Contacts of the helix formed by residues 383 - 396 (chain H) 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 ASP 383 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376H PHE* 4.0 1.8 - - - -
381H SER 3.9 2.2 + - - +
382H ALA* 1.3 70.5 - - - +
384H ILE* 1.3 67.4 + - - +
385H GLU* 2.9 42.5 + - - +
386H GLU* 3.2 33.9 + - - +
387H TRP* 3.1 19.6 - - - +
566H LYS* 4.6 4.4 - - - +
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Residues in contact with ILE 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376H PHE* 3.4 42.3 - - + -
382H ALA 3.7 1.8 + - - -
383H ASP* 1.3 74.1 + - - +
385H GLU* 1.3 66.6 + - + +
387H TRP* 3.4 0.8 + - - -
388H MET* 3.0 40.0 + - + +
577H LEU* 4.3 20.9 - - + -
599H TRP* 5.0 3.6 - - + -
602H ARG* 4.6 21.1 - - + +
603H LEU* 4.9 10.5 - - + -
606H GLU* 4.6 15.7 - - + +
607H PHE* 4.1 16.2 - - + -
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Residues in contact with GLU 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383H ASP* 2.9 20.5 + - - +
384H ILE* 1.3 81.8 - - + +
386H GLU* 1.3 60.3 + - - +
388H MET* 3.4 4.0 + - - +
389H ALA* 3.1 21.0 + - - +
607H PHE* 3.4 30.6 - - + -
615H MET* 4.4 0.7 - - - +
626H LEU* 3.5 35.6 - - + +
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Residues in contact with GLU 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383H ASP* 3.2 25.8 + - + +
385H GLU* 1.3 74.8 - - - +
387H TRP* 1.3 60.3 + - + +
389H ALA* 3.0 7.0 + - - +
390H GLY 3.0 22.2 + - - -
562H PHE* 3.1 38.4 - - + +
563H LEU* 3.6 7.6 - - - +
566H LYS* 2.7 40.7 + - - +
568H ILE* 3.8 16.3 - - + +
626H LEU* 4.1 17.3 - - + -
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Residues in contact with TRP 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375H MET* 3.5 24.4 - - + +
376H PHE* 3.8 16.6 - + + -
382H ALA* 4.1 9.8 - - + +
383H ASP 3.1 25.8 - - - +
384H ILE 3.4 4.9 + - - +
385H GLU 3.4 0.6 - - - -
386H GLU* 1.3 81.1 + - + +
388H MET* 1.3 58.5 + - - +
390H GLY* 3.4 2.3 + - - -
391H VAL* 3.1 27.3 + - - +
566H LYS* 4.3 14.8 - - + +
567H ARG 3.9 9.6 - - - -
568H ILE* 3.7 37.3 - - + +
571H SER* 3.2 34.1 - - - -
573H ILE* 3.5 22.9 - - + -
574H ALA* 3.9 14.8 - - - +
577H LEU* 3.6 18.2 - - + +
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Residues in contact with MET 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384H ILE* 3.0 35.0 + - + +
385H GLU* 3.6 6.7 - - - +
386H GLU 3.2 0.2 - - - -
387H TRP* 1.3 76.5 - - - +
389H ALA* 1.3 63.6 + - - +
391H VAL* 3.4 22.9 + - + +
392H ALA* 3.5 4.5 + - - +
577H LEU* 3.5 48.9 - - + +
581H TRP* 3.5 34.8 - - + -
603H LEU* 3.7 15.5 - - + -
607H PHE* 4.1 15.9 - - + -
612H TYR* 4.0 6.1 - - + -
615H MET* 3.8 22.9 - - + +
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Residues in contact with ALA 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H GLU 3.1 13.0 + - - +
386H GLU* 3.0 13.4 + - - +
388H MET* 1.3 77.5 - - - +
390H GLY* 1.3 62.4 + - - +
392H ALA* 3.0 15.9 + - - +
393H TRP* 3.1 12.5 + - - +
562H PHE* 4.2 2.2 - - + -
563H LEU* 4.4 2.0 - - - -
615H MET* 3.7 9.4 - - - -
625H VAL* 3.4 33.9 - - + +
626H LEU* 3.6 16.6 - - + -
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Residues in contact with GLY 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386H GLU 3.0 9.7 + - - -
387H TRP 3.4 5.1 + - - -
388H MET 3.3 0.4 - - - -
389H ALA* 1.3 73.3 - - - +
391H VAL* 1.3 58.2 + - - +
392H ALA 3.0 2.0 - - - -
393H TRP* 3.2 5.9 + - - +
394H LEU* 2.8 42.7 + - - +
563H LEU* 3.6 20.2 - - - +
568H ILE* 4.2 8.1 - - - -
569H ILE* 4.8 4.5 - - - -
574H ALA* 5.6 0.4 - - - -
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Residues in contact with VAL 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387H TRP 3.1 18.1 + - - +
388H MET* 3.5 28.3 - - + +
389H ALA 3.2 0.4 - - - -
390H GLY* 1.3 75.6 - - - +
392H ALA* 1.3 57.7 + - - +
394H LEU* 4.1 8.7 - - - +
395H HIS* 3.2 26.3 + - - +
574H ALA 3.8 20.0 - - - +
577H LEU* 3.9 5.8 - - + +
578H MET* 3.5 35.0 - - + +
581H TRP* 5.2 2.5 - - + -
582H TYR* 4.5 1.8 - - + -
612H TYR* 3.3 22.5 + - + +
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Residues in contact with ALA 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388H MET 3.5 4.9 + - - +
389H ALA 3.0 13.4 + - - +
390H GLY 3.0 0.6 - - - -
391H VAL* 1.3 77.8 - - - +
393H TRP* 1.3 64.9 + - - +
395H HIS* 3.2 3.6 + - - +
396H CYS* 3.0 29.7 + - - -
612H TYR* 4.4 6.3 + - + -
615H MET* 4.1 13.0 - - + -
616H LYS* 3.5 39.9 - - + +
619H VAL* 4.6 3.1 - - + -
625H VAL* 4.9 0.4 - - + -
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Residues in contact with TRP 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389H ALA 3.1 8.6 + - - +
390H GLY* 3.2 5.4 + - - +
392H ALA* 1.3 78.8 - - - +
394H LEU* 1.3 73.6 - - + +
396H CYS* 3.1 16.9 + - - +
397H LEU* 3.3 26.6 + - + +
430H SER 5.3 1.3 - - - -
431H GLY* 5.2 2.9 - - - -
434H THR* 3.9 18.6 - - + -
553H LEU* 3.2 55.4 + - + +
556H CYS* 3.4 26.5 - - - -
557H LEU* 3.7 27.0 - - + +
563H LEU* 4.4 11.7 - - + -
569H ILE* 3.5 44.6 - - + -
619H VAL* 4.3 5.3 - - + +
625H VAL* 4.7 3.1 - - + -
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Residues in contact with LEU 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390H GLY 2.8 22.5 + - - +
391H VAL* 4.1 5.8 - - - +
393H TRP* 1.3 91.9 - - + +
395H HIS* 1.3 61.5 + - - +
397H LEU* 3.2 27.2 - - + +
401H MET* 3.2 21.7 - - + +
434H THR* 4.8 3.1 - - + +
435H LEU* 5.5 6.3 - - + -
438H ALA* 5.9 0.7 - - + -
569H ILE* 3.1 32.5 - - - +
574H ALA* 3.9 30.5 - - + -
575H LEU* 4.0 24.0 - - + -
578H MET* 4.4 9.0 - - - -
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Residues in contact with HIS 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138 GLN 5.0 4.0 - - - -
148 ILE* 3.7 15.9 + - - +
391H VAL 3.2 19.0 + - - +
392H ALA 3.2 5.7 + - - +
394H LEU* 1.3 75.7 - - - +
396H CYS* 1.3 57.7 + - - +
397H LEU 3.2 2.7 - - - -
398H LEU 3.4 16.4 - - - +
400H LYS* 4.6 14.6 - - - -
401H MET* 3.8 7.3 + - + -
402H ASP* 2.9 38.2 + - + -
578H MET* 4.5 4.0 - - - -
582H TYR* 3.3 30.7 - + - +
616H LYS* 2.9 30.8 + - - +
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Residues in contact with CYS 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148 ILE* 3.4 12.7 - - + +
158 PHE* 4.0 18.6 - - - -
392H ALA 3.0 21.2 + - - +
393H TRP 3.1 8.0 + - - +
395H HIS* 1.3 76.8 - - - +
397H LEU* 1.3 60.0 + - - +
550H LYS* 3.6 1.0 + - - -
552H TYR* 2.7 29.0 + - + -
553H LEU* 3.4 8.2 - - + +
616H LYS* 4.1 25.6 - - - -
619H VAL* 3.6 36.1 - - + -
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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