Contacts of the helix formed by residues 314 - 318 (chain B) in PDB entry 2AXT
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 TYR 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ARG* 4.5 4.0 - - - -
275B TRP* 4.1 3.3 - - - -
311B PHE* 3.3 20.6 - + - +
312B TYR 3.1 5.5 + - - +
313B ASP* 1.3 78.2 - - - +
315B ILE* 1.3 60.4 + - + +
316B GLY* 2.8 31.5 + - - -
317B ASN* 2.9 35.9 + - - +
318B ASN 4.0 1.4 + - - -
334B ASP* 2.3 34.8 + - - +
426B PHE* 3.4 31.0 - + + -
428B GLU 3.8 19.5 - - - +
430B PHE* 4.5 8.1 - + + -
432B PHE* 3.2 22.2 - + - -
443B PHE* 3.6 3.9 - + - -
202O GLN* 2.8 26.7 + - - -
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Residues in contact with ILE 315 (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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275B TRP* 3.4 31.1 - - + +
314B TYR* 1.3 70.9 - - - +
316B GLY* 1.3 61.4 + - - +
317B ASN 3.0 1.1 - - - -
318B ASN* 2.8 32.8 + - + +
321B LYS* 3.6 24.7 - - + +
359B MET* 3.2 53.2 - - + +
361B ALA 4.4 2.7 - - - +
426B PHE* 2.8 44.2 + - + +
443B PHE* 3.9 13.2 - - + -
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Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 3.7 8.0 + - - -
314B TYR* 2.8 30.4 + - - -
315B ILE* 1.3 81.4 - - - +
317B ASN* 1.3 60.2 + - - +
318B ASN 3.3 1.7 - - - +
321B LYS* 5.8 0.8 - - - +
330B MET* 3.3 17.3 - - - +
334B ASP* 4.3 2.1 - - - +
443B PHE* 3.5 23.7 - - - +
444B ARG 4.9 1.2 - - - +
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Residues in contact with ASN 317 (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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56B TRP* 3.0 33.4 - - + -
57B ARG* 2.8 29.3 + - - -
270B PRO* 3.8 23.7 - - + +
311B PHE* 3.1 44.1 + - - +
312B TYR* 4.7 2.2 - - - +
314B TYR* 2.9 22.6 + - - +
316B GLY* 1.3 76.0 - - - +
318B ASN* 1.3 59.2 + - - +
319B PRO* 3.2 13.7 - - - +
330B MET* 3.7 11.3 - - - +
446B SER* 5.1 0.9 + - - -
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Residues in contact with ASN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B PRO* 5.9 0.2 - - - -
271B THR 5.5 0.7 - - - -
272B ARG* 3.2 19.8 + - - +
275B TRP* 3.4 27.7 - - + +
314B TYR 4.0 0.6 + - - +
315B ILE* 2.8 24.2 + - + +
316B GLY 3.3 1.1 - - - +
317B ASN* 1.3 77.5 - - - +
319B PRO* 1.3 66.2 - - - +
320B ALA* 2.8 22.9 + - - +
321B LYS* 2.9 25.5 + - + +
330B MET* 4.9 5.4 - - - +
361B ALA* 3.0 31.3 - - - +
444B ARG 5.4 0.3 - - - +
445B THR* 5.2 0.9 - - - -
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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