Contacts of the helix formed by residues 194 - 206 (chain D) in PDB entry 3B4V
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 SER 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175D PRO 4.2 2.8 + - - -
177D PRO* 3.8 18.2 - - - -
182D GLN* 3.8 19.1 - - - -
184D LEU* 4.4 3.1 - - - -
192D TYR* 3.3 6.5 - - - +
193D ILE* 1.3 80.6 - - - +
195D SER* 1.3 63.5 + - - +
196D CYS* 3.3 11.1 + - - +
197D HIS* 2.4 48.8 + - - +
198D MET* 3.3 8.8 + - - +
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Residues in contact with SER 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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98A GLN* 3.7 18.1 + - - +
117A EDO 3.4 33.1 - - - -
182D GLN* 4.5 5.5 + - - -
184D LEU* 3.9 19.5 - - - +
194D SER* 1.3 71.5 - - - +
196D CYS* 1.3 63.2 - - - +
198D MET* 3.2 3.4 + - - +
199D ARG* 2.9 43.8 + - - +
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Residues in contact with CYS 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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27A ASP* 6.5 0.2 - - + -
117A EDO 5.6 0.8 - - - -
170D ARG* 3.5 25.3 - - - -
174D CYS* 2.1 52.0 - - + -
175D PRO* 4.3 7.9 - - + -
194D SER* 3.2 11.0 + - - +
195D SER* 1.3 77.4 - - - +
197D HIS* 1.3 58.2 + - - +
199D ARG* 3.4 20.4 + - - +
200D GLN* 2.9 23.4 + - - +
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Residues in contact with HIS 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D CYS* 3.3 37.3 + - + +
175D PRO 3.4 17.7 - - - -
176D VAL* 5.4 1.2 - - - +
192D TYR* 4.2 15.6 - - + -
193D ILE* 3.4 35.3 - - + +
194D SER* 2.4 41.3 + - - +
196D CYS* 1.3 78.7 - - - +
198D MET* 1.3 57.6 + - - +
200D GLN* 3.1 11.0 + - - +
201D ALA* 2.9 26.7 + - - +
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Residues in contact with MET 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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97A GLY 3.9 4.5 - - - +
98A GLN* 3.9 16.4 - - + -
184D LEU* 4.2 11.9 - - + -
186D GLY* 4.2 5.4 - - - -
192D TYR* 3.8 39.9 - - + -
194D SER 3.3 4.1 + - - +
195D SER 3.2 7.2 + - - +
197D HIS* 1.3 76.3 - - - +
199D ARG* 1.3 53.2 + - - +
201D ALA* 3.2 2.5 + - - +
202D THR* 2.7 45.4 + - - +
209D ILE* 4.1 12.6 - - + -
210D GLY* 3.3 48.7 - - - +
211D VAL* 3.7 20.9 - - + +
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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
----------------------------------------------------------
27A ASP* 3.4 38.4 + - - +
28A TRP* 3.2 34.4 - - - +
94A TYR* 3.1 43.4 + - + +
98A GLN* 3.3 25.3 + - + +
117A EDO 3.5 26.5 + - - -
195D SER* 2.9 26.3 + - - +
196D CYS* 3.5 25.7 - - - +
198D MET* 1.3 76.9 - - - +
200D GLN* 1.3 52.9 + - - +
202D THR* 3.2 1.0 + - - -
203D CYS* 2.7 33.0 + - - +
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Residues in contact with GLN 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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170D ARG* 2.6 40.4 + - + +
171D ALA 3.3 9.1 + - - -
172D ALA 2.8 25.9 + - - -
173D PRO* 4.5 1.8 - - - +
174D CYS* 4.2 16.3 + - - +
196D CYS 2.9 14.2 + - - +
197D HIS* 3.1 14.7 + - - +
199D ARG* 1.3 76.4 - - - +
201D ALA* 1.3 60.9 + - - +
203D CYS* 4.0 3.5 - - - +
204D PHE* 3.0 44.1 + - + -
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Residues in contact with ALA 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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192D TYR* 3.5 40.8 - - + +
197D HIS 2.9 7.6 + - - +
198D MET 3.2 7.2 + - - +
200D GLN* 1.3 74.3 - - - +
202D THR* 1.3 64.8 + - - +
204D PHE* 4.2 2.5 - - - +
205D LEU* 3.1 26.2 + - - +
209D ILE* 4.0 7.3 - - + +
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Residues in contact with THR 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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94A TYR* 4.1 7.9 - - + -
98A GLN 3.8 17.3 + - - +
100A ILE* 4.0 14.9 - - + +
198D MET* 2.7 36.0 + - - +
199D ARG* 3.6 3.5 - - - -
201D ALA* 1.3 72.0 - - - +
203D CYS* 1.3 67.0 + - - +
205D LEU* 3.3 1.6 + - - +
206D GLY 3.1 18.0 + - - -
207D ARG 3.3 27.7 + - - +
208D SER* 3.8 14.8 - - - -
209D ILE* 3.8 19.5 - - - +
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Residues in contact with CYS 203 (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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30A ILE* 4.7 4.9 - - - -
94A TYR* 3.4 14.7 + - - +
100A ILE* 5.4 0.9 - - - -
155D SER* 4.5 3.6 - - - -
156D CYS 4.6 0.2 - - - +
157D VAL* 3.4 19.8 - - - +
167D VAL* 3.6 20.4 - - - -
168D VAL 4.7 0.2 - - - -
169D CYS* 2.0 61.3 - - + -
170D ARG 5.3 0.4 - - - +
199D ARG 2.7 20.6 + - - +
200D GLN* 4.0 3.4 - - - +
202D THR* 1.3 76.1 - - - +
204D PHE* 1.3 59.5 + - - +
206D GLY* 3.4 8.0 + - - -
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Residues in contact with PHE 204 (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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155D SER* 4.0 18.9 - - - -
169D CYS* 3.6 25.6 - - + -
170D ARG 3.5 25.8 - - - -
171D ALA* 4.5 9.0 - - + -
200D GLN* 3.0 35.9 + - + +
201D ALA* 4.4 2.5 - - - +
203D CYS* 1.3 74.3 - - - +
205D LEU* 1.3 64.4 + - - +
206D GLY* 3.5 0.7 + - - -
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Residues in contact with LEU 205 (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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188D ASN* 6.1 0.7 - - + +
201D ALA 3.1 18.6 + - - +
202D THR 3.8 2.5 - - - +
204D PHE* 1.3 76.5 - - - +
206D GLY* 1.3 59.0 + - - +
207D ARG* 3.7 55.1 + - + +
208D SER 4.6 0.7 - - - +
209D ILE* 3.6 31.4 - - + -
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Residues in contact with GLY 206 (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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145D CYS* 4.9 1.5 - - - -
156D CYS 3.5 22.4 - - - +
157D VAL* 3.2 9.3 - - - -
158D VAL* 2.9 27.9 + - - +
202D THR 3.1 5.1 + - - -
203D CYS 3.4 7.4 + - - -
204D PHE 3.2 2.9 - - - -
205D LEU* 1.3 78.6 - - - +
207D ARG* 1.3 63.5 + - - +
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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