Contacts of the strand formed by residues 210 - 216 (chain G) in PDB entry 2HU4
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 ILE 210 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E TYR* 4.6 10.1 - - + +
129E CYS* 5.8 1.3 - - - -
412E GLN* 3.4 55.4 - - + +
413E THR* 3.7 26.7 - - + +
419E ARG* 4.9 5.8 - - - +
206G LYS* 3.2 3.3 - - - -
207G TYR* 2.9 37.1 + - + +
208G ASN* 4.0 11.0 - - + +
209G GLY* 1.3 83.8 - - - +
211G ILE* 1.3 67.1 + - - +
212G THR* 3.2 10.5 + - + +
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Residues in contact with ILE 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ALA* 3.9 12.8 - - + +
99E VAL 3.9 10.3 - - - +
100E TYR* 3.8 29.9 - - + -
412E GLN* 5.6 0.4 + - - +
413E THR* 5.5 1.6 - - - +
419E ARG* 2.9 39.9 + - - +
447E CYS* 3.9 19.7 - - + -
449E VAL* 3.7 23.6 - - + -
204G VAL* 3.7 29.6 - - + -
205G LEU 3.3 10.3 - - - +
206G LYS* 4.1 6.5 - - + -
209G GLY 4.1 0.2 + - - -
210G ILE* 1.3 70.7 - - - +
212G THR* 1.3 62.4 + - - +
213G ASP 4.0 11.7 - - - +
214G THR* 5.0 0.2 - - - +
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Residues in contact with THR 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419E ARG* 5.2 1.8 - - - +
205G LEU 2.8 13.9 + - - -
207G TYR* 3.6 17.7 + - + -
210G ILE* 3.2 19.7 + - + +
211G ILE* 1.3 74.9 - - - +
213G ASP* 1.3 65.4 + - - +
259G LYS* 3.4 20.0 - - + +
260G GLY* 2.8 30.3 + - - +
261G LYS* 3.2 26.7 + - - +
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Residues in contact with ASP 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E VAL* 6.2 0.7 - - - -
451E SER* 3.9 12.7 + - - -
204G VAL* 3.9 0.9 - - - -
205G LEU* 2.9 34.9 + - + +
211G ILE* 3.7 8.6 - - - +
212G THR* 1.3 81.7 - - - +
214G THR* 1.3 87.3 + - - +
260G GLY 3.3 15.5 - - - +
261G LYS* 3.9 10.0 - - - +
262G VAL* 3.0 40.3 + - - +
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Residues in contact with THR 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ALA* 4.3 13.0 - - - +
449E VAL* 4.2 9.1 - - - +
451E SER* 2.9 29.0 + - - -
452E ASP 2.6 33.6 + - - +
202G VAL* 3.4 15.6 - - + +
203G ALA 3.4 8.7 + - - -
204G VAL* 4.5 3.6 - - - +
205G LEU 4.9 0.2 - - - +
213G ASP* 1.3 91.4 + - - +
215G ILE* 1.3 74.8 + - - +
216G LYS* 4.3 2.3 + - - +
262G VAL* 5.3 0.5 - - - +
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Residues in contact with ILE 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G VAL* 3.3 1.2 - - - -
203G ALA* 2.7 41.0 + - + +
205G LEU* 4.5 13.0 - - + -
214G THR* 1.3 83.7 - - - +
216G LYS* 1.3 67.0 + - - +
218G TRP* 4.6 10.3 - - + -
223G LEU* 3.6 4.5 - - + +
241G MET* 4.0 25.1 - - + -
255G PHE* 3.6 46.9 - - + -
257G MET* 5.8 1.1 - - - -
262G VAL* 4.1 18.8 - - + -
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Residues in contact with LYS 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E SER* 5.0 2.0 - - - +
452E ASP* 2.6 61.3 - - + +
454E VAL* 5.4 4.5 - - + -
200G GLY 5.3 2.2 - - - +
201G ALA 3.7 7.0 - - - +
202G VAL* 4.1 10.3 - - + +
214G THR* 4.3 2.8 + - - +
215G ILE* 1.3 76.3 - - - +
217G SER* 1.3 70.9 + - - +
218G TRP* 3.3 13.2 + - - +
223G LEU* 4.3 1.3 - - - -
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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
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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