Contacts of the helix formed by residues 422 - 437 (chain D) in PDB entry 2OIB
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 422 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ASN* 4.3 32.1 + - + +
207B ASN* 4.0 14.1 - - - +
285D TRP* 4.3 4.3 + - - -
414D ILE* 6.1 0.4 - - - -
420D ASP 3.7 2.6 + - - +
421D ALA* 1.3 75.4 - - - +
423D SER* 1.3 64.8 + - - +
424D THR* 3.3 12.5 + - - -
425D SER* 2.8 39.9 + - - -
426D VAL* 3.1 25.0 + - - +
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Residues in contact with SER 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D GLU* 2.7 32.8 + - - -
422D ASP* 1.3 72.9 - - - +
424D THR* 1.3 57.8 + - - +
426D VAL* 3.8 2.4 - - - +
427D GLU* 2.8 49.3 + - - +
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Residues in contact with THR 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D ASP* 3.3 10.1 + - - -
423D SER* 1.3 78.5 - - - +
425D SER* 1.3 58.5 + - - +
427D GLU* 3.4 7.1 + - - +
428D ALA* 2.9 28.0 + - + +
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Residues in contact with SER 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D TRP* 2.7 32.9 + - - -
289D CYS* 5.2 1.8 - - - -
422D ASP* 2.8 28.3 + - - -
424D THR* 1.3 75.1 - - - +
426D VAL* 1.3 60.1 + - - +
428D ALA* 3.2 8.2 + - - +
429D MET* 2.9 30.8 + - - +
457D MET* 3.8 27.7 - - - +
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Residues in contact with VAL 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D TRP* 3.6 31.4 - - + -
381D ILE* 4.1 16.6 - - + +
410D ILE* 4.5 10.1 - - + -
411D GLU* 5.0 1.3 - - - +
414D ILE* 3.6 38.4 - - + -
421D ALA* 3.9 20.2 - - + -
422D ASP 3.1 21.8 + - - +
423D SER 3.8 3.8 - - - +
425D SER* 1.3 76.7 + - - +
427D GLU* 1.3 57.1 + - + +
429D MET* 3.5 2.3 + - - +
430D TYR* 3.0 25.8 + - - +
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Residues in contact with GLU 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D ILE* 4.2 17.5 - - + -
411D GLU* 4.5 10.8 - - - +
423D SER* 2.8 38.4 + - - +
424D THR* 3.8 5.6 - - - +
426D VAL* 1.3 70.5 - - + +
428D ALA* 1.3 59.8 + - - +
430D TYR* 3.7 8.5 - - - +
431D SER* 2.9 29.3 + - - -
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Residues in contact with ALA 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424D THR* 2.9 16.8 + - + +
425D SER* 3.2 10.7 + - - +
427D GLU* 1.3 74.5 - - - +
429D MET* 1.3 63.7 + - - +
431D SER* 3.4 7.4 + - - -
432D VAL* 3.2 25.8 + - - +
453D LEU 5.8 0.7 - - - +
457D MET* 4.0 25.4 - - + -
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Residues in contact with MET 429 (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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285D TRP* 3.6 29.4 - - + -
288D ARG 4.3 2.9 - - - +
289D CYS* 4.2 10.1 - - - -
292D ALA* 3.7 23.3 - - + -
377D LEU* 4.1 25.4 - - + +
380D ILE* 3.8 15.9 - - + -
381D ILE* 3.7 19.1 - - + -
425D SER 2.9 18.1 + - - +
426D VAL 4.0 3.6 - - - +
428D ALA* 1.3 68.9 - - - +
430D TYR* 1.3 66.2 + - - +
432D VAL* 3.1 9.2 + - - +
433D ALA* 3.0 20.3 + - - +
454D LEU* 4.3 4.9 - - + -
457D MET* 3.8 25.4 - - + -
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Residues in contact with TYR 430 (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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378D LEU* 3.8 25.4 - - + -
381D ILE* 3.6 11.6 - - + +
399D ILE* 5.3 0.4 - - + -
400D LYS* 3.6 35.1 + - + +
403D ILE* 3.6 40.5 - - + +
404D GLU* 5.1 3.0 + - + +
410D ILE* 3.6 33.0 - - + -
426D VAL 3.0 17.8 + - - +
427D GLU* 3.7 8.7 - - - +
428D ALA 3.3 0.2 - - - -
429D MET* 1.3 76.0 - - - +
431D SER* 1.3 60.7 + - - +
433D ALA* 3.2 2.8 + - - +
434D SER* 2.8 42.7 + - - -
437D LEU* 6.5 0.2 - - + -
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Residues in contact with SER 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D GLU 2.9 18.3 + - - -
428D ALA* 3.6 8.1 - - - -
429D MET 3.2 0.2 - - - -
430D TYR* 1.3 80.5 - - - +
432D VAL* 1.3 62.3 + - - +
434D SER* 3.4 6.8 + - - -
435D GLN* 3.1 41.0 + - - +
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Residues in contact with VAL 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D LEU* 3.7 19.3 - - + -
428D ALA 3.2 14.8 + - - +
429D MET 3.1 7.7 + - - +
431D SER* 1.3 78.2 - - - +
433D ALA* 1.3 56.0 + - - +
435D GLN* 3.3 10.8 + - - +
436D CYS* 2.9 30.2 + - - -
445D PRO* 5.2 0.8 - - + +
450D VAL* 3.8 30.3 - - + -
453D LEU* 3.7 34.8 - - + +
454D LEU* 4.0 19.7 - - + -
457D MET* 6.2 0.4 - - + -
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Residues in contact with ALA 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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374D GLY 3.7 18.2 - - - +
377D LEU* 3.7 21.3 - - + +
378D LEU* 3.9 20.0 - - + +
381D ILE* 5.0 0.2 - - + -
429D MET 3.0 12.3 + - - +
430D TYR* 3.4 10.5 - - - +
432D VAL* 1.3 75.9 - - - +
434D SER* 1.3 57.7 + - - +
436D CYS* 3.3 5.9 + - - +
437D LEU* 3.0 37.3 + - - +
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Residues in contact with SER 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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400D LYS* 3.3 37.0 + - - +
404D GLU* 3.7 8.8 + - - -
430D TYR* 2.8 39.7 + - - -
431D SER* 3.7 7.6 - - - -
433D ALA* 1.3 71.7 - - - +
435D GLN* 1.3 62.3 + - - +
437D LEU* 3.1 9.8 + - - -
438D HIS* 3.5 4.7 + - - +
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Residues in contact with GLN 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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431D SER* 3.1 38.6 + - - +
432D VAL* 3.6 6.5 - - - +
434D SER* 1.3 72.1 - - - +
436D CYS* 1.3 66.0 + - - +
437D LEU 3.2 0.3 + - - -
438D HIS* 3.3 20.6 + - - +
443D LYS 4.7 1.4 - - - +
444D ARG* 3.7 1.7 - - - -
445D PRO* 3.3 32.6 - - + +
449D LYS* 4.7 8.8 + - - -
453D LEU* 3.8 27.5 - - + +
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Residues in contact with CYS 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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370D ILE* 3.4 40.6 - - - +
371D TYR* 3.3 12.4 - - - -
373D PHE* 4.5 5.6 - - - -
374D GLY* 3.6 15.7 - - - -
377D LEU* 4.6 0.7 - - - -
432D VAL* 2.9 30.2 + - - -
433D ALA 3.3 8.7 + - - +
435D GLN* 1.3 76.3 - - - +
437D LEU* 1.3 57.9 + - - +
438D HIS 3.3 0.2 - - - -
444D ARG* 3.2 23.6 - - - -
445D PRO* 4.0 2.4 - - - +
450D VAL* 3.8 22.7 - - - -
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Residues in contact with LEU 437 (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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371D TYR* 3.4 56.7 - - + +
374D GLY* 4.1 7.2 - - - +
375D VAL* 3.8 12.1 - - + +
378D LEU* 3.7 35.4 - - + -
397D LEU* 4.7 8.7 - - + +
400D LYS* 3.8 32.9 + - + +
433D ALA 3.0 20.1 + - - +
434D SER* 3.6 8.3 - - - +
435D GLN 3.1 1.2 - - - -
436D CYS* 1.3 77.3 - - - +
438D HIS* 1.3 64.7 + - - +
439D GLU* 3.3 8.5 + - - +
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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