Contacts of the helix formed by residues 191 - 199 (chain H) in PDB entry 3I6A
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 LEU 191 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147H TYR* 4.4 16.4 - - + +
153H LEU* 3.8 39.3 - - + -
187H ARG 3.3 9.9 + - - +
188H ILE* 3.2 31.7 + - + +
190H ASN* 1.3 74.7 - - - +
192H PRO* 1.3 79.9 - - + +
193H THR* 3.3 4.7 - - - +
194H VAL* 3.0 14.4 + - + +
195H LYS* 2.7 22.3 + - - +
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Residues in contact with PRO 192 (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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190H ASN 3.5 8.1 - - - +
191H LEU* 1.3 87.5 - - + +
193H THR* 1.3 66.3 + - + +
195H LYS* 3.6 8.5 - - + +
196H LYS* 3.0 25.1 + - - +
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Residues in contact with THR 193 (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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24H ALA* 3.2 20.4 - - - +
25H ALA* 2.6 26.0 + - - +
26H ALA 4.7 0.7 - - - -
27H GLY* 3.9 19.5 - - - -
191H LEU* 3.3 5.1 - - - +
192H PRO* 1.3 79.5 - - + +
194H VAL* 1.3 66.2 + - - +
196H LYS* 3.4 9.5 + - - +
197H PHE* 3.1 21.8 + - - +
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Residues in contact with VAL 194 (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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21H TRP* 4.3 20.4 - - + -
25H ALA* 3.8 29.2 - - + +
158H ILE* 4.1 13.7 - - + -
161H VAL* 5.7 0.2 - - + -
188H ILE* 3.2 33.2 - - + +
189H SER* 3.9 12.8 - - - +
191H LEU* 3.0 9.8 + - + +
193H THR* 1.3 81.6 + - - +
195H LYS* 1.3 64.7 + - - +
196H LYS 3.2 0.3 + - - -
197H PHE* 3.2 7.1 + - + +
198H LEU* 2.9 34.3 + - + +
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Residues in contact with LYS 195 (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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189H SER 3.4 14.8 + - - +
190H ASN* 3.3 47.6 + - - +
191H LEU 2.7 19.0 + - - +
192H PRO* 3.6 7.4 - - + +
194H VAL* 1.3 71.3 - - - +
196H LYS* 1.3 61.9 + - - +
198H LEU* 3.4 7.2 + - - +
199H GLN* 3.1 46.6 + - + +
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Residues in contact with LYS 196 (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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192H PRO 3.0 13.2 + - - +
193H THR* 3.5 13.2 - - + +
195H LYS* 1.3 75.4 - - - +
197H PHE* 1.3 59.2 + - - +
199H GLN* 2.8 38.3 + - - +
202H SER* 4.0 5.5 - - - -
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Residues in contact with PHE 197 (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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17H GLU* 4.6 0.4 - - - -
20H ARG* 3.8 17.9 - - + -
21H TRP* 3.4 68.4 - + - -
24H ALA* 3.3 24.5 - - + -
25H ALA 5.6 0.2 - - - +
30H PHE* 5.0 0.2 - + - -
193H THR 3.1 11.2 + - - +
194H VAL* 3.2 11.0 + - + +
196H LYS* 1.3 77.8 - - - +
198H LEU* 1.3 60.6 + - + +
199H GLN 3.6 0.2 - - - +
202H SER* 2.4 34.2 + - - -
203H PRO* 4.1 19.1 - - + -
204H ARG* 3.6 45.1 - - + +
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Residues in contact with LEU 198 (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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21H TRP* 3.9 20.4 - - + -
165H TYR* 3.3 36.3 - - + +
189H SER* 3.6 24.2 - - - +
194H VAL* 2.9 30.6 + - + +
195H LYS* 3.7 6.1 - - - +
197H PHE* 1.3 74.5 - - + +
199H GLN* 1.3 64.9 + - + +
200H PRO* 3.9 1.4 - - - +
204H ARG* 3.1 52.4 + - - +
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Residues in contact with GLN 199 (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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195H LYS* 3.1 36.7 + - + +
196H LYS* 2.8 20.3 + - - +
197H PHE 3.6 0.3 - - - +
198H LEU* 1.3 81.1 - - + +
200H PRO* 1.3 83.0 - - + +
201H GLY 3.6 0.2 + - - -
202H SER* 3.5 18.2 + - - -
204H ARG* 5.4 0.3 + - - -
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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