Contacts of the strand formed by residues 202 - 207 (chain H) 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 VAL 202 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98F ALA* 6.1 1.3 - - + -
99F VAL* 5.5 8.3 - - + -
452F ASP 3.9 6.3 - - - +
453F THR* 4.8 2.9 - - + -
454F VAL* 3.3 39.3 - - + +
458F TRP* 6.1 0.4 - - + -
193H GLY 3.6 2.3 - - - +
194H ILE* 4.2 1.8 - - - -
195H SER* 2.9 30.1 + - - +
200H GLY 4.3 2.5 - - - +
201H ALA* 1.3 74.4 - - - +
203H ALA* 1.3 65.6 + - - +
204H VAL* 3.6 13.3 + - + +
214H THR* 3.3 35.0 - - + +
215H ILE 3.5 4.9 - - - +
216H LYS* 4.3 5.2 - - + +
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Residues in contact with ALA 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H ILE* 4.3 7.0 - - + -
193H GLY 3.2 6.5 - - - +
194H ILE* 3.6 22.9 - - + -
202H VAL* 1.3 72.3 - - - +
204H VAL* 1.3 60.2 + - - +
205H LEU* 3.8 3.9 + - + +
214H THR* 3.3 6.8 - - - -
215H ILE* 2.8 44.1 + - + +
223H LEU* 4.3 4.9 - - + +
241H MET* 3.7 22.7 - - + -
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Residues in contact with VAL 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F ALA* 4.3 15.0 - - + -
99F VAL* 3.9 30.3 - - + +
175H SER* 4.6 7.7 + - - +
176H VAL 6.0 2.0 - - - +
191H THR* 3.8 2.9 + - - +
192H ILE* 3.8 0.3 - - - -
193H GLY* 2.8 32.5 + - - +
195H SER* 6.4 0.7 - - - -
202H VAL* 4.3 16.4 - - + +
203H ALA* 1.3 73.4 - - - +
205H LEU* 1.3 64.8 + - - +
206H LYS* 4.0 12.6 + - - +
211H ILE* 3.8 40.2 - - + -
213H ASP 3.9 3.1 - - - -
214H THR* 4.5 1.8 - - - +
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Residues in contact with LEU 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H LEU* 4.6 4.9 - - + -
191H THR 3.5 4.3 - - - +
192H ILE* 3.7 33.4 - - + -
203H ALA* 4.1 13.5 - - + +
204H VAL* 1.3 75.8 - - - +
206H LYS* 1.3 62.3 + - - +
211H ILE* 3.3 9.9 - - - +
212H THR* 2.9 22.8 + - - +
213H ASP* 3.0 29.7 + - + +
214H THR 4.6 0.4 - - - +
215H ILE* 4.3 11.9 - - + -
241H MET* 5.0 0.2 - - + -
257H MET* 4.0 19.3 - - - -
260H GLY 3.8 25.4 - - - +
262H VAL* 3.9 22.2 - - + -
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Residues in contact with LYS 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F TYR* 2.9 54.9 + - - +
173H PHE* 4.6 1.6 - - - -
174H GLU 3.2 25.6 + - - +
175H SER* 3.6 16.4 + - - +
189H TRP 3.4 1.2 - - - +
190H LEU* 3.1 10.3 - - - +
191H THR* 3.0 46.0 + - - +
204H VAL* 4.2 10.1 - - + +
205H LEU* 1.3 80.5 - - - +
207H TYR* 1.3 59.9 + - - +
208H ASN 4.0 0.7 - - - -
209H GLY* 3.9 22.8 + - - +
210H ILE 3.7 7.4 - - - +
211H ILE* 3.9 16.6 - - + +
212H THR* 4.0 2.7 - - - -
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Residues in contact with TYR 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H LYS* 6.0 1.2 - - - -
185H ASP* 2.7 38.0 + - - -
187H THR* 3.6 15.8 - - + +
188H SER* 2.4 32.4 + - - -
189H TRP 3.4 8.3 - - - -
190H LEU* 4.6 7.4 - - + -
206H LYS* 1.3 71.9 - - - +
208H ASN* 1.3 75.4 + - + +
210H ILE* 3.1 27.6 + - + +
212H THR* 3.7 21.2 + - + -
237H CYS* 6.3 0.2 - - - -
259H LYS* 3.6 39.4 - - + +
260H GLY* 3.7 13.7 - - - +
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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