Contacts of the helix formed by residues 429 - 441 (chain B) in PDB entry 2I91
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 LEU 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350B VAL* 6.6 0.2 - - + -
351B GLU* 5.4 9.6 - - + -
354B ASP* 3.0 28.3 - - - +
405B ARG* 6.3 1.1 - - - +
427B ASN 5.0 4.7 - - - +
428B MET* 1.3 75.3 - - - +
430B LEU* 1.3 67.6 + - - +
431B HIS* 3.2 12.6 - - + +
432B GLU* 2.9 26.6 + - + +
433B VAL* 3.0 9.6 + - - +
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 4.2 29.4 - - + -
328B LEU* 4.6 8.1 - - + -
354B ASP* 3.3 25.4 + - + +
357B PHE* 3.2 46.0 - - + -
358B TYR* 3.3 31.3 + - + +
394B VAL* 6.3 0.2 - - + -
398B ALA* 4.4 15.3 - - + -
401B MET* 5.9 0.2 - - + -
428B MET 3.9 1.2 + - - -
429B LEU* 1.3 72.2 - - - +
431B HIS* 1.3 59.4 + - - +
433B VAL* 3.2 23.1 - - + +
434B VAL* 3.0 23.1 + - + +
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Residues in contact with HIS 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.5 14.4 - - + +
332B LYS* 2.8 59.3 + - + +
350B VAL* 4.1 17.6 - - + +
354B ASP* 5.4 1.0 - - + +
429B LEU* 3.1 13.1 + - + +
430B LEU* 1.3 75.2 - - - +
432B GLU* 1.3 76.6 + - + +
433B VAL 3.3 0.2 - - - -
434B VAL* 3.7 7.2 - - - -
435B GLU* 3.4 24.5 + - - +
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Residues in contact with GLU 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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428B MET* 3.1 41.6 - - + +
429B LEU* 2.9 19.1 + - + +
431B HIS* 1.3 90.6 - - + +
433B VAL* 1.3 56.0 + - - +
434B VAL 3.2 0.4 - - - -
435B GLU* 4.1 8.2 - - - +
436B LYS* 2.7 63.2 + - - +
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Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 5.0 3.4 - - + +
397B ALA* 4.2 22.0 - - + -
398B ALA* 4.9 5.4 - - + +
401B MET* 4.4 21.1 - - + -
424B ILE* 3.5 26.7 - - + -
428B MET* 4.3 11.2 - - + -
429B LEU 3.0 20.6 - - - +
430B LEU* 3.2 23.6 - - + +
432B GLU* 1.3 74.0 - - - +
434B VAL* 1.3 65.6 + - + +
436B LYS* 3.9 0.6 - - - +
437B MET* 2.9 34.1 + - + +
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 4.5 14.8 - - + -
328B LEU* 5.4 2.0 - - + -
329B GLU* 3.8 30.7 - - + +
332B LYS* 4.4 1.8 - - - +
390B LEU* 5.1 1.3 - - + -
394B VAL* 3.7 37.9 - - + +
430B LEU* 3.0 21.7 + - + +
431B HIS* 3.6 12.8 - - - +
432B GLU 3.2 0.4 - - - -
433B VAL* 1.3 78.6 - - + +
435B GLU* 1.3 67.3 + - - +
437B MET* 3.2 14.7 + - - +
438B SER* 3.2 10.7 + - - +
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Residues in contact with GLU 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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332B LYS* 5.2 4.8 + - - +
431B HIS* 3.4 21.2 + - - +
432B GLU* 4.1 13.9 - - - +
434B VAL* 1.3 82.1 - - - +
436B LYS* 1.3 74.2 + - + +
438B SER* 2.7 30.0 - - - +
439B ASP* 2.8 16.3 - - - +
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Residues in contact with LYS 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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423B PRO* 3.3 26.4 - - + +
424B ILE* 4.0 11.2 - - + -
428B MET* 3.0 27.8 - - + -
432B GLU* 2.7 44.8 + - - +
433B VAL 4.0 4.3 - - - +
434B VAL 3.1 1.2 - - - -
435B GLU* 1.3 85.8 + - + +
437B MET* 1.3 53.7 + - - +
438B SER 3.0 5.1 + - - -
439B ASP* 3.7 10.8 + - - +
440B ILE* 2.6 31.4 + - - +
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Residues in contact with MET 437 (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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375B ILE* 3.8 14.8 - - + -
377B VAL* 3.6 31.6 - - + -
391B ASN* 5.4 0.8 + - - -
393B SER* 3.8 14.1 - - - +
394B VAL* 4.3 19.1 - - + -
397B ALA* 3.8 32.5 - - + -
414B ALA* 5.6 0.9 - - + -
423B PRO* 4.0 23.3 - - + -
424B ILE* 4.3 8.3 - - - -
433B VAL 2.9 22.7 - - - +
434B VAL* 3.2 7.3 + - - +
436B LYS* 1.3 74.7 - - - +
438B SER* 1.3 64.2 + - - +
440B ILE* 3.5 4.0 - - + -
441B THR* 2.8 31.0 + - - -
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN* 5.9 3.8 - - - +
394B VAL* 5.7 0.9 - - - +
434B VAL* 3.2 7.3 + - - +
435B GLU* 2.7 29.7 - - - +
437B MET* 1.3 79.6 - - - +
439B ASP* 1.3 62.1 + - - +
440B ILE 3.1 1.4 + - - -
441B THR* 3.7 10.3 + - - +
442B MET* 5.5 0.5 - - - +
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Residues in contact with ASP 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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435B GLU* 2.8 29.3 - - - +
436B LYS* 3.7 8.7 + - - +
437B MET 3.5 0.4 - - - -
438B SER* 1.3 75.3 - - - +
440B ILE* 1.3 57.6 + - + +
442B MET* 3.4 19.5 - - - +
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Residues in contact with ILE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B VAL* 3.7 36.1 - - + +
414B ALA* 4.1 5.2 - - + -
420B LEU* 4.7 13.0 - - + +
421B PRO 4.5 4.9 - - - +
423B PRO* 3.7 37.7 - - + -
436B LYS 2.6 31.6 - - - +
437B MET* 3.5 13.0 - - - +
438B SER 3.1 0.2 - - - -
439B ASP* 1.3 77.7 - - + +
441B THR* 1.3 64.2 + - - +
442B MET* 3.3 15.5 + - - +
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Residues in contact with THR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B VAL* 3.2 9.0 - - - +
378B SER 3.4 22.2 - - - +
379B ALA 4.5 0.2 - - - +
381B MET 3.9 2.9 - - - -
382B ASN* 3.3 40.7 - - - +
391B ASN* 4.5 4.1 + - - +
393B SER* 2.6 32.1 + - - +
437B MET 2.8 21.0 + - - -
438B SER 3.7 7.3 + - - +
440B ILE* 1.3 73.4 - - - +
442B MET* 1.3 71.0 + - - +
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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