Contacts of the helix formed by residues 434 - 446 (chain A) in PDB entry 1EAK
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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A ASP* 3.8 16.8 + - - -
418A GLY 4.0 7.7 + - - -
419A ALA* 3.6 18.8 + - - -
420A LEU 4.4 0.2 - - - -
431A PHE* 5.3 0.2 - - - -
432A ARG* 3.3 10.1 + - - +
433A LEU* 1.3 73.2 - - - +
435A GLN* 1.3 68.7 + - - +
436A ASP* 3.6 7.6 + - - +
437A ASP* 2.7 38.8 + - - +
438A ILE* 2.9 10.8 + - - +
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Residues in contact with GLN 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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432A ARG* 4.1 10.8 - - - +
433A LEU 3.7 2.0 + - - -
434A SER* 1.3 72.4 + - - +
436A ASP* 1.3 55.0 + - - +
438A ILE* 3.0 13.9 + - + +
439A LYS* 2.7 39.8 + - + +
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Residues in contact with ASP 436 (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 SER* 3.0 36.0 + - - -
416A ASP* 4.0 17.4 - - - +
419A ALA* 3.4 7.9 - - + +
421A MET* 5.6 0.2 - - - +
434A SER* 3.6 11.7 + - - +
435A GLN* 1.3 78.1 - - - +
437A ASP* 1.3 58.2 + - - +
439A LYS* 3.3 13.9 + - - +
440A GLY* 2.9 25.8 + - - -
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Residues in contact with ASP 437 (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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151A TRP* 4.1 8.5 - - + -
411A LEU* 4.7 1.6 - - - +
419A ALA* 3.6 7.0 - - - +
420A LEU* 2.7 29.9 + - - +
421A MET* 3.3 33.8 + - - +
433A LEU* 3.4 21.0 - - + +
434A SER* 2.7 32.3 + - - +
436A ASP* 1.3 74.0 - - - +
438A ILE* 1.3 57.2 + - - +
440A GLY* 2.8 18.4 + - - -
441A ILE* 2.8 19.1 + - - +
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Residues in contact with ILE 438 (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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154A VAL* 4.4 18.2 - - + -
432A ARG* 4.5 12.1 - - - +
433A LEU* 3.8 39.5 - - + +
434A SER 2.9 13.6 + - - +
435A GLN* 3.5 9.0 - - + +
437A ASP* 1.3 75.4 - - - +
439A LYS* 1.3 61.4 + - - +
441A ILE* 4.2 6.7 - - - -
442A GLN* 2.9 58.3 + - + +
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Residues in contact with LYS 439 (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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435A GLN* 2.7 23.9 + - + +
436A ASP* 3.6 14.6 - - - +
438A ILE* 1.3 73.3 - - - +
440A GLY* 1.3 57.3 + - - +
442A GLN* 4.3 3.9 - - - +
443A GLU* 3.1 45.3 + - + +
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Residues in contact with GLY 440 (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 LEU* 3.4 20.0 - - - +
436A ASP* 2.9 11.3 + - - -
437A ASP* 2.8 8.8 + - - -
439A LYS* 1.3 76.6 - - - +
441A ILE* 1.3 63.4 + - - +
442A GLN 3.4 0.2 + - - -
443A GLU* 3.5 20.8 + - - +
444A LEU* 3.5 8.1 + - - +
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Residues in contact with ILE 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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151A TRP* 3.6 35.0 - - + -
154A VAL* 3.7 24.5 - - + -
155A THR* 3.5 18.8 - - + -
157A LEU* 4.6 1.6 - - + -
409A MET* 3.8 20.2 - - + -
411A LEU* 3.6 22.1 - - + +
437A ASP 2.8 17.8 + - - +
438A ILE* 3.8 5.4 - - - +
440A GLY* 1.3 71.3 - - - -
442A GLN* 1.3 59.7 + - + +
444A LEU* 3.1 6.9 + - + +
445A TYR* 2.8 57.1 + - + +
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Residues in contact with GLN 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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154A VAL* 2.8 37.8 + - - +
438A ILE* 2.9 38.6 + - + +
439A LYS* 4.3 3.5 - - - +
440A GLY 3.3 0.4 - - - -
441A ILE* 1.3 79.4 - - + +
443A GLU* 1.3 62.7 + - - +
444A LEU 2.8 4.9 - - - -
446A GLY* 2.4 41.8 + - - +
447A ALA* 3.2 26.4 - - - +
448A SER 4.2 0.6 - - - +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LYS* 4.9 10.2 + - - -
439A LYS* 3.1 38.4 + - + +
440A GLY* 3.7 14.4 - - - +
441A ILE 3.5 0.2 - - - -
442A GLN* 1.3 77.1 - - - +
444A LEU* 1.3 66.7 + - + +
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LYS* 4.9 19.7 - - + -
117A PRO 4.0 20.9 - - - +
118A LYS* 3.6 27.7 - - + -
409A MET 3.2 27.1 - - - +
410A GLY* 4.1 14.4 - - - +
411A LEU* 4.6 9.4 - - + +
440A GLY 3.5 9.4 + - - +
441A ILE* 3.1 9.8 + - + +
442A GLN 2.7 1.4 + - - -
443A GLU* 1.3 88.5 - - + +
445A TYR* 1.3 72.2 + - + +
446A GLY 3.7 0.2 - - - -
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Residues in contact with TYR 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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118A LYS* 4.8 7.4 - - + +
119A TRP* 3.0 47.4 + - + -
121A LYS 4.7 0.2 - - - -
122A ASN* 4.6 11.9 - - - +
155A THR* 4.2 5.6 - - - -
156A PRO* 3.4 25.6 - - + +
157A LEU* 3.5 32.3 - - + -
409A MET* 2.5 36.7 + - + -
441A ILE* 2.8 43.4 + - + +
444A LEU* 1.3 88.1 - - + +
446A GLY* 1.3 67.8 + - - +
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Residues in contact with GLY 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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154A VAL 3.9 1.4 - - - +
155A THR* 3.8 6.1 - - - -
156A PRO* 3.3 8.5 - - - +
442A GLN* 2.4 39.3 + - - -
443A GLU 4.5 0.2 - - - -
444A LEU 3.7 0.4 - - - -
445A TYR* 1.3 73.0 - - - +
447A ALA* 1.3 67.0 + - - -
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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