Contacts of the helix formed by residues 194 - 207 (chain K) in PDB entry 3A68
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 GLY 194 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D ARG* 3.3 35.0 - - - +
192K GLY 3.8 0.2 + - - -
193K LYS* 1.3 72.1 - - - +
195K HIS* 1.3 66.9 + - - -
196K GLY 3.2 1.2 + - - -
197K VAL* 3.2 6.2 + - - +
198K TRP* 3.0 22.7 + - - +
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Residues in contact with HIS 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D ARG 3.7 4.2 + - - -
191D VAL* 3.7 24.5 + - + +
195D HIS* 3.7 43.7 + + - +
196D GLY* 3.8 21.8 + - - -
199D HIS* 2.9 30.4 + - - +
193K LYS 3.7 2.4 + - - -
194K GLY* 1.3 71.3 - - - +
196K GLY* 1.3 62.5 + - - +
198K TRP* 3.4 12.8 + + - +
199K HIS* 2.9 20.0 + - + +
195Q HIS* 3.6 22.0 + + + +
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Residues in contact with GLY 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191K VAL* 3.4 33.7 + - - +
192K GLY 3.5 10.5 + - - -
193K LYS 4.2 2.2 + - - -
194K GLY 3.2 0.8 - - - -
195K HIS* 1.3 79.1 - - - +
197K VAL* 1.3 57.1 + - - +
199K HIS* 3.2 4.2 + - - +
200K PHE 2.9 24.1 + - - -
195Q HIS* 3.8 16.3 + - - -
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Residues in contact with VAL 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ARG* 3.8 21.8 - - - +
77K LEU* 4.2 9.0 - - + -
127K GLY* 6.5 0.4 - - - -
128K ASP* 5.8 0.2 - - - +
129K ALA* 3.6 28.7 - - + -
130K LEU* 5.7 2.7 - - + +
188K LEU* 4.1 20.0 - - + +
191K VAL* 4.3 4.5 - - + -
192K GLY 3.1 22.4 + - - +
193K LYS* 3.7 17.9 - - + -
194K GLY 3.2 10.8 + - - +
196K GLY* 1.3 70.2 - - - +
198K TRP* 1.3 67.9 + - - +
200K PHE* 3.3 3.3 + - + +
201K ASP* 2.9 22.7 + - + +
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Residues in contact with TRP 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D GLN* 2.8 46.7 + - + +
190D ARG* 4.1 14.8 - - - +
191D VAL* 3.5 25.1 - - + -
199D HIS* 3.6 43.5 - + + -
200D PHE* 3.8 25.6 - + - -
203D MET* 3.8 21.5 - - + -
76K ALA 5.1 1.3 - - - -
77K LEU* 4.5 7.0 - - + -
194K GLY 3.0 13.4 + - - +
195K HIS* 3.7 12.6 - + - +
197K VAL* 1.3 77.2 - - - +
199K HIS* 1.3 72.0 + - - +
201K ASP* 3.2 10.3 + - - +
202K GLN* 2.9 55.4 + - + +
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Residues in contact with HIS 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D HIS* 3.5 32.4 + + + -
195K HIS 2.9 17.7 + - - +
196K GLY 3.5 4.3 - - - +
198K TRP* 1.3 81.0 - - + +
200K PHE* 1.3 65.4 + - - +
202K GLN* 3.1 10.1 + - + +
203K MET* 3.0 21.6 + - + +
195Q HIS* 2.9 25.3 + - + +
198Q TRP* 3.6 20.0 - + + -
199Q HIS* 3.6 43.2 + + - -
202Q GLN* 5.7 1.4 - - - +
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Residues in contact with PHE 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K LEU* 4.2 9.0 - - + -
133K MET* 4.6 1.6 - - + -
184K TYR* 3.6 41.3 - + + -
187K GLN* 3.8 31.9 - - + -
188K LEU* 3.5 35.0 - - + -
191K VAL* 4.4 7.0 - - + -
196K GLY 2.9 12.9 + - - +
197K VAL 3.6 6.3 - - - +
199K HIS* 1.3 75.2 - - - +
201K ASP* 1.3 61.7 + - - +
203K MET* 3.1 30.7 + - + +
204K LEU* 2.9 44.0 + - + +
198Q TRP* 3.9 16.7 - + + -
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Residues in contact with ASP 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K ALA 4.8 0.5 - - - +
77K LEU* 3.4 28.9 - - + +
78K ARG* 3.1 10.0 + - - +
79K GLY* 2.8 20.7 + - - -
80K LEU* 2.7 40.3 + - + +
197K VAL 2.9 14.3 + - - +
198K TRP* 3.4 11.2 - - + +
200K PHE* 1.3 83.1 - - - +
202K GLN* 1.3 64.3 + - - +
204K LEU* 3.2 3.4 + - - +
205K LEU* 2.8 27.5 + - - +
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Residues in contact with GLN 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D HIS* 5.8 0.9 - - - +
203D MET* 3.3 22.4 - - - +
78K ARG* 3.0 27.2 + - - +
198K TRP* 2.9 53.9 + - + +
199K HIS* 3.4 14.4 - - + +
201K ASP* 1.3 80.3 - - - +
203K MET* 1.3 62.9 + - - +
205K LEU* 3.3 8.1 + - - +
206K HIS* 3.1 52.0 + - - +
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Residues in contact with MET 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K TYR* 4.8 2.2 - - + -
187K GLN* 3.9 3.4 - - - +
199K HIS* 3.0 13.6 + - + +
200K PHE* 3.1 43.3 + - + +
202K GLN* 1.3 77.1 - - - +
204K LEU* 1.3 66.6 + - + +
206K HIS* 3.2 5.2 + - - +
207K GLU* 2.8 54.6 + - - +
78Q ARG* 3.7 21.8 - - - +
198Q TRP* 3.9 10.8 - - + -
202Q GLN* 3.3 30.1 - - - +
206Q HIS* 6.0 0.2 - - + -
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Residues in contact with LEU 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K GLY* 3.7 21.3 - - - +
80K LEU* 3.8 23.6 - - + -
82K LYS* 5.2 3.8 + - - +
83K PHE* 3.9 16.2 - - + -
133K MET* 3.8 19.5 - - + -
180K ARG* 5.2 1.8 - - - +
184K TYR* 3.4 36.6 - - + +
200K PHE* 2.9 21.2 + - + +
201K ASP* 3.6 8.7 - - - +
203K MET* 1.3 76.9 - - + +
205K LEU* 1.3 65.9 + - - +
206K HIS 3.2 0.7 + - - -
207K GLU* 3.3 22.4 + - + +
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Residues in contact with LEU 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78K ARG* 3.7 61.7 - - + +
79K GLY* 3.7 8.7 - - - +
82K LYS* 3.4 39.7 + - + +
201K ASP 2.8 17.3 + - - +
202K GLN* 3.5 15.0 - - - +
203K MET 3.3 0.2 - - - -
204K LEU* 1.3 76.4 - - - +
206K HIS* 1.3 82.7 + - + +
207K GLU 5.0 0.2 - - - +
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Residues in contact with HIS 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D MET* 6.0 0.4 - - + -
82K LYS* 5.5 0.4 - - - +
202K GLN* 3.1 42.6 + - - +
203K MET* 3.2 5.1 + - - +
204K LEU 3.1 0.4 - - - -
205K LEU* 1.3 96.1 - - + +
207K GLU* 1.3 66.9 + - - +
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Residues in contact with GLU 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K LYS* 5.2 5.2 + - - -
180K ARG* 4.5 5.7 + - - -
184K TYR* 2.7 37.2 + - - -
203K MET* 2.8 31.1 + - - +
204K LEU* 3.3 17.9 + - + +
205K LEU 5.0 1.0 - - - +
206K HIS* 1.3 82.8 - - - +
78Q ARG* 3.2 27.4 + - - +
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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