Contacts of the helix formed by residues 431 - 444 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B TRP* 5.2 3.6 - - - -
397B LEU* 3.9 11.9 - - - +
430B SER* 1.3 79.5 - - - +
432B LYS* 1.3 61.6 + - - +
433B THR 3.6 1.1 - - - -
434B THR* 3.4 19.6 - - - -
435B LEU* 2.9 26.7 + - - +
547B PHE* 3.3 16.6 - - - -
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Residues in contact with LYS 432 (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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418A LYS* 4.6 4.9 - - - +
540A ARG* 5.8 1.3 - - - +
424B PHE* 3.9 15.8 - - + +
426B GLY 3.2 28.9 - - - +
427B PRO 2.9 22.1 + - - -
428B ILE* 4.8 0.4 - - - +
429B ASP* 3.6 15.9 - - - +
430B SER* 3.0 22.8 + - - +
431B GLY* 1.3 73.4 - - - +
433B THR* 1.3 66.3 + - - +
434B THR 2.9 6.1 + - - -
435B LEU* 3.0 1.6 + - - +
436B ALA* 2.7 38.9 + - - +
474B ASP* 4.7 3.6 - - - -
527B THR* 4.9 8.1 - - + -
528B MET 3.9 3.8 - - - +
529B ASN* 3.3 20.9 - - - +
547B PHE* 3.4 27.3 - - + -
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Residues in contact with THR 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LYS* 5.5 5.5 + - - -
499A ASP* 5.7 0.4 - - - -
502A ASP* 4.1 24.1 + - + +
504A SER* 3.5 28.5 - - - +
505A VAL* 5.0 3.4 - - + +
540A ARG* 4.6 4.7 + - - -
431B GLY 3.6 0.2 - - - -
432B LYS* 1.3 87.6 + - - +
434B THR* 1.3 58.1 + - - +
437B ALA* 3.1 24.9 + - - +
473B GLU* 3.1 34.6 + - - +
474B ASP* 4.4 6.8 + - - -
527B THR* 5.9 0.7 - - - -
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Residues in contact with THR 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A SER* 5.4 1.3 - - - -
393B TRP* 3.9 15.0 - - + -
394B LEU* 4.8 1.6 - - + -
397B LEU* 5.3 1.6 - - + -
431B GLY* 3.4 21.0 - - - -
432B LYS 2.9 0.8 - - - -
433B THR* 1.3 79.9 - - - +
435B LEU* 1.3 59.5 + - - +
437B ALA 4.1 0.2 - - - -
438B ALA* 3.5 7.8 + - - +
569B ILE* 3.2 51.3 - - + +
570B GLN* 3.5 26.5 - - + +
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Residues in contact with LEU 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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394B LEU* 5.5 5.2 - - + -
397B LEU* 4.4 6.3 - - + -
398B LEU* 4.1 3.8 - - + -
401B MET* 3.8 34.1 - - + -
404B VAL* 6.4 1.6 - - + -
405B VAL* 5.5 1.3 - - + -
424B PHE* 3.5 28.7 - - + -
431B GLY 2.9 15.4 + - - +
434B THR* 1.3 75.2 - - - +
436B ALA* 1.3 63.2 + - - +
437B ALA 2.9 5.6 + - - -
438B ALA* 3.1 2.9 + - + -
439B LEU* 2.9 50.8 + - + +
545B ILE* 5.6 1.6 - - + -
547B PHE* 3.6 15.5 - - + -
569B ILE 5.4 0.4 - - - -
575B LEU* 4.2 20.2 - - + -
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Residues in contact with ALA 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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424B PHE* 3.8 14.5 - - + -
432B LYS 2.7 20.9 + - - +
433B THR* 4.6 0.4 - - - -
435B LEU* 1.3 73.5 - - - +
437B ALA* 1.3 58.5 + - - +
439B LEU* 4.2 6.8 - - - +
440B LEU* 3.7 14.0 + - - +
471B VAL* 3.7 22.8 - - + +
473B GLU* 3.8 12.6 - - - +
525B ILE* 4.6 7.5 - - + +
527B THR* 3.7 26.2 - - + -
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A SER* 3.0 31.3 - - - +
505A VAL* 3.8 12.8 - - + -
433B THR 3.1 22.2 + - - +
434B THR 4.1 3.1 - - - +
435B LEU 2.9 0.8 - - - -
436B ALA* 1.3 78.9 - - - +
438B ALA* 1.3 66.4 + - - +
439B LEU 3.2 0.4 - - - -
440B LEU* 3.1 20.8 + - - +
441B GLU* 3.4 5.9 + - - +
570B GLN* 4.3 9.1 - - + +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 5.8 0.7 - - + -
434B THR 3.5 12.1 + - - +
435B LEU* 3.1 5.4 + - + +
437B ALA* 1.3 77.5 - - - +
439B LEU* 1.3 57.5 + - - +
441B GLU* 3.1 3.0 + - - -
442B LEU* 2.9 24.8 + - - +
569B ILE 4.4 4.0 - - - +
570B GLN* 3.7 20.8 + - - -
571B SER 3.5 20.2 - - - +
572B GLY* 3.4 9.0 - - - +
575B LEU* 3.5 22.4 - - + -
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Residues in contact with LEU 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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405B VAL* 4.5 14.4 - - + -
408B PHE* 4.4 27.6 - - + -
424B PHE* 3.6 19.7 - - + -
435B LEU* 2.9 36.2 + - + +
436B ALA 4.4 3.1 - - - +
438B ALA* 1.3 76.2 - - - +
440B LEU* 1.3 63.9 + - - +
442B LEU* 3.6 13.3 - - + +
443B CYS* 3.0 29.1 + - - +
469B LEU* 4.7 2.5 - - - +
525B ILE* 3.5 28.5 - - + -
575B LEU* 3.5 20.6 - - + -
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A VAL* 4.7 11.7 - - + -
506A LYS* 5.0 10.3 - - + +
436B ALA 3.7 11.5 + - - +
437B ALA 3.1 15.1 + - - +
439B LEU* 1.3 78.9 - - - +
441B GLU* 1.3 54.8 + - - +
444B GLY* 2.8 29.5 + - - -
445B GLY 3.4 32.4 + - - +
446B LYS* 3.4 8.1 - - - +
447B ALA* 3.8 29.6 - - + +
469B LEU* 3.5 24.2 - - + -
471B VAL* 3.5 13.4 - - + +
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LYS* 5.2 10.6 + - - -
364B ARG* 2.8 48.7 + - - +
368B LEU* 3.7 6.6 - - + +
371B ARG* 3.4 24.6 + - - +
437B ALA 3.4 5.3 + - - +
438B ALA* 3.1 8.1 + - - +
440B LEU* 1.3 78.4 - - + +
442B LEU* 1.3 61.5 + - - +
443B CYS 3.3 0.7 - - - -
570B GLN 5.0 1.1 - - - +
571B SER* 3.5 11.8 + - - -
572B GLY* 2.8 30.4 + - - +
573B ILE* 4.1 3.4 + - - +
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Residues in contact with LEU 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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364B ARG* 3.5 6.9 - - - +
365B PHE* 3.9 13.2 - - + -
368B LEU* 3.5 27.1 - - + +
405B VAL* 3.7 24.5 - - + -
409B LEU* 4.3 11.2 - - + -
438B ALA 2.9 15.3 + - - +
439B LEU* 3.2 11.9 + - + +
441B GLU* 1.3 78.3 - - - +
443B CYS* 1.3 60.2 + - - +
572B GLY* 3.6 20.8 - - - +
575B LEU* 3.6 27.4 - - + -
576B LEU* 3.8 12.1 - - + +
579B LEU* 3.8 22.7 - - + -
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Residues in contact with CYS 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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360B MET 5.4 0.2 - - - +
361B LEU* 3.7 25.7 - - + +
364B ARG* 3.2 20.3 - - - +
408B PHE* 3.9 14.6 - - - -
409B LEU* 3.5 31.6 - - - -
412B MET* 5.2 0.2 - - - -
439B LEU* 3.0 14.5 + - - +
442B LEU* 1.3 84.2 - - - +
444B GLY* 1.3 60.1 + - - +
468B PHE* 3.8 10.6 - - + +
469B LEU* 3.5 28.9 - - + -
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Residues in contact with GLY 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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364B ARG* 4.2 17.5 - - - -
440B LEU 2.8 22.4 + - - -
441B GLU 4.1 0.6 + - - -
443B CYS* 1.3 75.8 - - - +
445B GLY* 1.3 58.5 + - - -
468B PHE* 3.4 23.5 - - - +
469B LEU* 3.4 13.6 - - - +
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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