Contacts of the helix formed by residues 430 - 440 (chain B) in PDB entry 2EIT
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 430 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B THR* 3.6 12.8 - - - -
428B VAL* 3.5 3.5 - - - +
429B LYS* 1.3 102.5 - - + +
431B PHE* 1.3 60.1 + - - +
432B ALA* 3.5 11.7 + - - +
433B GLU* 3.0 25.0 + - - +
434B ALA* 3.0 26.3 + - - +
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Residues in contact with PHE 431 (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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296B ILE* 3.8 21.8 - - + -
298B ASP* 3.9 12.1 - - + -
331B THR* 3.8 5.7 - - + +
430B ASP* 1.3 76.0 - - - +
432B ALA* 1.3 58.1 + - - +
434B ALA* 3.1 6.4 + - - +
435B LEU* 2.9 50.9 + - + +
449B VAL* 3.7 31.4 - - + -
456B HIS* 3.4 71.5 - + + +
459B TRP* 3.6 22.9 - + + -
460B ALA* 4.2 8.5 - - + -
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Residues in contact with ALA 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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430B ASP* 3.3 12.8 + - - +
431B PHE* 1.3 76.1 - - - +
433B GLU* 1.3 62.6 + - - +
435B LEU* 3.2 6.3 + - - +
436B GLU* 3.1 32.5 + - - +
459B TRP* 3.5 34.2 - - + -
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Residues in contact with GLU 433 (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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427B ARG 4.9 0.3 - - - +
428B VAL* 3.5 17.2 - - + +
429B LYS* 2.8 50.5 + - - +
430B ASP* 3.0 22.4 + - - +
432B ALA* 1.3 73.6 - - - +
434B ALA* 1.3 59.9 + - - +
436B GLU* 3.3 17.4 + - + +
437B VAL* 2.9 35.6 + - + +
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Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE* 3.6 33.9 - - + +
329B ILE* 3.8 16.1 - - + +
331B THR* 4.6 2.0 - - + -
428B VAL* 3.7 14.1 - - + +
430B ASP 3.0 14.5 + - - +
431B PHE* 3.2 12.6 - - - +
433B GLU* 1.3 75.7 - - - +
435B LEU* 1.3 58.2 + - - +
437B VAL* 3.4 1.4 + - - +
438B ALA* 2.8 30.0 + - - +
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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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296B ILE* 3.9 16.6 - - + -
431B PHE* 2.9 32.1 + - + +
432B ALA 3.6 7.2 - - - +
433B GLU 3.2 0.4 - - - -
434B ALA* 1.3 74.1 - - - +
436B GLU* 1.3 64.9 + - + +
438B ALA* 3.3 1.3 + - - +
439B ASN* 3.0 37.2 + - - +
459B TRP* 3.7 45.8 - - + +
460B ALA* 4.2 9.9 - - + -
463B GLU* 4.7 6.5 - - + -
464B PHE* 3.7 36.8 - - + -
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Residues in contact with GLU 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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432B ALA* 3.1 23.3 + - - +
433B GLU* 3.6 20.7 - - + +
435B LEU* 1.3 76.5 - - + +
437B VAL* 1.3 63.2 + - + +
439B ASN* 3.3 6.3 + - - +
440B ASP* 3.1 26.5 + - - +
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Residues in contact with VAL 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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327B ARG* 2.9 17.9 + - - +
329B ILE* 3.8 17.0 - - + -
409B PRO* 4.1 29.4 - - + -
426B ILE* 4.0 26.2 - - + -
428B VAL* 3.8 19.1 - - + -
433B GLU* 2.9 26.4 + - + +
434B ALA 3.9 3.1 - - - +
436B GLU* 1.3 75.9 - - + +
438B ALA* 1.3 64.9 + - - +
439B ASN 3.3 0.3 + - - -
440B ASP* 3.3 15.8 + - - +
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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
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296B ILE* 3.9 8.1 - - + -
327B ARG* 2.8 24.2 + - - +
329B ILE* 3.6 17.4 - - + +
434B ALA 2.8 19.5 + - - +
435B LEU* 3.6 6.3 - - - +
437B VAL* 1.3 74.9 - - - +
439B ASN* 1.3 61.9 + - - +
440B ASP 3.5 0.2 + - - -
441B THR* 4.2 4.2 + - - +
443B TYR 5.8 0.2 - - - +
464B PHE* 3.7 36.8 - - + -
466B VAL* 5.9 1.2 - - - +
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Residues in contact with ASN 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 LEU* 3.0 26.9 + - - +
436B GLU* 3.9 4.6 - - - +
437B VAL 3.2 0.2 - - - -
438B ALA* 1.3 77.0 - - - +
440B ASP* 1.3 56.5 - - - +
441B THR* 2.9 12.9 + - - +
443B TYR 5.8 0.2 - - - -
463B GLU* 2.9 24.0 + - - +
464B PHE* 3.8 6.5 - - - +
465B HIS* 2.8 36.9 + - - +
466B VAL* 5.6 0.2 - - - +
489B LYS* 2.9 25.0 + - - +
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Residues in contact with ASP 440 (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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327B ARG* 4.8 0.2 + - - -
409B PRO* 5.7 4.8 - - + +
410B LYS* 2.6 41.4 + - - +
415B GLN* 2.9 29.6 + - - -
436B GLU 3.1 17.4 + - - +
437B VAL* 3.3 11.1 + - - +
439B ASN* 1.3 74.8 - - - +
441B THR* 1.3 54.4 + - - +
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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