Contacts of the strand formed by residues 200 - 204 (chain D) in PDB entry 1HJV
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 200 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LYS* 4.4 22.0 - - + -
25D VAL* 3.8 26.2 - - + -
53D HIS* 4.1 22.2 - + - -
55D ILE* 4.7 3.4 - - + -
93D LEU* 4.0 16.2 - - + -
136D ASP* 5.1 0.7 - - - -
173D LEU* 5.0 7.4 - - + -
174D LEU 4.1 0.4 + - - -
175D SER* 3.3 46.9 - - - -
176D ALA 3.6 1.9 + - - -
198D LEU* 3.1 3.5 - - - +
199D ASP* 1.3 91.6 - - + +
201D ILE* 1.3 66.8 + - - +
202D SER* 3.8 21.5 - - - -
252D SER 5.1 1.3 - - - +
253D LYS* 3.6 16.6 - - - +
255D VAL* 4.0 17.9 - - + -
347D ALA* 5.3 0.2 - - + -
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Residues in contact with ILE 201 (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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176D ALA 3.7 3.8 - - - +
178D LEU* 3.6 37.7 - - + -
191D ILE* 4.9 4.9 - - + -
194D ILE* 5.1 0.9 - - + -
195D SER* 4.0 25.8 - - - +
198D LEU* 3.7 29.2 - - + -
200D PHE* 1.3 77.0 - - - +
202D SER* 1.3 68.5 + - - +
203D ILE 3.9 0.9 - - - +
244D MET* 4.8 3.6 - - - -
249D ALA* 4.8 5.2 - - + -
250D PRO* 6.1 0.2 - - + -
253D LYS* 2.7 23.3 + - + +
254D LEU* 3.8 18.2 - - + -
255D VAL* 2.5 37.6 + - - +
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Residues in contact with SER 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 4.6 2.6 - - - +
27D TYR* 4.9 4.9 + - - -
55D ILE* 5.8 0.2 - - - +
136D ASP* 5.4 1.0 + - - -
176D ALA 3.0 10.8 + - - -
177D ALA* 3.5 8.9 - - - -
178D LEU 3.0 23.2 + - - -
200D PHE* 3.8 19.4 - - - -
201D ILE* 1.3 80.6 + - - +
203D ILE* 1.3 61.4 + - - +
204D MET* 3.3 5.1 + - - +
255D VAL* 3.4 10.0 - - - +
350D MET* 3.8 34.6 - - - +
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Residues in contact with ILE 203 (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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178D LEU 3.8 3.4 - - - +
179D SER 4.0 4.5 - - - +
180D ALA* 3.5 24.9 - - + -
185D ILE* 4.6 0.7 - - + -
201D ILE* 3.9 2.7 - - - +
202D SER* 1.3 69.3 - - - +
204D MET* 1.3 53.9 + - - +
205D THR* 2.7 24.3 + - + -
240D ALA* 3.6 42.0 - - + +
241D VAL* 4.0 12.3 - - + +
244D MET* 3.7 31.6 - - + -
254D LEU* 4.8 11.2 - - + +
255D VAL 3.0 21.0 + - - +
256D MET* 4.1 8.7 - - - -
257D GLY* 2.9 23.2 + - - -
346D LEU* 6.1 0.2 - - + -
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Residues in contact with MET 204 (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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140D LEU* 4.3 5.6 - - - -
177D ALA* 3.8 19.5 - - + +
178D LEU 3.1 21.0 + - - +
179D SER* 4.8 1.1 - - - -
180D ALA* 3.1 16.4 + - - +
202D SER 3.8 8.1 - - - +
203D ILE* 1.3 66.8 - - - +
205D THR* 1.3 59.1 + - - +
206D TYR* 3.0 47.7 + - + +
350D MET* 4.0 7.2 - - + -
2L NAG 3.4 20.0 + - - +
3L NAG 2.9 63.9 - - + +
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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