Contacts of the helix formed by residues 5385 - 5397 (chain c) 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 GLN5385 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5383c ASP* 3.3 21.7 + - - +
5384c ILE* 1.3 76.5 - - - +
5386c PRO* 1.3 77.7 - - + +
5387c TRP* 3.1 36.6 - - + +
5388c GLN* 3.1 22.7 + - - +
5389c GLU* 3.5 3.6 + - - +
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Residues in contact with PRO5386 (chain c).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5384c ILE 4.2 2.5 - - - +
5385c GLN* 1.3 87.4 - - + +
5387c TRP* 1.3 63.4 + - - +
5388c GLN 2.9 7.6 + - - -
5389c GLU* 3.0 22.7 + - + +
5390c ARG* 3.1 31.3 + - - +
5116v GLU* 3.8 27.1 - - + +
5117v VAL* 4.1 16.6 - - + +
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Residues in contact with TRP5387 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5364c PRO* 4.4 8.3 - - + -
5365c TRP* 3.7 27.1 - - + -
5368c PRO* 5.1 7.9 - - + -
5385c GLN* 3.1 40.2 - - + +
5386c PRO* 1.3 78.1 - - - +
5388c GLN* 1.3 75.8 + - + +
5390c ARG* 3.6 30.8 + - - +
5391c ARG* 3.0 56.8 + - - +
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Residues in contact with GLN5388 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5315c MET* 5.7 4.5 - - + -
5319c ILE* 5.2 0.7 - - - -
5365c TRP* 2.8 36.2 + - + +
5368c PRO* 4.1 19.8 - - - +
5369c LEU* 4.4 13.1 - - + +
5383c ASP 3.9 4.7 - - - +
5384c ILE* 3.6 17.0 - - + +
5385c GLN* 3.4 25.9 + - - +
5386c PRO 2.9 0.8 - - - -
5387c TRP* 1.3 112.7 - - + +
5389c GLU* 1.3 58.1 + - - +
5390c ARG 3.1 1.6 - - - -
5391c ARG* 4.1 4.7 - - - -
5392c ALA* 2.6 39.9 + - - +
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Residues in contact with GLU5389 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5316c THR* 4.8 4.0 + - - -
5319c ILE* 3.9 41.5 - - + +
5320c ARG* 5.7 1.6 + - - -
5323c LYS* 3.0 35.1 + - - +
5384c ILE* 5.1 4.6 - - + +
5385c GLN 3.5 4.8 + - - +
5386c PRO* 3.0 16.7 + - + +
5388c GLN* 1.3 78.0 - - - +
5390c ARG* 1.3 58.2 + - - +
5392c ALA* 3.9 3.1 - - - +
5393c ALA* 3.2 22.7 + - - +
5117v VAL* 3.6 28.4 - - + +
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Residues in contact with ARG5390 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5386c PRO* 3.1 31.7 + - - +
5387c TRP* 3.6 28.0 + - - +
5389c GLU* 1.3 75.4 - - - +
5391c ARG* 1.3 64.2 + - - +
5392c ALA 3.2 1.1 - - - -
5393c ALA* 3.2 7.8 + - - +
5394c GLU* 2.8 28.4 + - - +
5116v GLU* 2.8 29.0 + - - +
5117v VAL* 4.4 14.8 - - + +
5126v ILE* 3.0 51.7 - - - +
5127v PHE* 3.8 26.9 - - + -
5552v HEM 5.4 2.6 - - + +
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Residues in contact with ARG5391 (chain c).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5102c GLY* 5.5 4.6 + - - -
5188c THR* 5.9 0.4 - - - +
5300c GLU* 3.6 27.3 + - - +
5364c PRO* 5.8 2.4 - - - +
5365c TRP* 3.4 35.4 - - + +
5387c TRP* 3.0 39.5 + - - +
5388c GLN* 3.0 5.0 + - - +
5390c ARG* 1.3 78.4 - - - +
5392c ALA* 1.3 63.3 + - - +
5394c GLU* 3.2 7.8 + - + +
5395c TYR* 3.1 59.6 + - + -
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Residues in contact with ALA5392 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5312c ALA* 3.1 29.5 - - + +
5315c MET* 3.5 36.1 - - + -
5316c THR* 3.6 11.0 + - - +
5365c TRP* 4.7 10.4 - - + -
5388c GLN 2.6 22.4 + - - +
5389c GLU* 3.9 5.6 - - - +
5391c ARG* 1.3 74.6 - - - +
5393c ALA* 1.3 60.6 + - - +
5395c TYR* 4.9 0.4 - - - -
5396c MET* 3.2 8.1 + - - +
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Residues in contact with ALA5393 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5316c THR* 3.8 11.2 + - + +
5389c GLU 3.2 15.6 + - - +
5390c ARG* 3.2 9.1 + - - +
5391c ARG 3.2 0.6 - - - -
5392c ALA* 1.3 77.6 - - - +
5394c GLU* 1.3 65.9 + - - +
5396c MET* 3.3 5.0 + - - +
5397c THR* 3.1 28.8 + - - +
5074v THR* 4.2 18.8 - - + +
5117v VAL* 6.4 0.9 - - + -
5552v HEM 4.2 18.6 - - + -
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Residues in contact with GLU5394 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5080c PRO* 4.2 3.9 - - - +
5082c TYR* 2.6 30.3 + - - +
5083c GLU* 3.5 8.0 - - - +
5390c ARG 2.8 17.2 + - - +
5391c ARG* 3.4 12.6 - - - +
5393c ALA* 1.3 72.0 - - - +
5395c TYR* 1.3 71.9 + - + +
5397c THR* 2.8 20.4 + - - -
5398c HIS* 2.8 43.4 + - - -
5065v SER* 5.5 0.5 + - - -
5127v PHE* 6.0 3.5 - - - -
5552v HEM 5.5 6.5 - - - +
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Residues in contact with TYR5395 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5082c TYR* 4.5 8.5 - + - -
5299c SER* 4.0 24.8 + - - -
5300c GLU* 4.3 6.9 - - - +
5304c PRO* 3.6 21.6 - - + +
5308c GLU* 3.6 24.2 - - + -
5309c ALA* 3.6 13.2 - - - +
5312c ALA* 4.1 9.4 - - + -
5365c TRP* 3.5 37.9 - + - -
5391c ARG* 3.1 49.7 + - + +
5392c ALA 4.1 3.1 - - - +
5394c GLU* 1.3 88.7 - - + +
5396c MET* 1.3 65.1 + - - +
5397c THR 3.0 1.8 - - - -
5398c HIS* 3.0 13.0 + - + -
5399c ALA 3.4 8.8 + - - -
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Residues in contact with MET5396 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5341a LEU* 3.3 49.9 - - + +
5343a LEU* 4.2 8.9 - - + +
5309c ALA* 4.1 12.8 - - - +
5312c ALA* 4.0 0.6 - - - +
5313c GLN* 3.7 42.6 - - + +
5316c THR* 3.7 28.0 - - - +
5317c PHE* 4.2 2.9 - - + -
5392c ALA 3.2 16.1 + - - +
5393c ALA 3.3 10.7 + - - +
5395c TYR* 1.3 75.7 - - - +
5397c THR* 1.3 64.7 + - + +
5398c HIS 3.3 1.4 + - - -
5399c ALA* 4.2 5.2 + - - +
5073v LYS* 3.5 24.0 - - + +
5074v THR* 3.8 13.5 - - + -
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Residues in contact with THR5397 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5341a LEU* 5.6 1.3 - - - -
5393c ALA 3.1 13.9 + - - +
5394c GLU* 2.8 20.8 + - - -
5395c TYR 3.0 0.2 - - - -
5396c MET* 1.3 80.5 - - + +
5398c HIS* 1.3 76.2 + - - +
5399c ALA 3.7 0.9 - - - -
5419c PHE* 5.8 0.7 - - - -
5065v SER* 3.6 33.2 + - - +
5066v CYS* 4.6 6.9 - - + +
5073v LYS* 4.4 12.8 - - + +
5074v THR* 3.8 24.7 - - + -
5552v HEM 5.4 2.9 - - + +
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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