Contacts of the helix formed by residues 5175 - 5189 (chain d) 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 VAL5175 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5560a CLA 3.5 37.2 - - + +
5562a PHO 4.0 15.9 - - + +
5048d TRP* 6.1 0.2 - - + -
5073d PHE* 4.0 30.0 + - + +
5074d LEU* 3.4 34.9 + - + +
5076d VAL 3.9 2.0 + - - -
5174d GLY* 1.3 73.4 - - - +
5176d ALA* 1.3 65.3 + - - +
5178d ILE* 3.3 20.6 + - - +
5179d PHE* 3.4 25.6 + - + -
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Residues in contact with ALA5176 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5194a MET* 4.4 9.0 - - + -
5317a TRP* 4.1 15.3 - - + -
5318a ALA* 4.5 5.8 - - - +
5321a ILE* 3.5 24.8 - - + +
5074d LEU 3.1 16.4 + - - +
5075d THR* 4.6 2.0 - - - -
5175d VAL* 1.3 75.2 - - - +
5177d ALA* 1.3 54.9 + - - +
5178d ILE 2.5 17.7 + - - -
5179d PHE* 2.8 25.0 + - + +
5180d ARG* 3.0 13.0 + - - +
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Residues in contact with ALA5177 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5317a TRP* 3.7 33.6 - - + +
5074d LEU 5.0 0.2 + - - -
5075d THR 6.2 0.4 - - - -
5076d VAL 5.3 0.4 + - - -
5077d ALA* 3.7 30.3 - - + -
5171d PRO* 4.9 0.3 - - - +
5172d SER* 3.8 27.2 + - - -
5174d GLY* 3.8 10.4 - - - +
5175d VAL 3.3 0.4 - - - -
5176d ALA* 1.3 76.0 - - - +
5178d ILE* 1.3 58.3 + - - +
5180d ARG* 4.2 8.4 - - - +
5181d PHE* 4.1 10.2 + - - +
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Residues in contact with ILE5178 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5560a CLA 4.0 58.3 - - + +
5562a PHO 4.6 7.9 - - + -
5157d PHE* 5.1 3.1 - - + -
5171d PRO* 3.9 24.9 - - + -
5172d SER 4.1 0.2 - - - +
5173d PHE* 4.1 14.6 - - - +
5174d GLY 3.4 16.3 + - - +
5175d VAL* 3.3 13.9 + - - +
5176d ALA 2.5 6.5 + - - -
5177d ALA* 1.3 77.2 - - - +
5179d PHE* 1.3 69.0 + - + +
5180d ARG 2.8 4.3 - - - -
5181d PHE* 2.5 26.7 + - + +
5182d LEU* 2.9 14.6 + - + +
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Residues in contact with PHE5179 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5193a LEU* 3.0 58.8 - - + -
5194a MET* 3.7 21.8 - - - -
5198a HIS* 6.1 0.4 - - - -
5199a GLN* 4.0 5.6 - - + -
5321a ILE* 4.1 12.3 - - + -
5560a CLA 3.3 48.2 - + + -
5175d VAL* 3.5 23.3 - - + -
5176d ALA* 2.8 20.5 + - + +
5178d ILE* 1.3 88.9 - - + +
5180d ARG* 1.3 60.1 + - - +
5182d LEU* 3.2 12.1 - - + +
5183d LEU* 3.1 30.5 + - - +
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Residues in contact with ARG5180 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5317a TRP* 3.6 38.8 - - + -
5320a ILE* 3.8 8.7 - - + -
5321a ILE* 4.5 14.5 - - + +
5168d PHE* 5.0 6.7 + - - -
5169d PHE* 4.3 23.0 + - - +
5170d ALA 5.0 4.6 + - - -
5171d PRO* 5.9 0.2 - - - +
5176d ALA 3.0 13.5 + - - +
5177d ALA 4.2 6.7 - - - +
5178d ILE 2.8 0.2 - - - -
5179d PHE* 1.3 76.6 - - - +
5181d PHE* 1.3 86.0 + - - +
5183d LEU* 3.4 5.0 + - - +
5184d PHE* 2.9 57.4 + - - +
5329d MET* 4.2 5.2 - - + +
5333d ASP* 2.7 43.6 + - - +
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Residues in contact with PHE5181 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5560a CLA 3.9 11.2 - - + -
5156d VAL* 4.2 5.8 - - + -
5160d TYR* 4.1 7.6 - + - -
5169d PHE 3.5 15.9 - - - -
5170d ALA 4.0 0.4 - - - -
5171d PRO* 3.3 50.3 - - + -
5177d ALA 4.1 5.1 + - - +
5178d ILE* 2.5 25.7 + - - +
5180d ARG* 1.3 97.8 - - - +
5182d LEU* 1.3 60.4 + - - +
5184d PHE* 4.0 0.8 - - - +
5185d PHE* 3.2 55.2 + + - +
5286d VAL* 6.2 0.2 - - + -
5354d CLA 3.6 30.1 - - + -
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Residues in contact with LEU5182 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5193a LEU* 3.5 32.1 - - + -
5558a CLA 3.7 26.7 - - + -
5560a CLA 3.7 32.8 - - + -
5178d ILE* 2.9 14.5 + - + +
5179d PHE* 3.2 21.8 - - + +
5181d PHE* 1.3 75.8 - - - +
5183d LEU* 1.3 67.5 + - - +
5185d PHE* 3.0 7.6 + - - +
5186d GLN 3.0 17.3 + - - -
5354d CLA 3.5 42.7 - - + +
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Residues in contact with LEU5183 (chain d).
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* 4.3 10.1 - - + +
5193a LEU* 3.8 20.9 - - + -
5321a ILE* 4.6 8.7 - - + +
5324a ALA* 4.2 19.7 - - + -
5325a ASN* 4.1 17.0 - - - +
5328a MET* 3.5 31.4 - - + -
5558a CLA 3.9 19.7 - - + -
5179d PHE 3.1 17.4 + - - +
5180d ARG* 4.0 3.4 - - - +
5182d LEU* 1.3 71.4 - - - +
5184d PHE* 1.3 57.0 + - - +
5186d GLN* 3.0 10.2 + - + +
5187d GLY* 2.7 34.1 + - - -
5325d ILE* 4.1 7.7 - - + +
5329d MET* 4.6 1.3 - - + -
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Residues in contact with PHE5184 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5362b PHE* 3.0 38.4 - + - -
5160d TYR* 4.0 5.2 - - - -
5169d PHE* 4.8 6.5 - + + -
5180d ARG* 2.9 51.7 + - - +
5181d PHE 4.0 3.6 - - - +
5183d LEU* 1.3 75.3 - - - +
5185d PHE* 1.3 74.2 + + - +
5187d GLY* 4.9 0.2 - - - -
5188d PHE* 2.8 62.6 + + + +
5189d HIS* 3.7 20.9 - - - -
5329d MET* 4.3 19.7 - - + +
5333d ASP* 4.9 2.5 - - - -
5334d GLN* 4.3 8.1 - - - -
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Residues in contact with PHE5185 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5160d TYR* 3.4 41.3 - + - -
5181d PHE* 3.2 50.7 + + - +
5182d LEU 3.0 10.6 + - - +
5184d PHE* 1.3 86.8 - + - +
5186d GLN* 1.3 64.2 + - - +
5189d HIS* 2.8 34.0 + + - +
5190d ASN 2.9 6.2 + - - -
5191d TRP* 4.0 17.3 - + + -
5286d VAL* 4.5 14.6 - - + -
5289d LEU* 3.2 35.4 - - + -
5354d CLA 3.6 22.0 - - + -
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Residues in contact with GLN5186 (chain d).
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* 3.0 36.8 - - + +
5558a CLA 5.9 2.0 - - + -
5182d LEU 3.0 8.6 + - - +
5183d LEU* 3.5 12.8 - - + +
5185d PHE* 1.3 75.7 - - - +
5187d GLY* 1.3 57.8 + - - +
5190d ASN* 3.1 31.3 + - - +
5192d THR* 2.5 38.1 + - - +
5318d ASN* 4.9 2.0 + - - +
5322d ASN* 2.6 36.7 + - - +
5325d ILE* 4.5 8.7 - - + -
5354d CLA 3.4 20.1 - - + +
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Residues in contact with GLY5187 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5183d LEU 2.7 19.2 + - - -
5184d PHE 3.6 0.9 - - - -
5186d GLN* 1.3 75.1 - - - +
5188d PHE* 1.3 63.5 + - - +
5190d ASN 4.7 0.2 - - - -
5296d TYR* 4.5 0.5 - - - -
5322d ASN* 3.5 15.9 - - - +
5325d ILE* 3.9 23.1 - - - -
5326d ARG* 3.2 26.7 + - - +
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Residues in contact with PHE5188 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5362b PHE* 3.7 25.5 - + + +
5363b PHE* 3.6 30.7 - + - -
5364b GLU* 4.7 1.7 - - - +
5184d PHE* 2.8 60.9 + + + +
5187d GLY* 1.3 78.9 - - - -
5189d HIS* 1.3 63.1 + - + +
5190d ASN 3.6 0.7 - - - -
5294d ARG* 3.2 25.9 + - - +
5296d TYR* 3.9 10.4 - - - -
5325d ILE* 5.0 0.4 - - + -
5326d ARG* 3.5 39.4 + - + +
5329d MET* 4.2 12.3 - - - -
5330d ALA* 4.6 6.7 - - + -
5334d GLN* 3.9 19.3 - - - -
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Residues in contact with HIS5189 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5362b PHE* 4.9 2.2 - + - -
5160d TYR* 2.7 25.7 + + - -
5164d GLN* 4.5 2.0 - - - -
5184d PHE* 3.7 14.5 - + - -
5185d PHE* 2.8 45.8 + + + +
5188d PHE* 1.3 73.0 - - + +
5190d ASN* 1.3 73.4 + - - +
5191d TRP* 3.3 4.0 + - - +
5289d LEU* 3.7 38.5 - - + +
5292d ASN* 3.1 23.1 - - - -
5294d ARG* 3.1 45.2 + - - +
5295d SER 4.3 1.2 + - - +
5296d TYR* 4.0 5.3 - - - -
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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
------------------------------------------------------------
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