Contacts of the helix formed by residues 5316 - 5332 (chain a) 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 THR5316 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5302a PHE* 4.3 5.9 + - - +
5305a SER* 5.8 0.8 - - - -
5306a VAL* 3.1 43.0 - - + +
5315a ASN* 1.3 75.9 - - - +
5317a TRP* 1.3 60.4 + - - +
5318a ALA* 3.6 16.2 + - - +
5319a ASP* 2.8 32.3 + - - +
5320a ILE 3.7 0.7 + - - -
5063d LEU* 3.4 11.0 - - - +
5064d ALA* 3.7 13.0 - - + +
5071d CYS* 3.7 19.5 - - - -
5075d THR* 4.2 10.6 - - - +
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Residues in contact with TRP5317 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5316a THR* 1.3 73.8 - - - +
5318a ALA* 1.3 61.5 + - - +
5319a ASP 3.0 1.2 + - - -
5320a ILE* 3.2 22.5 + - + +
5321a ILE* 3.1 25.0 + - - +
5061d HIS* 3.4 39.3 - + - -
5063d LEU* 3.5 16.4 - - + +
5064d ALA 5.1 1.8 - - - -
5065d SER* 4.8 6.6 - - - -
5075d THR 4.4 14.5 + - - +
5077d ALA* 4.2 9.4 - - + -
5079d SER* 2.7 29.3 + - - -
5172d SER* 4.1 12.1 - - - -
5176d ALA* 4.1 6.3 - - + -
5177d ALA* 3.7 36.9 - - + +
5180d ARG* 3.6 50.5 - - + -
5333d ASP* 4.8 3.1 - - - -
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Residues in contact with ALA5318 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5194a MET* 4.7 6.1 - - + -
5302a PHE* 3.9 26.0 - - + +
5303a ASN* 3.7 8.5 - - - +
5316a THR* 2.9 14.2 + - - +
5317a TRP* 1.3 77.8 - - - +
5319a ASP* 1.3 58.3 + - - +
5321a ILE* 3.2 16.5 - - - +
5322a ASN* 3.2 18.5 + - - +
5075d THR* 3.7 24.2 - - + +
5176d ALA* 4.5 2.3 - - - +
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Residues in contact with ASP5319 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5302a PHE 4.2 2.3 - - - +
5303a ASN* 3.6 13.7 - - - +
5304a HIS* 3.4 35.8 + - - -
5305a SER 5.2 1.0 + - - -
5306a VAL* 5.4 0.5 - - - +
5315a ASN* 3.3 33.5 + - + +
5316a THR* 2.8 36.7 + - - +
5318a ALA* 1.3 76.0 - - - +
5320a ILE* 1.3 55.4 + - - +
5321a ILE 2.9 1.6 - - - -
5322a ASN* 3.0 3.6 + - - +
5323a ARG* 2.7 36.5 + - - +
5332d GLN* 5.3 0.9 - - - +
5163v TYR 5.2 3.4 - - - +
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Residues in contact with ILE5320 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5315a ASN* 4.9 5.2 - - + +
5316a THR 3.7 0.6 + - - +
5317a TRP* 3.2 19.4 + - + +
5319a ASP* 1.3 76.2 - - - +
5321a ILE* 1.3 65.6 + - - +
5323a ARG* 3.4 6.3 + - + +
5324a ALA* 3.2 17.3 + - - +
5063d LEU* 3.8 29.2 - - + -
5180d ARG* 3.8 13.2 - - + -
5329d MET* 4.1 6.0 - - + +
5332d GLN* 3.5 45.1 - - + +
5333d ASP* 2.8 35.7 - - + +
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Residues in contact with ILE5321 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5187a GLN* 4.6 2.0 - - - +
5191a ASN* 3.6 15.3 - - - +
5193a LEU* 6.2 1.3 - - + -
5194a MET* 4.2 11.0 - - + -
5317a TRP 3.1 12.2 + - - +
5318a ALA* 3.2 15.5 - - - +
5320a ILE* 1.3 77.8 - - - +
5322a ASN* 1.3 56.4 + - + +
5324a ALA* 2.7 30.0 + - - +
5325a ASN* 2.9 31.8 + - - +
5176d ALA* 3.5 37.9 - - + +
5179d PHE* 4.1 21.5 - - + -
5180d ARG* 4.5 15.7 - - + +
5183d LEU* 4.6 7.4 - - + +
5329d MET* 5.7 0.4 - - - -
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Residues in contact with ASN5322 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5191a ASN* 5.7 3.4 + - - -
5303a ASN* 3.0 34.0 - - - +
5318a ALA 3.2 2.9 + - - +
5319a ASP* 3.0 8.0 + - - +
5321a ILE* 1.3 80.8 - - + +
5323a ARG* 1.3 57.4 + - - +
5325a ASN* 3.1 10.5 + - - +
5326a LEU* 2.9 34.7 + - - +
5411c ALA 3.0 12.7 + - - -
5412c THR* 3.0 46.1 - - - +
5163v TYR* 4.9 5.9 - - - +
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Residues in contact with ARG5323 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5319a ASP 2.7 20.5 + - - +
5320a ILE* 3.4 12.8 - - + +
5321a ILE 2.9 0.2 + - - -
5322a ASN* 1.3 75.5 - - - +
5324a ALA* 1.3 61.7 + - - +
5326a LEU* 3.0 27.3 + - - +
5327a GLY 3.5 8.8 + - - -
5328d TRP* 3.1 52.0 + - - +
5329d MET* 4.0 11.4 - - - +
5331d PRO* 5.9 2.4 - - - +
5332d GLN* 3.0 32.0 - - + +
5346d LEU* 5.0 4.8 - - - +
5160v LYS 2.7 25.5 + - - -
5161v VAL* 2.7 25.1 + - - +
5163v TYR* 3.0 19.4 + - - -
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Residues in contact with ALA5324 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5320a ILE 3.2 1.2 + - - +
5321a ILE 2.7 12.7 + - - +
5323a ARG* 1.3 73.7 - - - +
5325a ASN* 1.3 63.4 + - - +
5326a LEU 3.3 0.2 - - - -
5327a GLY* 3.7 1.9 + - - +
5328a MET* 3.0 28.3 + - - +
5183d LEU* 4.2 13.9 - - + -
5325d ILE* 3.7 17.1 - - + +
5329d MET* 3.3 43.9 - - + +
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Residues in contact with ASN5325 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5187a GLN* 2.6 45.6 + - - +
5188a ALA* 3.2 17.2 - - - +
5191a ASN* 3.5 6.0 + - - -
5321a ILE* 2.9 46.5 + - - +
5322a ASN* 3.1 13.9 + - - +
5324a ALA* 1.3 76.9 - - - +
5326a LEU* 1.3 59.2 + - - +
5328a MET* 3.0 11.2 + - - +
5329a GLU* 2.8 25.3 + - - +
5411c ALA* 6.3 0.9 - - + -
5412c THR* 4.2 14.6 - - + -
5183d LEU* 4.1 3.6 - - - +
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Residues in contact with LEU5326 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5322a ASN* 2.9 21.5 + - - +
5323a ARG* 3.0 41.5 - - - +
5325a ASN* 1.3 76.4 - - - +
5327a GLY* 1.3 57.2 + - - +
5329a GLU* 2.7 29.3 + - - +
5330a VAL* 2.8 18.3 + - + +
5412c THR* 3.1 38.4 - - + +
5328d TRP* 3.9 16.8 - - + -
5160v LYS* 3.6 26.5 - - + +
5163v TYR* 4.3 12.6 - - + -
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Residues in contact with GLY5327 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5323a ARG 3.5 7.4 + - - -
5324a ALA 3.7 3.1 + - - -
5325a ASN 3.3 0.6 - - - -
5326a LEU* 1.3 78.6 - - - +
5328a MET* 1.3 61.5 + - - +
5330a VAL* 4.8 0.4 - - - -
5331a MET* 3.5 15.6 + - - +
5321d LEU 4.3 0.2 - - - +
5324d GLY* 3.3 43.8 - - - -
5325d ILE* 4.1 0.7 - - - -
5328d TRP* 3.8 18.3 - - - +
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Residues in contact with MET5328 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5184a ILE* 3.1 39.5 - - + +
5185a VAL* 5.5 0.7 - - - -
5187a GLN* 4.0 8.3 - - + -
5188a ALA* 3.2 14.1 - - + -
5324a ALA* 3.0 21.7 + - + +
5325a ASN* 3.0 15.2 + - - +
5326a LEU 2.9 0.8 - - - -
5327a GLY* 1.3 76.3 - - - +
5329a GLU* 1.3 66.3 + - - +
5330a VAL 3.1 0.9 + - - -
5332a HIS* 3.2 28.6 + - - +
5558a CLA 5.9 0.2 - - - -
5183d LEU* 3.5 35.0 - - + -
5321d LEU* 3.9 13.1 - - + +
5325d ILE* 3.3 31.2 - - + -
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Residues in contact with GLU5329 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5188a ALA* 3.6 12.5 - - + +
5189a GLU* 6.0 2.7 - - + -
5325a ASN 2.8 12.3 + - - +
5326a LEU* 2.7 14.8 + - - +
5328a MET* 1.3 72.7 - - - +
5330a VAL* 1.3 58.7 + - + +
5332a HIS* 2.5 39.0 + - + -
5342a ASP* 5.0 8.4 + - - +
5410c VAL* 3.9 15.5 - - + +
5412c THR* 2.5 38.6 + - + +
5352d LEU* 3.4 21.2 - - + +
5160v LYS* 2.8 28.0 + - - -
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Residues in contact with VAL5330 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5326a LEU* 2.8 21.1 + - - +
5327a GLY 4.2 3.4 - - - +
5329a GLU* 1.3 77.2 - - + +
5331a MET* 1.3 64.1 + - - +
5332a HIS 3.4 5.5 + - - +
5334a ARG* 5.0 0.2 - - - -
5337a HIS* 5.8 0.2 + - - -
5328d TRP* 3.7 28.0 - - + +
5347d PRO 3.8 4.5 - - - +
5348d ARG* 3.1 46.9 - - + +
5349d GLY* 3.4 13.9 + - - +
5352d LEU* 3.5 31.9 - - - +
5160v LYS* 4.2 10.1 - - - +
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Residues in contact with MET5331 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5327a GLY 3.5 7.1 + - - +
5328a MET 3.5 2.9 + - - +
5330a VAL* 1.3 73.1 - - + +
5332a HIS* 1.3 64.3 + - - +
5333a GLU 3.5 0.5 + - - -
5334a ARG* 3.4 24.1 + - + +
5383b PHE* 4.6 9.4 - - + -
5320d LEU* 3.7 53.9 - - + +
5321d LEU* 4.6 4.0 - - - -
5323d GLU* 4.9 4.5 - - + -
5324d GLY* 3.7 27.6 - - - -
5347d PRO* 3.5 44.2 - - + +
5348d ARG* 3.6 11.7 - - - -
5349d GLY* 4.2 2.9 - - - +
5183o LEU* 5.9 2.9 - - + -
5187o GLY* 6.2 0.2 - - - -
5194o TYR* 5.2 1.8 - - + +
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Residues in contact with HIS5332 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5185a VAL* 4.0 28.7 - - + -
5188a ALA* 6.4 0.4 - - + -
5189a GLU* 3.2 4.3 + - + -
5328a MET 3.2 14.4 + - - +
5329a GLU* 2.5 39.8 + - + -
5330a VAL 3.3 5.0 - - - +
5331a MET* 1.3 75.3 - - - +
5333a GLU* 1.3 85.9 + - + +
5334a ARG 3.2 0.5 + - - -
5337a HIS* 3.9 7.5 + + - -
5342a ASP* 3.5 10.3 - - - -
5565a OEC 2.3 36.6 + - - -
5321d LEU* 3.6 19.9 - - + +
5352d LEU* 3.7 10.8 - - + -
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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