Contacts of the helix formed by residues 383 - 399 (chain D) in PDB entry 2IHU
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 ARG 383 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D TYR* 3.5 51.4 - - + +
379D GLU 4.9 1.2 - - - +
380D ASP* 4.8 7.1 - - - +
381D GLY 3.3 18.2 + - - +
382D MET* 1.3 91.6 + - - +
384D VAL* 1.3 66.9 + - - +
385D HIS* 3.3 28.0 - - + +
386D GLN* 3.0 24.7 + - - +
387D VAL* 3.4 11.3 + - - +
559D VAL* 4.9 0.2 - - - -
560D ASN* 3.2 50.4 + - - +
561D TYR* 5.1 5.4 - - - +
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Residues in contact with VAL 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D ARG* 1.3 72.2 - - - +
385D HIS* 1.3 63.6 + - - +
387D VAL* 3.1 8.0 + - + +
388D ILE* 3.0 30.2 + - + +
413D PHE* 4.0 17.9 - - + -
416D TYR* 3.6 40.4 - - + -
460D ILE* 4.6 7.6 - - + -
488D VAL* 4.8 4.5 - - + -
559D VAL* 4.3 16.8 - - + -
560D ASN 5.1 1.0 + - - -
561D TYR* 3.5 36.8 - - + +
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Residues in contact with HIS 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D PHE* 3.1 72.0 - + + +
372D LEU* 3.9 8.1 - - - +
374D ASP* 2.8 31.3 + - + +
378D TYR* 4.8 1.6 - - - -
383D ARG* 3.4 28.7 - - + +
384D VAL* 1.3 77.9 - - - +
386D GLN* 1.3 67.7 + - + +
388D ILE* 4.8 1.6 - - - -
389D ASP* 3.0 28.9 + - - +
416D TYR* 3.7 19.8 + - + -
420D PHE* 4.3 10.5 - - + -
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Residues in contact with GLN 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D ASP* 2.9 26.9 + - - +
375D PRO 4.4 0.2 - - - -
376D GLU 2.8 27.5 + - - +
378D TYR* 3.8 15.7 - - - -
382D MET* 3.8 23.5 - - + +
383D ARG* 3.0 27.3 + - - +
385D HIS* 1.3 86.4 - - + +
387D VAL* 1.3 59.1 + - - +
389D ASP* 3.5 1.9 + - - +
390D SER* 2.7 34.3 + - - -
536D ARG* 3.5 32.5 + - - +
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Residues in contact with VAL 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D MET* 4.2 12.1 - - + -
383D ARG 3.7 13.0 - - - +
384D VAL* 3.1 13.9 + - - +
386D GLN* 1.3 76.7 - - - +
388D ILE* 1.3 58.3 + - - +
390D SER* 3.3 5.0 + - - -
391D MET* 3.1 34.6 + - - +
460D ILE* 4.0 18.2 - - + -
486D VAL* 3.8 28.5 - - + -
488D VAL* 4.0 9.9 - - + -
539D LEU* 3.7 14.5 - - + +
557D VAL* 4.1 24.0 - - + -
559D VAL* 4.3 2.2 - - + -
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Residues in contact with ILE 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D VAL* 3.0 24.4 + - + +
385D HIS* 4.2 3.6 - - - +
387D VAL* 1.3 73.4 - - - +
389D ASP* 1.3 60.1 + - - +
391D MET* 3.2 10.3 + - + +
392D ASN* 2.8 31.8 + - - +
406D ILE* 6.2 1.1 - - + -
413D PHE 4.2 2.5 - - - +
416D TYR* 3.4 34.5 - - + -
417D GLY* 3.4 17.5 - - - +
420D PHE* 3.7 15.0 - - + -
421D ALA* 3.7 35.7 - - + +
460D ILE* 4.1 20.6 - - + -
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Residues in contact with ASP 389 (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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372D LEU* 3.0 50.3 - - + +
373D ALA* 5.0 2.2 - - - -
385D HIS 3.0 17.3 + - - +
386D GLN 3.7 4.9 - - - +
388D ILE* 1.3 77.1 - - - +
390D SER* 1.3 60.3 + - - +
392D ASN* 3.4 8.7 + - - +
393D THR* 3.0 35.3 + - - -
536D ARG* 2.9 22.1 + - - +
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Residues in contact with SER 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D GLN 2.7 21.2 + - - -
387D VAL 3.5 7.2 - - - -
389D ASP* 1.3 76.9 - - - +
391D MET* 1.3 64.5 + - - +
393D THR* 3.3 4.1 + - - -
394D VAL* 3.1 27.9 + - - +
536D ARG* 4.3 17.1 + - - +
539D LEU* 3.5 27.9 - - - +
540D LEU* 3.8 24.2 - - - +
543D LEU* 3.7 3.4 - - - -
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Residues in contact with MET 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D VAL* 3.1 20.6 + - + +
388D ILE* 3.2 13.9 + - + +
390D SER* 1.3 75.3 - - - +
392D ASN* 1.3 57.1 + - - +
394D VAL 3.5 0.3 + - - -
395D MET* 2.8 32.9 + - - +
406D ILE* 4.3 20.4 - - + -
458D PHE* 3.7 36.8 - - + -
459D LEU 4.0 10.8 - - - +
460D ILE* 4.0 40.8 - - + +
486D VAL* 4.0 15.9 - - + -
539D LEU* 5.5 0.2 - - + -
543D LEU* 3.8 21.8 - - + -
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Residues in contact with ASN 392 (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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372D LEU* 4.5 9.1 - - - +
388D ILE* 2.8 28.7 + - - +
389D ASP* 3.6 11.5 + - - +
391D MET* 1.3 68.0 - - - +
393D THR* 1.3 61.1 + - - +
395D MET* 3.8 5.0 - - - +
396D GLU* 2.9 32.9 + - - +
406D ILE* 3.7 6.6 - - - +
420D PHE 2.9 26.9 + - - -
421D ALA* 3.5 5.4 - - - -
422D ARG* 2.8 38.1 + - + +
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Residues in contact with THR 393 (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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389D ASP* 3.0 23.6 + - - -
390D SER* 3.3 9.0 + - - -
392D ASN* 1.3 78.0 - - - +
394D VAL* 1.3 61.8 + - - +
396D GLU* 3.4 9.9 + - - +
397D GLU* 3.2 42.0 + - + +
540D LEU* 4.2 12.5 - - + +
544D ARG* 4.1 11.0 - - - +
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Residues in contact with VAL 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D SER 3.1 16.7 + - - +
391D MET 4.2 2.0 - - - +
393D THR* 1.3 72.7 - - - +
395D MET* 1.3 59.2 + - - +
397D GLU* 3.3 8.6 + - + +
398D ALA* 2.8 28.1 + - + +
458D PHE* 4.0 12.1 - - + -
540D LEU* 3.8 18.6 - - + +
543D LEU* 3.8 25.6 - - + +
544D ARG* 3.8 48.9 - - + +
547D ALA* 4.2 6.1 - - + -
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Residues in contact with MET 395 (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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391D MET 2.8 20.7 + - - +
392D ASN* 3.8 4.5 - - - +
394D VAL* 1.3 77.4 - - - +
396D GLU* 1.3 57.8 + - - +
398D ALA* 4.5 1.1 - - - +
399D ALA* 3.0 44.1 + - + +
403D GLU 5.1 1.3 - - - +
404D GLY* 3.8 23.3 - - - -
405D THR 3.3 30.5 - - - +
406D ILE* 4.0 15.9 - - + -
422D ARG* 4.1 17.3 - - + +
456D PRO* 3.6 19.7 - - + +
458D PHE* 3.5 35.5 - - + -
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Residues in contact with GLU 396 (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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392D ASN 2.9 18.6 + - - +
393D THR* 3.6 9.2 - - - +
394D VAL 3.3 0.2 - - - -
395D MET* 1.3 76.2 - - - +
397D GLU* 1.3 56.8 + - + +
399D ALA* 3.5 6.8 - - - +
422D ARG* 3.6 40.7 + - - +
602D K 3.0 18.5 - - - -
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Residues in contact with GLU 397 (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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393D THR* 3.2 23.9 + - + +
394D VAL* 3.5 10.7 - - + +
396D GLU* 1.3 77.4 - - + +
398D ALA* 1.3 60.3 + - - +
544D ARG* 2.8 52.6 + - - +
602D K 2.9 17.7 - - - -
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Residues in contact with ALA 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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394D VAL* 2.8 20.4 + - + +
395D MET* 4.2 2.2 - - - +
397D GLU* 1.3 74.2 - - - +
399D ALA* 1.3 60.3 + - - +
400D GLU* 4.1 1.7 + - - +
456D PRO* 3.7 25.7 - - + +
458D PHE* 4.7 1.3 - - + -
547D ALA* 4.0 26.9 - - + +
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Residues in contact with ALA 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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395D MET* 3.0 23.5 + - + +
396D GLU* 3.5 6.2 - - - +
398D ALA* 1.3 78.6 - - - +
400D GLU* 1.3 67.1 + - - +
403D GLU 3.5 25.8 - - - +
422D ARG* 6.0 1.1 - - - +
456D PRO* 3.7 24.0 - - + -
602D K 2.8 24.0 - - - -
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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