLU 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A SER* 1.3 74.2 - - - +
441A GLU* 1.3 66.7 + - - +
443A GLU* 3.2 9.5 - - - +
444A ASP* 2.8 40.7 + - - +
5B ARG* 3.8 18.5 - - + +
108B GLU* 3.3 24.6 + - - +
109B ASN* 5.6 8.9 + - - +
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Residues in contact with GLU 441 (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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439A SER* 3.1 9.9 + - - +
440A GLU* 1.3 85.6 + - - +
442A MET* 1.3 59.0 + - - +
443A GLU 3.0 0.7 - - - -
444A ASP* 2.6 29.0 + - + +
445A ARG* 2.8 30.9 + - - +
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Residues in contact with MET 442 (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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411A ASP* 2.9 58.6 - - - +
414A ILE* 3.2 27.6 - - + -
415A LEU* 3.9 11.4 - - + -
418A VAL* 3.6 18.2 - - + -
438A TRP* 3.8 13.7 - - + -
439A SER* 3.3 6.9 + - - +
441A GLU* 1.3 78.3 - - + +
443A GLU* 1.3 64.3 + - - +
445A ARG* 3.2 29.1 + - + +
446A LEU* 2.9 25.0 + - + +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A TRP* 2.6 40.5 + - + +
439A SER 2.8 14.5 + - - +
440A GLU* 3.2 17.7 - - - +
442A MET* 1.3 77.2 - - - +
444A ASP* 1.3 63.7 + - - +
446A LEU* 3.1 18.1 + - - +
447A GLN* 3.1 23.1 + - + +
460A SER 5.3 1.0 - - - +
5B ARG* 3.8 31.4 + - + +
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Residues in contact with ASP 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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440A GLU* 2.8 29.4 + - - +
441A GLU* 2.6 21.8 + - + +
443A GLU* 1.3 71.0 - - - +
445A ARG* 1.3 61.8 + - + +
447A GLN* 2.9 18.5 + - - +
448A ALA* 3.0 10.8 + - - +
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Residues in contact with ARG 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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415A LEU* 3.6 43.9 - - - +
418A VAL* 4.5 13.4 - - + +
441A GLU* 2.8 29.4 + - + +
442A MET* 3.6 26.7 - - + +
444A ASP* 1.3 72.6 - - + +
446A LEU* 1.3 62.8 + - - +
448A ALA* 3.0 24.4 - - - +
449A LEU* 3.0 9.0 + - - +
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Residues in contact with LEU 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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414A ILE* 4.8 6.7 - - + -
418A VAL* 4.6 15.7 - - + -
431A LEU* 6.0 2.2 - - + -
433A LEU* 4.6 6.7 - - + -
438A TRP* 3.2 50.0 - - + +
442A MET* 2.9 16.6 + - + +
443A GLU* 3.3 13.2 - - - +
444A ASP 3.0 0.4 - - - -
445A ARG* 1.3 77.6 - - - +
447A GLN* 1.3 60.4 + - - +
449A LEU* 3.3 23.5 - - + +
450A GLU* 3.1 32.5 + - - +
458A VAL* 4.4 22.0 - - + -
460A SER 5.3 0.7 - - - +
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Residues in contact with GLN 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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443A GLU* 3.1 19.9 + - + +
444A ASP* 2.9 11.7 + - - +
446A LEU* 1.3 73.9 - - - +
448A ALA* 1.3 66.4 + - - +
450A GLU* 2.8 30.7 - - - +
451A LYS* 3.3 17.6 + - - +
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Residues in contact with ALA 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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444A ASP 3.0 8.1 + - - +
445A ARG* 3.0 18.6 - - - +
447A GLN* 1.3 77.1 - - - +
449A LEU* 1.3 65.4 + - - +
451A LYS* 2.8 17.4 + - - +
452A ASP* 2.9 16.4 + - - +
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Residues in contact with LEU 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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418A VAL* 3.6 29.2 - - + -
421A VAL* 4.2 16.6 - - + -
422A ARG* 4.0 29.8 - - + +
431A LEU* 6.2 2.7 - - + -
445A ARG 3.0 7.0 + - - +
446A LEU* 3.3 22.9 - - + +
448A ALA* 1.3 78.8 - - - +
450A GLU* 1.3 58.2 + - - +
451A LYS 2.9 0.5 + - - -
452A ASP* 3.0 5.4 + - + +
453A LYS* 2.7 45.3 + - + +
456A LEU* 3.9 21.8 - - + -
458A VAL* 4.7 6.5 - - + -
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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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446A LEU* 3.1 23.9 + - - +
447A GLN* 2.8 41.6 - - - +
448A ALA 3.3 0.2 - - - -
449A LEU* 1.3 79.0 - - - +
451A LYS* 1.3 59.5 + - - +
453A LYS 4.3 5.2 - - - -
454A PRO* 3.9 20.1 - - - +
456A LEU* 4.6 8.7 - - - +
457A ARG* 5.6 0.9 - - - -
458A VAL* 3.1 48.7 - - + +
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Residues in contact with LYS 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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447A GLN* 3.3 13.5 + - - +
448A ALA* 2.8 10.6 + - - +
450A GLU* 1.3 79.0 - - - +
452A ASP* 1.3 63.8 + - - +
454A PRO* 4.0 11.1 - - - +
112D PRO* 5.6 3.5 - - - +
140D GLN* 5.8 0.5 + - - -
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Residues in contact with ASP 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 ALA* 2.9 15.5 + - + +
449A LEU* 3.9 5.8 - - + +
451A LYS* 1.3 78.4 - - - +
453A LYS* 1.3 60.3 + - + +
454A PRO* 3.3 4.6 - - - +
140D GLN* 5.7 1.1 - - - +
142D ARG* 2.6 34.1 + - - +
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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