Contacts of the helix formed by residues 191 - 197 (chain D) in PDB entry 1M6X
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 ARG 191 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D THR* 4.6 2.0 - - - -
190D GLY* 1.3 78.2 - - - +
192D PHE* 1.3 67.7 + - - +
193D SER* 3.2 7.8 + - - +
194D ASP* 2.5 39.0 + - - +
195D ILE* 3.4 9.7 + - - +
222D THR* 5.2 1.2 - - - -
223D LYS* 3.7 34.9 - - - +
224D THR* 4.7 7.9 + - - +
304D SER 6.0 0.9 - - - -
305D HIS* 3.9 17.3 - - + +
308D ARG* 3.7 31.4 - - - +
328D GLY 5.4 0.8 + - - -
329D ASN* 4.9 9.1 + - - +
330D TRP* 5.3 0.8 - - - +
14H T 2.4 51.3 + - - -
15H T 5.6 0.2 + - - -
23J A 3.8 15.5 - - - -
24J T 3.2 11.0 - - - +
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Residues in contact with PHE 192 (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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181D LEU* 3.8 28.7 - - + -
185D THR* 4.7 10.2 - - - +
191D ARG* 1.3 71.0 - - - +
193D SER* 1.3 55.7 + - - +
195D ILE* 3.0 6.1 + - - +
196D LYS* 2.7 59.1 + - + +
275D LEU* 4.4 3.4 - - + -
276D LYS 3.7 11.0 - - - -
277D ASP* 3.6 16.8 - - - -
279D LEU* 4.1 10.3 - - + -
280D VAL* 3.5 48.7 - - + -
304D SER* 3.8 26.2 + - - +
305D HIS* 5.1 1.2 + - - -
24J T 2.9 23.1 + - - +
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Residues in contact with SER 193 (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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191D ARG* 3.6 9.2 + - - +
192D PHE* 1.3 74.2 - - - +
194D ASP* 1.3 61.8 + - - -
196D LYS* 3.8 16.4 - - - +
197D ASN* 2.9 38.0 + - - +
219D VAL* 4.1 0.7 - - - +
221D GLU 4.9 6.1 - - - +
222D THR* 5.9 0.9 - - - -
223D LYS 5.1 5.1 + - - -
23J A 2.9 19.8 + - - -
24J T 2.7 39.4 + - - -
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Residues in contact with ASP 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D GLY* 3.3 12.7 - - - -
191D ARG* 2.5 53.6 + - - +
192D PHE 3.1 0.8 - - - -
193D SER* 1.3 78.1 + - - +
195D ILE* 1.3 62.6 + - + +
198D VAL* 3.4 2.3 - - - +
219D VAL* 3.0 35.2 - - + +
222D THR* 3.7 27.4 - - - +
223D LYS 5.1 0.2 + - - -
228D ARG* 4.1 15.2 + - - -
230D ILE* 3.9 11.6 - - + +
308D ARG* 4.6 1.0 + - - -
328D GLY 5.1 1.6 - - - +
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Residues in contact with ILE 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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180D PHE* 4.4 4.0 - - + -
181D LEU* 4.1 6.1 - - + -
184D ALA* 3.8 40.4 - - + +
185D THR* 3.7 23.3 - - + +
188D ASN* 4.3 2.0 - - + +
190D GLY* 5.4 1.3 - - - -
191D ARG 3.6 12.8 - - - +
192D PHE 3.0 5.0 + - - +
194D ASP* 1.3 78.8 - - + +
196D LYS* 1.3 64.2 + - - +
198D VAL* 3.0 23.8 + - + +
230D ILE* 4.1 27.6 - - + -
232D PHE* 5.4 2.2 - - + -
274D LEU* 3.6 19.2 - - + +
275D LEU* 3.9 17.5 - - + -
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Residues in contact with LYS 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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192D PHE* 2.7 47.5 + - + +
193D SER* 4.0 11.7 - - - +
195D ILE* 1.3 74.8 - - - +
197D ASN* 1.3 98.3 + - - +
198D VAL 3.2 0.2 - - - -
221D GLU* 5.0 0.2 + - - -
258D ARG* 4.9 0.4 - - - +
260D ASN* 4.7 8.3 - - - +
273D GLN* 3.6 9.4 + - - +
274D LEU 3.2 23.7 + - - -
275D LEU* 3.4 31.2 + - - +
276D LYS 4.3 0.2 - - - -
277D ASP* 2.7 43.9 + - - +
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Residues in contact with ASN 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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193D SER* 2.9 23.5 + - - +
195D ILE 3.4 0.2 - - - -
196D LYS* 1.3 109.6 + - - +
198D VAL* 1.3 63.7 + - - +
199D ASP 3.5 2.4 + - - -
219D VAL* 3.6 22.0 - - + +
220D THR 4.5 1.7 + - - -
221D GLU* 3.2 42.9 + - + +
257D LYS* 3.7 21.5 - - - +
260D ASN* 4.7 0.2 - - - +
270D GLN* 3.9 15.4 + - - +
273D GLN* 4.1 7.2 + - - +
274D LEU 4.8 0.2 - - - -
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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