Contacts of the helix formed by residues 193 - 202 (chain D) in PDB entry 5HVO
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 VAL 193 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D PHE* 3.8 12.3 - - + -
117D PHE* 3.7 18.6 - - + -
122D TRP* 3.3 60.3 - - + +
191D LEU* 3.3 21.3 - - + -
192D PRO* 1.3 78.7 - - + +
194D ARG* 1.3 64.3 + - - +
195D GLY 3.3 2.5 - - - -
196D GLN* 3.2 26.5 + - - +
197D LEU* 3.3 13.1 + - + +
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Residues in contact with ARG 194 (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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410C GLU* 2.5 42.0 + - - -
425C ASN* 3.8 11.6 - - - +
431C GLU* 5.8 0.6 + - - -
188D TYR* 2.8 54.8 + - + +
189D ARG* 2.6 43.1 + - - +
191D LEU* 3.0 17.7 + - - +
192D PRO* 3.3 3.6 + - - +
193D VAL* 1.3 77.9 - - - +
195D GLY* 1.3 65.3 + - - +
198D LEU* 3.5 8.7 + - - +
225D LEU* 3.9 30.6 - - + +
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Residues in contact with GLY 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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193D VAL 3.3 0.6 - - - -
194D ARG* 1.3 83.3 - - - +
196D GLN* 1.3 69.1 + - - +
198D LEU* 3.5 5.3 + - - +
199D ARG* 3.0 49.7 + - - +
225D LEU* 5.8 2.5 - - - -
226D LEU* 4.6 9.6 - - - +
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Residues in contact with GLN 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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122D TRP* 3.7 29.6 - - + +
155D LEU* 3.6 12.2 - - + +
158D GLU* 4.3 2.1 - - - +
192D PRO 4.3 3.7 + - - +
193D VAL* 3.2 37.0 + - - +
195D GLY* 1.3 77.2 + - - +
197D LEU* 1.3 58.7 + - - +
199D ARG* 3.4 20.1 + - - +
200D GLY 2.9 22.9 + - - -
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Residues in contact with LEU 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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99D PHE* 4.8 2.0 - - + -
104D LEU* 3.8 27.6 - - + -
122D TRP* 3.5 34.5 - - + -
125D TYR* 4.2 11.7 - - + +
154D MET* 4.0 24.4 - - + +
155D LEU* 4.2 7.6 - - + -
188D TYR* 3.1 18.2 - - + +
191D LEU* 3.4 31.2 - - + -
193D VAL* 3.3 8.1 + - + +
195D GLY 3.3 0.6 - - - -
196D GLN* 1.3 75.4 - - - +
198D LEU* 1.3 64.6 + - - +
200D GLY* 3.2 1.4 + - - -
201D VAL* 3.2 29.0 + - - +
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Residues in contact with LEU 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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182D PHE* 4.1 17.5 - - + -
188D TYR* 3.8 16.2 - - + +
194D ARG 3.5 11.8 + - - +
195D GLY* 3.5 7.1 + - - +
196D GLN 3.4 0.4 - - - -
197D LEU* 1.3 78.4 - - - +
199D ARG* 1.3 57.9 + - - +
201D VAL* 3.3 3.4 + - - +
202D LEU* 2.9 38.7 + - + +
218D PHE* 3.4 36.5 - - + -
221D SER* 3.6 32.1 - - - +
222D CYS* 4.1 10.3 - - - +
225D LEU* 4.3 7.9 - - + -
226D LEU* 4.1 18.6 - - + -
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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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158D GLU* 3.9 11.9 - - - +
195D GLY* 3.0 37.9 + - - +
196D GLN* 3.8 22.5 + - - +
198D LEU* 1.3 75.8 - - - +
200D GLY* 1.3 63.2 + - - +
202D LEU* 3.3 13.7 + - - +
203D HIS* 3.0 23.3 + - + -
226D LEU* 3.3 42.0 - - + +
237D TYR* 3.4 28.5 - - + +
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Residues in contact with GLY 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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154D MET 3.0 17.3 - - - -
155D LEU* 4.2 4.7 - - - -
157D PRO* 3.2 9.2 - - - +
158D GLU* 3.1 43.0 + - - +
196D GLN 2.9 15.1 + - - -
197D LEU 3.2 2.2 + - - -
199D ARG* 1.3 78.6 - - - +
201D VAL* 1.3 57.6 + - - +
202D LEU 3.6 0.2 + - - -
203D HIS 3.8 1.6 + - - -
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Residues in contact with VAL 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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154D MET* 3.4 37.5 - - + +
157D PRO* 4.3 5.2 - - - -
176D PHE* 4.0 29.8 - - + -
197D LEU 3.2 15.9 + - - +
198D LEU* 4.0 3.4 - - - +
200D GLY* 1.3 73.2 - - - +
202D LEU* 1.3 57.3 + - - +
203D HIS 3.1 4.9 - - - -
204D CYS* 3.2 25.0 + - - +
207D ILE* 3.2 33.2 - - + +
218D PHE* 4.7 11.0 - - + -
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Residues in contact with LEU 202 (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 LEU 2.9 28.4 + - - +
199D ARG* 3.3 6.8 + - - +
201D VAL* 1.3 74.6 - - - +
203D HIS* 1.3 58.0 + - - +
204D CYS 3.2 6.2 - - - +
207D ILE* 4.4 4.3 - - + -
218D PHE* 3.9 18.8 - - + -
222D CYS* 4.1 8.3 - - - -
226D LEU* 4.1 11.4 - - + -
228D LEU* 3.7 28.3 - - + -
235D VAL* 3.5 32.3 - - + -
237D TYR* 3.8 29.5 - - + +
240D ARG* 5.1 3.5 - - - -
242D VAL* 3.3 29.2 - - + +
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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