Contacts of the helix formed by residues 189 - 198 (chain D) in PDB entry 3EVK
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 ASP 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D TYR* 3.0 29.4 + - + +
187D LYS 3.2 1.1 - - - -
188D ASN* 1.3 81.5 - - - +
190D ARG* 1.3 61.0 + - - +
191D GLY* 3.4 6.1 + - - -
192D SER* 3.1 37.7 + - - +
193D TYR 3.5 11.6 + - - -
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Residues in contact with ARG 190 (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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178B TRP* 6.2 0.8 - - - -
133D ALA 3.5 23.6 + - - -
134D LYS* 3.4 26.3 + - - +
136D VAL* 2.8 27.5 + - - +
138D GLY 3.0 24.7 + - - +
177D VAL* 3.7 23.7 + - + -
179D GLU* 5.3 4.6 + - - +
182D TYR* 3.5 39.7 + - + +
188D ASN 2.9 10.6 + - - +
189D ASP* 1.3 70.5 - - - +
191D GLY* 1.3 60.0 + - - +
193D TYR* 3.1 6.8 + - + +
194D VAL* 2.9 38.4 + - + +
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Residues in contact with GLY 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LYS* 3.4 29.1 - - - +
189D ASP* 3.3 6.6 + - - -
190D ARG* 1.3 78.7 - - - +
192D SER* 1.3 57.1 + - - +
194D VAL 3.5 0.2 + - - -
195D ASP* 3.0 34.2 + - - +
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Residues in contact with SER 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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186D TYR* 3.3 22.5 - - - -
189D ASP* 3.1 29.2 + - - +
191D GLY* 1.3 72.9 - - - +
193D TYR* 1.3 59.4 + - - +
195D ASP* 3.6 10.8 - - - +
196D ASN* 3.0 41.8 + - - +
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Residues in contact with TYR 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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33D TYR 5.2 0.4 - - - -
34D ILE* 4.3 22.6 - - + +
93D PHE* 4.0 12.8 - - - -
175D LEU* 3.3 25.4 - - + +
176D ASP 2.7 29.8 + - - -
177D VAL* 4.2 6.7 - - + -
181D ALA* 3.8 23.4 + - + +
182D TYR* 3.5 33.2 - + + -
186D TYR* 3.7 36.3 - + + -
189D ASP 3.5 6.2 + - - +
190D ARG* 3.1 10.9 + - + +
192D SER* 1.3 77.2 + - - +
194D VAL* 1.3 70.6 + - + +
196D ASN* 3.3 2.4 + - - +
197D TRP* 3.1 21.5 + - + +
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Residues in contact with VAL 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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130D SER* 4.1 18.8 - - - +
133D ALA* 3.9 25.8 - - + -
134D LYS* 3.9 25.4 - - + -
175D LEU* 3.8 24.5 - - + -
177D VAL* 4.0 13.7 - - + -
190D ARG* 2.9 21.6 + - + +
191D GLY 3.7 7.6 - - - +
193D TYR* 1.3 77.0 - - + +
195D ASP* 1.3 62.8 + - - +
197D TRP* 3.3 15.8 + - - +
198D TRP* 3.4 15.3 + - + +
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Residues in contact with ASP 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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130D SER* 4.8 4.0 + - - -
134D LYS* 2.9 28.4 + - - -
191D GLY 3.0 21.8 + - - +
192D SER* 3.6 10.7 - - - +
193D TYR 3.3 0.2 - - - -
194D VAL* 1.3 77.6 - - - +
196D ASN* 1.3 61.8 + - - +
198D TRP* 3.6 22.4 + - - +
199D ASN* 3.9 5.9 + - - +
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Residues in contact with ASN 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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33D TYR* 3.4 40.7 - - + +
186D TYR* 3.3 31.8 + - - +
192D SER* 3.0 25.3 + - - +
193D TYR 4.0 1.8 - - - +
195D ASP* 1.3 75.8 - - - +
197D TRP* 1.3 63.7 + - - +
198D TRP 3.2 0.7 - - - -
199D ASN* 3.0 28.1 + - - +
200D VAL 4.2 0.5 + - - -
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Residues in contact with TRP 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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34D ILE* 4.4 11.4 - - + -
93D PHE* 3.9 5.8 - + - -
96D ASN* 5.4 1.6 - - + -
97D MET* 3.7 36.2 - - + +
129D PHE* 3.8 20.2 - + - -
173D LEU* 3.6 36.8 - - + -
174D ALA 3.7 18.2 - - - -
175D LEU* 3.6 38.7 - - + +
193D TYR* 3.1 17.9 + - + +
194D VAL 3.3 9.2 + - - +
196D ASN* 1.3 75.9 - - - +
198D TRP* 1.3 88.3 + + - +
200D VAL* 2.9 35.1 + - + +
201D VAL* 3.4 25.6 + - + +
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Residues in contact with TRP 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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104D GLY* 3.3 14.2 - - - -
105D GLY 4.1 6.6 + - - +
122D PHE* 4.5 5.2 - + + -
125D PHE* 3.9 14.8 - + - -
126D LYS* 3.7 41.0 - - + +
129D PHE* 3.6 39.5 - + + -
130D SER* 3.1 28.0 + - - -
173D LEU* 4.5 1.8 - - + -
194D VAL* 3.4 26.2 + - + +
195D ASP* 3.6 18.5 + - - +
196D ASN 3.2 0.6 - - - -
197D TRP* 1.3 95.1 - + - +
199D ASN* 1.3 61.1 - - - +
200D VAL 3.2 3.9 + - - -
201D VAL* 3.4 21.7 + - + +
203D TRP* 4.0 27.8 - + - -
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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