Contacts of the helix formed by residues 434 - 446 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416B ASP* 4.1 7.1 + - - -
418B GLY 4.4 6.5 - - - -
419B ALA* 3.8 16.9 - - - +
420B LEU* 4.4 0.6 - - - +
432B ARG* 3.7 1.9 + - - -
433B LEU* 1.3 74.2 - - - +
435B GLN* 1.3 53.1 + - - +
436B ASP* 3.0 19.9 + - - +
437B ASP* 2.4 48.4 + - - -
438B ILE* 2.7 17.9 + - - -
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Residues in contact with GLN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B LEU 4.1 0.8 + - - -
434B SER* 1.3 71.8 + - - +
436B ASP* 1.3 63.4 + - - +
438B ILE* 3.7 23.3 - - - +
439B LYS* 2.8 31.0 + - + +
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Residues in contact with ASP 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B SER* 2.6 36.1 + - - -
416B ASP* 4.4 12.1 - - - +
419B ALA* 3.7 7.9 - - + +
421B MET* 5.4 0.2 - - - +
434B SER* 2.8 13.4 + - - +
435B GLN* 1.3 79.3 - - - +
437B ASP* 1.3 59.5 - - - +
439B LYS* 3.4 18.3 + - - +
440B GLY* 2.8 25.1 + - - -
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Residues in contact with ASP 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B TRP* 4.2 8.2 - - + -
411B LEU* 5.0 1.5 - - - +
419B ALA* 3.7 4.5 - - - +
420B LEU* 2.7 32.1 + - - +
421B MET* 3.0 37.2 + - - +
433B LEU* 3.5 16.8 - - + -
434B SER* 2.4 40.2 + - - +
436B ASP* 1.3 68.6 - - - +
438B ILE* 1.3 67.6 + - - +
439B LYS 3.1 0.9 - - - -
440B GLY* 3.0 2.1 + - - -
441B ILE* 2.8 27.3 + - - +
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Residues in contact with ILE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B VAL* 4.1 16.2 - - + -
433B LEU* 3.7 33.0 - - + +
434B SER 2.7 39.7 + - - +
435B GLN* 3.7 22.7 - - - +
437B ASP* 1.3 71.9 - - - +
439B LYS* 1.3 58.6 + - - +
441B ILE* 3.2 8.8 - - - +
442B GLN* 2.8 69.6 + - + +
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Residues in contact with LYS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B GLN* 2.8 25.9 + - + +
436B ASP* 3.4 17.4 + - - +
438B ILE* 1.3 79.3 - - - +
440B GLY* 1.3 64.7 + - - +
442B GLN* 3.9 4.7 - - - +
443B GLU* 3.1 42.8 + - + +
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Residues in contact with GLY 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B LEU* 3.6 19.6 - - - +
436B ASP 2.8 18.7 + - - -
437B ASP* 3.0 3.1 + - - -
439B LYS* 1.3 75.0 - - - +
441B ILE* 1.3 63.2 + - - +
443B GLU* 3.2 24.6 - - - +
444B LEU* 3.8 7.8 + - - +
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Residues in contact with ILE 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B TRP* 3.3 40.2 - - + -
154B VAL* 3.5 28.3 - - + -
155B THR* 3.6 16.6 - - + -
157B LEU* 4.7 2.9 - - + -
409B MET* 3.9 17.9 - - + -
411B LEU* 3.7 15.4 - - + +
437B ASP 2.8 14.9 + - - +
438B ILE* 3.2 12.6 - - - +
440B GLY* 1.3 71.1 - - - -
442B GLN* 1.3 62.5 + - - +
444B LEU* 3.0 20.5 + - - +
445B TYR* 3.0 36.5 + - + +
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Residues in contact with GLN 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B VAL* 3.2 26.3 + - - +
438B ILE* 2.8 44.2 + - + +
439B LYS* 4.0 4.8 + - - +
441B ILE* 1.3 77.6 - - + +
443B GLU* 1.3 57.9 + - - +
444B LEU 2.9 5.4 - - - -
446B GLY* 2.4 55.0 + - - +
447B ALA* 3.3 24.9 - - + +
448B SER* 4.6 1.6 + - - +
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LYS* 5.8 0.2 - - - -
439B LYS* 3.1 34.0 + - + +
440B GLY* 3.2 24.1 - - - +
442B GLN* 1.3 75.2 - - - +
444B LEU* 1.3 62.2 + - + +
446B GLY 4.5 0.2 - - - -
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LYS* 5.5 11.9 - - + -
117B PRO 4.6 4.0 - - - +
118B LYS* 2.8 55.3 + - + +
409B MET 3.4 23.3 - - - +
410B GLY* 3.7 24.5 - - - +
411B LEU* 4.3 13.7 - - + -
440B GLY 4.0 5.8 - - - +
441B ILE 3.0 9.5 + - - +
442B GLN 2.9 0.6 - - - -
443B GLU* 1.3 88.1 - - + +
445B TYR* 1.3 70.4 + - + +
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Residues in contact with TYR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LYS* 4.8 5.8 - - + +
119B TRP* 3.1 32.9 + + + -
121B LYS 4.7 0.9 - - - -
122B ASN* 4.7 8.1 - - - +
155B THR* 4.1 7.4 - - - -
156B PRO* 3.0 36.8 - - + +
157B LEU* 3.2 36.3 - - + -
409B MET* 2.3 67.7 + - + +
441B ILE* 3.0 28.0 + - + +
444B LEU* 1.3 87.4 - - + +
446B GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B VAL 3.7 2.1 - - - +
155B THR* 3.9 2.6 - - - +
156B PRO* 3.7 6.4 - - - +
442B GLN* 2.4 43.7 + - - +
443B GLU 4.5 0.2 - - - -
444B LEU 3.7 0.6 - - - -
445B TYR* 1.3 74.6 - - - +
447B ALA* 1.3 61.9 + - - -
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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