Contacts of the helix formed by residues 431 - 444 (chain D) in PDB entry 4E2I
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 GLY 431 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393D TRP* 5.2 3.4 - - - -
397D LEU* 3.9 11.5 - - - +
430D SER* 1.3 79.7 - - - +
432D LYS* 1.3 62.3 + - - +
433D THR 3.6 1.3 - - - -
434D THR* 3.2 20.5 + - - -
435D LEU* 2.9 26.3 + - - +
547D PHE* 3.3 16.3 - - - -
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Residues in contact with LYS 432 (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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418C LYS* 4.6 4.5 - - - +
540C ARG* 5.7 1.6 - - - +
424D PHE* 3.9 16.9 - - + +
426D GLY 3.1 28.7 - - - +
427D PRO 2.9 22.0 + - - -
428D ILE* 4.8 0.2 - - - +
429D ASP* 3.5 16.1 - - - +
430D SER* 3.0 22.8 + - - +
431D GLY* 1.3 73.2 - - - +
433D THR* 1.3 67.0 + - - +
434D THR 2.9 5.4 + - - -
435D LEU* 3.0 1.6 + - - +
436D ALA* 2.7 39.2 + - - +
474D ASP* 4.7 3.6 - - - -
527D THR* 4.9 7.9 - - + -
528D MET 3.9 4.0 - - - +
529D ASN* 3.3 20.4 - - - +
547D PHE* 3.4 27.1 - - + -
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Residues in contact with THR 433 (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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418C LYS* 5.6 4.6 + - - -
499C ASP* 5.5 1.6 - - - -
502C ASP* 4.0 26.2 + - + +
504C SER* 3.4 26.6 - - - +
505C VAL* 4.9 2.7 - - + -
540C ARG* 4.6 4.9 + - - -
432D LYS* 1.3 86.9 + - - +
434D THR* 1.3 58.0 + - - +
436D ALA* 4.6 0.2 - - - -
437D ALA* 3.1 24.6 - - - +
473D GLU* 3.1 34.0 + - - +
474D ASP* 4.4 6.8 + - - -
527D THR* 5.5 0.9 - - - +
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Residues in contact with THR 434 (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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504C SER* 5.2 2.3 + - - -
393D TRP* 3.9 15.6 - - + -
394D LEU* 4.8 2.5 - - + -
397D LEU* 5.3 1.3 - - + -
431D GLY* 3.4 21.6 - - - -
432D LYS 2.9 1.0 - - - -
433D THR* 1.3 79.9 - - - +
435D LEU* 1.3 59.5 + - - +
437D ALA 4.1 0.2 - - - -
438D ALA* 3.5 7.4 + - - +
569D ILE* 3.2 51.0 - - + +
570D GLN* 3.5 26.7 - - + +
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Residues in contact with LEU 435 (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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394D LEU* 5.5 5.6 - - + -
397D LEU* 4.4 7.0 - - + -
398D LEU* 4.1 3.4 - - + -
401D MET* 3.8 34.5 - - + -
404D VAL* 6.4 1.1 - - + -
405D VAL* 5.5 1.6 - - + -
424D PHE* 3.5 28.7 - - + -
431D GLY 2.9 15.5 + - - +
434D THR* 1.3 75.8 - - - +
436D ALA* 1.3 63.2 + - - +
437D ALA 2.9 6.1 + - - -
438D ALA* 3.1 2.7 + - + +
439D LEU* 2.9 51.3 + - + +
545D ILE* 5.6 1.8 - - + -
547D PHE* 3.6 15.3 - - + -
569D ILE 5.4 0.2 - - - -
575D LEU* 4.2 19.5 - - + -
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Residues in contact with ALA 436 (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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424D PHE* 3.8 14.0 - - + -
432D LYS 2.7 20.5 + - - +
433D THR* 4.6 0.7 - - - -
435D LEU* 1.3 73.3 - - - +
437D ALA* 1.3 58.6 + - - +
439D LEU* 4.3 6.8 - - - +
440D LEU* 3.7 13.9 + - - +
471D VAL* 3.7 23.3 - - + +
473D GLU* 3.8 12.6 - - - +
525D ILE* 4.6 6.6 - - + +
527D THR* 3.7 27.4 - - + -
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Residues in contact with ALA 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C SER* 2.9 31.4 - - - +
505C VAL* 3.6 15.0 - - + -
433D THR 3.1 22.0 + - - +
434D THR 4.1 3.1 - - - +
435D LEU 2.9 0.6 - - - -
436D ALA* 1.3 78.7 - - - +
438D ALA* 1.3 67.9 + - - +
439D LEU 3.2 0.2 - - - -
440D LEU* 3.0 20.2 + - - +
441D GLU* 3.4 6.4 + - - +
570D GLN* 4.3 7.4 - - + +
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Residues in contact with ALA 438 (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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394D LEU* 5.8 0.7 - - + -
434D THR 3.5 12.0 + - - +
435D LEU* 3.1 5.9 + - - +
437D ALA* 1.3 77.5 - - - +
439D LEU* 1.3 58.3 + - - +
441D GLU* 3.1 3.2 + - - +
442D LEU* 2.9 24.6 + - - +
569D ILE 4.4 3.6 - - - +
570D GLN* 3.7 22.8 + - - -
571D SER 3.5 18.6 - - - +
572D GLY* 3.4 9.0 - - - +
575D LEU* 3.5 22.9 - - + -
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Residues in contact with LEU 439 (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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405D VAL* 4.4 15.3 - - + -
408D PHE* 4.4 27.4 - - + -
424D PHE* 3.6 20.2 - - + -
435D LEU* 2.9 34.4 + - + +
436D ALA 4.4 3.4 - - - +
438D ALA* 1.3 76.2 - - - +
440D LEU* 1.3 62.5 + - - +
442D LEU* 3.6 13.0 - - + +
443D CYS* 3.0 29.3 + - - +
469D LEU* 4.7 2.1 - - - +
525D ILE* 3.5 28.7 - - + -
575D LEU* 3.5 19.7 - - + -
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Residues in contact with LEU 440 (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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505C VAL* 4.8 12.3 - - + -
506C LYS* 4.9 11.9 - - + +
436D ALA 3.7 11.3 + - - +
437D ALA 3.0 14.6 + - - +
439D LEU* 1.3 79.8 - - - +
441D GLU* 1.3 56.0 + - - +
444D GLY* 2.8 29.5 + - - -
445D GLY 3.4 32.2 + - - +
446D LYS* 3.4 8.1 - - - +
447D ALA* 3.8 29.2 - - + +
469D LEU* 3.5 24.5 - - + -
471D VAL* 3.5 13.4 - - + +
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Residues in contact with GLU 441 (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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506C LYS* 4.9 13.9 + - - -
364D ARG* 2.8 49.1 + - - +
368D LEU* 3.7 6.3 - - + +
371D ARG* 3.4 24.3 + - - +
437D ALA 3.4 5.9 + - - +
438D ALA* 3.1 8.5 + - - +
440D LEU* 1.3 77.2 - - + +
442D LEU* 1.3 60.4 + - - +
443D CYS 3.3 0.7 - - - -
570D GLN 5.0 1.0 - - - +
571D SER* 3.6 12.3 + - - -
572D GLY* 2.8 29.6 + - - +
573D ILE* 4.1 2.8 + - - +
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Residues in contact with LEU 442 (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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364D ARG* 3.5 7.3 - - - +
365D PHE* 3.9 13.0 - - + -
368D LEU* 3.5 26.4 - - + +
405D VAL* 3.7 24.5 - - + -
409D LEU* 4.3 11.0 - - + -
438D ALA 2.9 16.4 + - - +
439D LEU* 3.6 10.1 - - + +
441D GLU* 1.3 78.5 - - - +
443D CYS* 1.3 60.9 + - - +
572D GLY* 3.6 20.8 - - - +
575D LEU* 3.6 27.1 - - + -
576D LEU* 3.8 11.9 - - + +
579D LEU* 3.8 23.1 - - + -
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Residues in contact with CYS 443 (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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360D MET 5.4 0.2 - - - +
361D LEU* 3.7 26.2 - - + +
364D ARG* 3.2 20.1 - - - +
408D PHE* 4.0 13.9 - - - -
409D LEU* 3.5 32.3 - - - -
412D MET* 5.2 0.2 - - - -
439D LEU* 3.0 15.2 + - - +
442D LEU* 1.3 82.7 - - - +
444D GLY* 1.3 59.2 + - - +
468D PHE* 3.8 10.5 - - + +
469D LEU* 3.5 29.4 - - + -
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Residues in contact with GLY 444 (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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364D ARG* 4.2 17.3 - - - -
440D LEU 2.8 22.9 + - - -
441D GLU 4.1 0.6 + - - -
442D LEU 3.8 0.4 - - - -
443D CYS* 1.3 75.7 - - - +
445D GLY* 1.3 58.3 + - - -
468D PHE* 3.4 23.7 - - - +
469D LEU* 3.4 13.1 - - - +
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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