Contacts of the helix formed by residues 429 - 439 (chain B) in PDB entry 2XAF
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 ASN 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425B ARG 3.6 8.0 + - - -
426B ARG 4.1 6.6 + - - -
427B ARG 3.5 4.4 - - - +
428B PHE* 1.3 80.4 - - - +
430B ILE* 1.3 52.8 + - - +
431B ASP* 2.7 10.1 + - + +
432B GLU* 2.7 58.5 + - + +
433B VAL* 3.1 7.4 + - + -
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Residues in contact with ILE 430 (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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392B VAL* 6.5 0.2 - - + -
395B ILE* 4.0 24.2 - - + -
420B PHE* 4.0 20.0 - - + -
421B PHE* 3.7 29.4 - - + +
424B TYR 4.0 3.1 - - - -
425B ARG* 3.5 41.1 + - + +
428B PHE* 2.9 19.3 + - + -
429B ASN* 1.3 73.8 - - - +
431B ASP* 1.3 62.7 + - - +
433B VAL* 3.9 6.3 - - + -
434B LEU* 2.9 44.0 + - + +
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Residues in contact with ASP 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ARG* 2.5 44.7 + - - +
429B ASN* 2.7 4.4 + - - +
430B ILE* 1.3 78.0 - - - +
432B GLU* 1.3 66.5 + - + +
434B LEU* 3.5 4.0 - - - +
435B GLN* 2.9 29.7 + - - +
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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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429B ASN* 2.7 51.6 + - + +
431B ASP* 1.3 74.2 - - + +
433B VAL* 1.3 66.6 + - + +
435B GLN* 3.1 28.4 + - - +
436B GLU* 2.9 29.8 + - + +
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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
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392B VAL* 4.2 19.3 - - + +
395B ILE* 3.0 33.2 - - + -
396B ARG* 3.7 25.1 - - + +
428B PHE* 3.6 24.0 - - + +
429B ASN* 3.1 2.1 + - + +
430B ILE* 3.7 11.0 - - + +
432B GLU* 1.3 81.8 - - + +
434B LEU* 1.3 61.1 + - - +
436B GLU* 3.3 7.8 + - - +
437B TRP* 3.2 17.5 + - - +
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Residues in contact with LEU 434 (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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395B ILE* 3.9 10.5 - - + -
399B GLY* 3.0 40.4 - - - +
400B ARG* 4.5 32.1 - - - +
421B PHE* 3.7 27.8 - - + -
430B ILE* 2.9 26.2 + - + +
431B ASP* 3.5 4.0 - - - +
433B VAL* 1.3 77.7 - - - +
435B GLN* 1.3 58.5 + - - +
437B TRP* 2.9 22.7 + - + +
438B GLU* 3.1 16.3 + - - +
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Residues in contact with GLN 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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431B ASP* 2.9 14.7 + - - +
432B GLU* 3.3 37.3 + - - +
434B LEU* 1.3 75.8 - - - +
436B GLU* 1.3 70.3 + - + +
438B GLU* 3.2 22.0 + - - +
439B ALA* 3.2 18.5 + - - +
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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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396B ARG* 3.9 34.0 + - - +
432B GLU* 2.9 19.5 + - + +
433B VAL* 3.4 11.2 - - - +
435B GLN* 1.3 84.0 - - + +
437B TRP* 1.3 61.4 - - - +
439B ALA* 3.5 22.2 + - - +
440B GLU* 4.2 3.3 + - - +
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Residues in contact with TRP 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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395B ILE 4.3 5.8 - - - +
396B ARG* 3.4 31.4 - - - +
397B LYS* 3.9 6.3 + - - -
398B TYR* 3.7 22.4 - - - +
399B GLY* 3.3 32.5 - - - -
400B ARG* 4.6 15.5 - - + -
433B VAL 3.2 8.8 + - - +
434B LEU* 2.9 15.0 + - + +
436B GLU* 1.3 75.6 - - - +
438B GLU* 1.3 76.9 - - + +
440B GLU* 3.1 37.6 + - + +
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Residues in contact with GLU 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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400B ARG* 3.2 31.9 + - - +
434B LEU 3.1 16.2 + - - +
435B GLN* 3.2 25.0 + - - +
437B TRP* 1.3 88.2 - - + +
439B ALA* 1.3 55.4 + - - +
440B GLU 2.9 15.8 + - - -
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Residues in contact with ALA 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 GLN 3.2 10.6 + - - +
436B GLU* 3.5 17.9 - - - +
437B TRP 3.3 1.0 - - - -
438B GLU* 1.3 73.6 - - - +
440B GLU* 1.3 61.8 + - + +
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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