Contacts of the strand formed by residues 194 - 201 (chain D) in PDB entry 1UHG
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 GLN 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191D GLU 5.9 0.4 + - - -
192D ASP 4.2 9.7 + - - +
193D THR* 1.3 76.1 - - - +
195D ALA* 1.3 71.4 + - - +
196D MET* 3.5 14.4 + - + +
209D GLN* 4.2 6.7 - - - +
210D MET* 2.9 33.6 + - - +
281D TYR* 5.9 2.4 - - - -
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Residues in contact with ALA 195 (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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194D GLN* 1.3 83.0 - - - +
196D MET* 1.3 59.0 + - - +
207D PRO* 4.8 14.8 - - + -
208D VAL 3.2 10.5 - - - +
209D GLN* 3.7 18.3 + - - +
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Residues in contact with MET 196 (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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194D GLN* 4.3 12.1 - - + +
195D ALA* 1.3 75.8 - - - +
197D PRO* 1.3 86.6 - - + +
207D PRO* 4.3 2.7 - - - -
208D VAL* 2.9 30.5 + - - +
210D MET* 3.7 38.4 - - + -
281D TYR* 3.5 34.1 - - + -
359D ARG* 3.8 24.5 - - - +
361D ASP* 4.1 15.0 - - - +
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Residues in contact with PRO 197 (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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196D MET* 1.3 101.4 - - + +
198D PHE* 1.3 58.8 + - - +
199D ARG* 4.0 6.1 + - + +
205D SER* 4.2 19.5 - - - +
206D LYS 3.6 9.6 - - - +
207D PRO* 4.3 3.6 - - + -
208D VAL* 4.9 0.2 - - - -
210D MET* 5.0 0.2 - - - +
361D ASP* 3.7 15.3 - - - +
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Residues in contact with PHE 198 (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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197D PRO* 1.3 71.8 - - - +
199D ARG* 1.3 61.9 + - - +
200D VAL* 3.2 16.9 + - + +
205D SER* 3.2 1.5 - - - -
206D LYS* 2.7 38.6 + - + +
208D VAL* 3.7 21.8 - - + -
210D MET* 4.3 1.6 - - + -
283D PRO* 4.3 1.1 - - + -
360D ALA 3.4 20.2 - - - -
361D ASP* 3.4 12.6 - - - -
362D HIS* 3.2 35.2 - - - -
363D PRO* 3.6 10.8 - - + -
364D PHE* 4.1 11.9 - + - -
382D CYS 4.2 3.8 - - - -
383D VAL 3.3 24.7 - - - -
385D PRO* 3.7 34.3 - - + -
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Residues in contact with ARG 199 (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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197D PRO* 4.9 7.0 - - + +
198D PHE* 1.3 70.0 - - - +
200D VAL* 1.3 62.6 + - - +
201D THR 3.4 10.3 - - - +
202D GLU 5.8 2.9 - - - +
204D GLU 3.5 6.5 - - - -
205D SER* 3.5 16.6 - - - +
247D ASP 5.3 2.4 + - - -
248D GLU* 6.1 0.6 - - - +
249D VAL* 4.1 23.6 - - + +
361D ASP* 2.8 34.5 + - - +
362D HIS* 3.0 39.5 + - - +
363D PRO* 3.1 24.1 - - - +
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Residues in contact with VAL 200 (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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198D PHE* 3.2 15.4 + - + +
199D ARG* 1.3 75.2 - - - +
201D THR* 1.3 67.8 + - + +
204D GLU* 3.0 49.7 + - + +
205D SER* 4.2 2.0 - - - +
206D LYS* 5.1 10.5 - - + -
249D VAL* 5.3 1.8 - - - +
363D PRO* 3.9 20.5 - - - +
383D VAL* 3.5 22.4 - - + +
384D SER* 5.1 7.0 - - - +
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Residues in contact with THR 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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199D ARG* 4.1 9.4 - - - +
200D VAL* 1.3 86.0 + - + +
202D GLU* 1.3 76.1 + - - +
203D GLN* 3.1 10.3 + - - +
204D GLU* 2.9 55.9 + - + +
249D VAL* 4.4 7.4 - - - -
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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