Contacts of the helix formed by residues 397 - 409 (chain D) 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 LEU 397 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D THR* 4.5 0.7 - - + -
135D LEU* 3.4 34.3 - - + -
140D VAL* 3.9 19.7 - - + -
143D ALA* 4.3 12.3 - - + -
144D PHE* 3.9 13.7 - - + -
173D PHE* 3.9 24.0 - - + -
207D PHE* 3.5 33.7 - - + -
213D TRP* 3.8 20.6 - - + -
214D THR 3.0 8.8 + - - +
215D LEU* 4.8 2.1 - - + +
395D TYR 3.3 2.0 + - - -
396D SER* 1.3 70.7 - - - +
398D PHE* 1.3 53.8 + - - +
401D ALA* 2.5 39.6 + - - +
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Residues in contact with PHE 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ALA* 4.1 16.9 - - + +
146D ARG* 3.5 57.2 - - + +
147D ALA* 3.6 20.6 - - - -
150D VAL* 3.7 21.5 - - + -
215D LEU* 5.5 3.4 - - + +
396D SER* 3.2 6.7 + - - +
397D LEU* 1.3 76.3 - - - +
399D LEU* 1.3 74.1 + - + +
401D ALA* 3.7 1.0 - - - +
402D ALA* 2.6 43.7 + - + +
431D PHE* 3.7 33.7 - + + -
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Residues in contact with LEU 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D SER* 3.2 20.7 + - - +
398D PHE* 1.3 102.5 - - + +
400D VAL* 1.3 64.3 + - - +
402D ALA* 3.4 4.9 - - - +
403D HIS* 3.0 23.4 + - - +
420D LEU* 4.0 8.9 - - + +
425D TYR* 4.3 10.3 - - + -
426D THR 3.9 12.3 - - - +
427D TYR* 3.7 19.1 - - + -
428D THR* 3.6 33.2 - - - +
431D PHE* 3.7 30.1 - - + -
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Residues in contact with VAL 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D LEU* 4.4 14.4 - - + -
192D ALA* 4.1 14.1 - - + -
207D PHE* 4.6 1.6 - - + -
213D TRP* 3.8 29.4 - - + -
395D TYR* 4.1 7.9 - - + -
396D SER 2.9 20.6 + - - +
397D LEU 4.0 0.2 - - - +
399D LEU* 1.3 70.6 - - - +
401D ALA* 1.3 65.9 + - - +
403D HIS* 3.1 7.6 + - + +
404D GLN* 2.9 43.0 + - + +
425D TYR* 4.0 24.2 - - + -
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Residues in contact with ALA 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 3.7 13.7 - - + -
147D ALA* 3.8 5.4 - - + -
207D PHE* 3.4 25.7 - - + -
397D LEU 2.5 25.6 + - - +
398D PHE* 3.7 1.8 - - - +
400D VAL* 1.3 71.2 - - - +
402D ALA* 1.3 65.3 + - - +
404D GLN* 2.9 3.5 + - - +
405D PHE* 2.8 49.3 + - + -
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Residues in contact with ALA 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ALA* 3.7 14.0 - - - +
150D VAL* 5.4 2.5 - - + -
151D TRP* 2.5 33.2 + - - +
398D PHE* 2.6 42.2 + - + +
399D LEU* 3.4 9.0 - - - +
401D ALA* 1.3 72.1 - - - +
403D HIS* 1.3 62.6 + - - +
405D PHE* 3.6 3.3 + - - -
406D GLY 3.3 1.4 + - - -
420D LEU* 4.1 15.9 - - + -
431D PHE* 5.2 2.9 - - + -
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Residues in contact with HIS 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D CYS* 5.3 2.0 - - + -
399D LEU 3.0 10.9 + - - +
400D VAL* 3.3 11.4 - - + +
401D ALA 3.0 0.2 + - - -
402D ALA* 1.3 77.7 - - - +
404D GLN* 1.3 66.3 + - - +
406D GLY 2.8 20.8 + - - -
407D HIS* 3.2 5.4 + + - -
420D LEU* 2.7 25.2 + - + +
421D MET* 3.2 52.1 + - + +
422D ALA 3.2 25.3 + - - -
423D PRO* 4.9 0.7 - - + -
997D ZN 2.5 34.0 - - - -
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Residues in contact with GLN 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D CYS* 4.0 20.4 - - - +
104D ASN* 3.9 2.3 - - - +
192D ALA* 3.1 33.5 - - + +
193D HIS* 2.4 37.0 - - - +
194D ALA* 3.0 14.8 + - + +
205D SER* 4.1 10.3 - - - -
207D PHE* 4.1 9.9 - - + -
400D VAL* 2.9 29.3 + - - +
401D ALA* 2.9 9.6 + - - +
403D HIS* 1.3 81.0 - - - +
405D PHE* 1.3 56.2 + - - +
407D HIS* 2.7 27.9 + - - +
408D ALA 2.9 9.0 + - - -
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Residues in contact with PHE 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 3.4 25.8 - + - -
147D ALA* 3.4 33.2 - - + -
148D PHE* 3.3 52.9 - + + -
151D TRP* 3.7 16.2 - - + +
169D ILE* 4.3 3.1 - - + -
171D ILE* 3.5 15.7 - - + -
205D SER* 3.7 22.4 - - - -
207D PHE* 4.4 1.6 - + - -
401D ALA* 2.8 32.1 + - + +
402D ALA* 3.9 1.6 - - - -
404D GLN* 1.3 73.1 - - - +
406D GLY* 1.3 60.1 + - - +
408D ALA* 2.5 28.8 + - + +
409D MET* 2.8 17.4 + - + +
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Residues in contact with GLY 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D TRP* 3.3 30.2 - - - +
402D ALA 3.3 4.4 + - - -
403D HIS 2.8 11.4 + - - -
405D PHE* 1.3 77.1 - - - +
407D HIS* 1.3 62.6 + - - +
409D MET* 2.8 17.3 + - - +
410D GLY 3.1 9.5 + - - -
411D LEU* 3.1 17.5 + - - +
421D MET* 4.1 2.5 - - - -
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Residues in contact with HIS 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ASN* 3.6 26.2 + - + +
105D PRO 5.4 0.4 - - - -
194D ALA* 3.7 14.8 - - + +
195D PHE 3.7 8.4 - - - +
196D ALA* 3.8 3.8 - - - +
197D PRO* 3.7 3.8 - - - +
403D HIS* 3.2 22.1 + + - -
404D GLN* 2.7 16.4 + - - +
406D GLY* 1.3 75.2 - - - +
408D ALA* 1.3 56.8 + - - +
409D MET 3.0 5.4 + - - -
410D GLY* 3.0 13.9 + - - -
411D LEU 2.7 26.4 + - - +
412D GLU* 3.9 8.5 - - + +
413D HIS* 2.9 26.0 + + - -
421D MET* 3.6 3.2 - - + +
997D ZN 2.6 34.6 - - - -
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Residues in contact with ALA 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D TRP* 2.7 32.4 + - - -
169D ILE* 3.9 15.0 - - + -
194D ALA* 4.2 0.9 - - + +
195D PHE 3.5 12.1 + - - -
197D PRO* 3.0 9.3 - - - +
203D GLY* 3.4 26.5 - - - +
205D SER* 4.1 4.5 - - - +
404D GLN 2.9 6.2 + - - +
405D PHE* 2.5 27.0 + - - +
407D HIS* 1.3 71.1 - - - +
409D MET* 1.3 50.4 + - - -
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Residues in contact with MET 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LYS* 3.9 2.9 - - - -
119D TRP* 3.6 19.7 - - + +
124D ILE* 4.2 2.7 - - + -
148D PHE* 5.5 0.7 - - - -
151D TRP* 4.9 4.9 - - + -
157D LEU* 3.4 29.4 - - + -
159D PHE* 3.2 43.3 - - + -
169D ILE* 4.2 7.2 - - - -
197D PRO* 3.3 12.1 - - - +
405D PHE* 2.8 20.4 + - - +
406D GLY* 2.8 7.6 + - - +
408D ALA* 1.3 86.1 - - - +
410D GLY* 1.3 56.8 + - - +
411D LEU* 3.8 0.9 - - + +
441D ILE* 3.7 26.7 - - + -
444D LEU* 3.8 6.5 - - - +
445D TYR* 2.7 26.6 + - + +
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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