Contacts of the strand formed by residues 202 - 207 (chain H) in PDB entry 6H25
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 202 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85H VAL* 3.1 53.8 - - + +
86H GLY* 4.0 12.6 - - - -
87H ARG* 4.6 6.1 - - + -
99H GLU* 4.4 11.2 - - - -
100H THR* 4.5 13.2 - - - -
101H ASN* 3.5 19.7 - - - -
171H LEU* 4.4 15.9 - - + -
172H VAL 3.7 2.0 - - - +
173H GLN* 3.5 39.3 - - + -
196H ILE 4.7 0.2 - - - -
198H GLY* 3.1 27.7 + - - +
200H ASN* 3.1 16.2 + - - +
201H GLY* 1.3 86.7 - - - +
203H ILE* 1.3 67.9 + - - +
204H TRP 4.2 0.4 - - - -
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Residues in contact with ILE 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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170H VAL 4.0 0.5 - - - +
171H LEU* 3.6 4.5 - - - +
172H VAL* 2.9 39.5 + - + +
174H VAL* 3.7 36.8 - - + -
179H VAL* 4.8 5.4 - - + -
195H VAL* 3.9 16.8 - - + -
196H ILE 3.5 2.7 - - - -
197H LEU* 3.7 21.5 - - + -
200H ASN 5.7 0.2 - - - +
202H PHE* 1.3 83.4 - - - +
204H TRP* 1.3 61.8 + - - +
205H ILE* 4.2 7.9 + - + +
241H ILE* 3.7 32.3 - - + -
251H LEU* 4.1 21.8 - - + -
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Residues in contact with TRP 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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10E GLU* 4.1 4.0 - - + -
85H VAL* 4.8 11.0 - - + +
140H LEU* 3.6 26.5 - - + -
166H LEU* 3.5 43.2 - - + +
167H GLY 4.2 9.9 - - - +
168H GLN 3.1 26.7 - - - -
169H GLY* 3.5 14.1 - - - -
170H VAL* 3.1 34.8 - - - -
171H LEU* 3.8 16.4 - - + -
195H VAL* 3.3 7.4 - - - +
196H ILE* 2.9 50.0 + - + +
202H PHE 4.2 0.4 - - - -
203H ILE* 1.3 74.5 - - - +
205H ILE* 1.3 65.1 + - - +
206H TYR* 3.3 40.1 - + + +
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Residues in contact with ILE 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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169H GLY* 3.1 4.0 - - - -
170H VAL* 2.9 44.0 + - + +
172H VAL* 5.6 3.1 - - + -
193H ALA* 4.6 7.0 - - + -
194H SER 3.7 7.9 - - - +
195H VAL* 4.1 14.8 - - + -
203H ILE* 4.2 5.8 - - + +
204H TRP* 1.3 79.5 - - - +
206H TYR* 1.3 64.3 + - - +
234H ILE* 3.7 34.5 - - + +
237H LEU* 4.1 10.5 - - + -
238H ARG* 3.9 32.8 - - + +
241H ILE* 3.8 24.2 - - + -
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Residues in contact with TYR 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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167H GLY* 5.8 5.6 - - - -
168H GLN 5.6 1.8 - - - +
169H GLY* 4.2 5.2 - - - +
186H PHE* 4.9 7.8 - - - +
193H ALA* 3.8 0.7 - - - -
194H SER* 2.9 67.7 + - - +
195H VAL 4.3 0.6 + - - -
196H ILE* 4.0 27.4 - - + +
204H TRP* 3.3 33.7 - + + +
205H ILE* 1.3 74.9 - - - +
207H PRO* 1.3 90.3 - - + +
209H PRO* 4.3 15.0 - - + -
234H ILE* 4.4 5.2 - - - -
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Residues in contact with PRO 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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13E TYR* 5.8 1.8 - - + -
168H GLN* 5.4 5.8 - - + +
169H GLY* 4.6 12.1 - - - +
192H GLY 4.4 2.0 - - - +
193H ALA* 4.5 1.1 - - - -
206H TYR* 1.3 101.7 - - + +
208H THR* 1.3 65.0 + - - +
209H PRO* 3.5 2.9 - - - +
226H VAL* 4.1 23.3 - - + -
230H ASP* 3.3 28.7 - - - +
234H ILE* 3.7 24.4 - - + -
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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