Contacts of the strand formed by residues 203 - 211 (chain C) in PDB entry 1HYH
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 PHE 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194C ASN* 3.2 6.8 - - - -
195C LEU* 2.7 69.4 + - + -
196C GLY* 4.4 1.8 - - - -
201C SER 3.9 9.2 - - - +
202C GLN* 1.3 78.0 - - - +
204C VAL* 1.4 72.1 + - - +
205C ALA* 3.4 10.7 + - + -
231C GLU* 4.8 6.5 - - - +
303C LEU* 5.5 0.2 - - + -
307C GLU* 3.4 44.6 - - + -
310C LYS* 3.8 34.3 - - + +
311C LEU* 3.8 24.5 - - + -
314C SER* 4.8 0.2 - - - -
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Residues in contact with VAL 204 (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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175C MET* 3.8 23.1 - - + -
193C TYR 3.9 7.6 - - - +
194C ASN* 3.8 20.1 - - - +
203C PHE* 1.4 81.2 - - - +
205C ALA* 1.3 60.8 + - - +
206C TRP* 3.1 56.2 + - + +
209C VAL* 4.0 8.5 - - + -
231C GLU* 3.6 33.1 + - + +
234C ALA* 6.3 1.6 - - + -
307C GLU* 4.8 1.6 - - - +
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Residues in contact with ALA 205 (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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193C TYR* 2.9 18.1 + - + +
195C LEU* 3.9 27.6 - - + -
203C PHE* 3.4 8.9 + - + -
204C VAL* 1.3 71.2 - - - +
206C TRP* 1.3 48.0 + - - +
207C SER 3.1 5.2 - - - -
208C THR* 2.5 46.1 + - + +
209C VAL* 3.9 2.6 + - - +
303C LEU* 3.9 17.0 - - + -
307C GLU* 3.6 10.8 - - - -
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Residues in contact with TRP 206 (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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175C MET* 4.4 5.8 - - + -
179C VAL* 4.0 18.8 - - + -
204C VAL* 3.1 31.3 + - + +
205C ALA* 1.3 71.0 - - - +
207C SER* 1.3 60.2 + - - +
208C THR 3.1 1.5 + - - -
209C VAL* 3.3 32.8 + - + +
215C PRO* 6.1 0.3 - - - +
216C ILE* 3.8 20.5 - - + +
217C VAL* 3.6 25.5 + - + +
227C LEU* 3.4 50.8 - - + +
230C ILE* 3.5 27.8 - - + -
231C GLU* 3.5 36.3 + - + -
307C GLU* 3.4 5.5 + - - +
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Residues in contact with SER 207 (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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205C ALA 3.0 0.8 + - - -
206C TRP* 1.3 77.2 - - - +
208C THR* 1.3 64.4 + - - +
209C VAL 5.2 0.7 - - - -
210C ARG* 6.1 0.3 - - - +
215C PRO* 5.8 3.7 - - - +
217C VAL* 4.5 9.4 - - - +
302C ASP 3.9 15.0 + - - -
303C LEU* 4.3 0.2 - - - -
304C THR* 3.8 15.9 - - - -
307C GLU* 2.6 33.5 + - - -
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Residues in contact with THR 208 (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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191C SER* 3.4 9.5 + - - -
192C GLY* 3.2 16.3 + - - -
193C TYR* 3.2 37.5 + - + -
205C ALA* 2.5 32.8 + - + +
207C SER* 1.3 87.6 - - - +
209C VAL* 1.3 60.9 + - - +
210C ARG* 3.6 6.6 + - - +
301C LEU* 4.4 12.1 - - + -
302C ASP 5.6 2.0 - - - +
303C LEU* 4.3 10.8 - - + -
210D ARG* 6.1 4.3 - - - +
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Residues in contact with VAL 209 (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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175C MET* 4.1 9.4 - - + -
179C VAL* 4.7 1.6 - - + -
190C VAL* 4.1 16.6 - - + -
191C SER 3.1 17.7 - - - +
192C GLY* 4.0 7.0 - - - -
204C VAL* 4.0 11.2 - - + -
205C ALA 3.9 13.2 - - - +
206C TRP* 3.3 30.6 + - + +
207C SER 5.2 0.3 - - - -
208C THR* 1.3 78.4 - - - +
210C ARG* 1.3 65.2 + - - +
211C VAL* 5.3 0.2 - - + -
215C PRO* 3.7 2.4 - - - +
216C ILE* 3.0 52.5 + - + +
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Residues in contact with ARG 210 (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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189C SER 4.1 2.6 - - - +
190C VAL* 3.8 2.6 - - - +
191C SER* 3.2 40.9 + - - +
207C SER 6.1 0.2 - - - +
208C THR 4.3 6.3 - - - +
209C VAL* 1.3 79.7 - - - +
211C VAL* 1.3 66.9 + - - +
212C MET 4.4 0.2 - - - -
213C GLY* 2.9 30.9 + - - +
214C GLN 3.4 7.0 - - - +
215C PRO* 3.8 31.4 - - + +
208D THR* 6.0 4.9 - - - +
210D ARG* 4.5 30.3 - - - +
302D ASP* 5.1 6.1 + - - +
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Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C VAL* 3.5 26.9 - - + -
183C PHE* 4.1 14.6 - - + -
185C LEU* 3.4 29.2 - - + -
189C SER 4.9 1.3 - - - -
190C VAL* 4.0 5.4 - - + -
209C VAL* 5.3 0.4 - - + -
210C ARG* 1.3 78.3 - - - +
212C MET* 1.3 75.4 + - + +
213C GLY 3.3 1.6 - - - -
214C GLN* 3.0 23.4 + - - +
216C ILE* 4.1 18.2 - - + -
219C LEU* 3.5 27.4 - - + +
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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