Contacts of the helix formed by residues 190 - 206 (chain A) in PDB entry 2D2C
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A SER* 2.8 12.0 + - - +
186A ALA* 2.9 23.5 + - + +
189A PHE* 1.3 81.8 - - + +
191A LEU* 1.3 65.5 + - + +
192A PRO* 3.0 0.7 - - - -
193A TRP* 2.6 32.3 + - - +
194A LEU* 3.7 23.1 + - + -
52N PHE* 3.9 32.5 - - + -
56N PHE* 4.5 7.0 - - + -
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.9 12.1 - - + +
130A SER* 3.4 45.5 - - - +
131A PHE* 3.7 23.6 - - + +
134A THR* 4.5 3.6 - - + +
186A ALA* 3.2 39.5 - - + +
187A HIS* 3.8 1.1 - - - +
190A VAL* 1.3 88.1 - - + +
192A PRO* 1.3 58.0 - - + +
193A TRP 2.5 12.5 + - - -
194A LEU* 3.0 18.0 + - + -
195A ILE* 2.9 19.6 + - - +
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Residues in contact with PRO 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 5.2 6.7 - - + -
48A PHE* 5.7 1.5 - - + -
131A PHE* 3.4 14.6 - - + -
186A ALA 3.0 13.7 - - - +
187A HIS 3.4 11.9 - - - +
188A THR 2.8 33.4 - - - +
189A PHE 3.1 13.2 - - - +
190A VAL 3.0 1.8 - - - -
191A LEU* 1.3 90.0 - - + +
193A TRP* 1.3 56.9 + - - -
195A ILE* 3.8 7.2 - - + +
196A ALA* 3.9 10.2 - - - +
301A HEM 4.5 14.1 - - + -
193N TRP* 3.4 25.6 - - + -
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Residues in contact with TRP 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PHE* 2.8 63.9 - + - -
190A VAL* 2.6 14.6 + - - +
191A LEU 2.5 5.3 + - - -
192A PRO* 1.3 72.9 - - - +
194A LEU* 1.3 71.3 + - + +
196A ALA* 2.9 10.5 - - + +
197A VAL* 2.8 32.6 + - + +
48N PHE* 4.3 25.9 - + + -
188N THR 4.4 0.4 - - - -
192N PRO* 3.4 32.8 - - + -
193N TRP* 3.1 58.4 - + - +
196N ALA* 5.7 4.8 - - + +
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.2 23.8 - - + -
190A VAL* 4.1 26.5 - - + +
191A LEU* 3.0 17.2 + - + +
193A TRP* 1.3 77.2 - - + +
195A ILE* 1.3 69.6 + - - +
197A VAL* 2.6 25.0 + - + +
198A PHE* 2.8 22.9 + - + -
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.8 34.5 - - + -
93A MET* 4.6 8.5 - - + -
124A LEU* 3.6 10.8 - - + +
127A ILE* 3.1 25.5 - - + +
128A THR* 4.5 16.4 - - - +
131A PHE* 3.9 16.2 - - + -
191A LEU 2.9 17.2 + - - +
192A PRO* 3.8 15.7 - - + +
194A LEU* 1.3 77.6 - - - +
196A ALA* 1.3 74.6 + - - +
198A PHE 3.4 0.2 + - - -
199A MET* 2.7 48.6 + - + +
302A HEM 5.4 2.0 - - + -
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 6.2 2.0 - - + -
192A PRO 3.9 10.1 - - - +
193A TRP* 2.9 20.9 - - + +
194A LEU 2.7 3.6 + - - -
195A ILE* 1.3 83.7 - - + +
197A VAL* 1.3 67.2 + - + +
199A MET* 2.8 16.7 + - - +
200A LEU* 2.9 24.4 - - + +
193N TRP* 5.7 4.5 - - - +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A TRP* 2.8 24.8 + - + +
194A LEU* 2.6 15.6 + - + +
196A ALA* 1.3 75.2 - - + +
198A PHE* 1.3 73.4 + - + +
200A LEU* 2.7 26.2 + - - +
201A LEU* 2.8 33.5 + - + +
1305N OPC 6.1 10.1 - - + -
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A SER* 4.2 16.4 + - - -
123A ILE* 3.4 47.1 - - + -
124A LEU* 3.5 22.6 - - + +
127A ILE* 4.5 2.2 - - + -
194A LEU* 2.8 35.6 + - + +
195A ILE* 4.6 0.9 - - - -
197A VAL* 1.3 85.0 - - + +
199A MET* 1.3 56.6 + - - +
201A LEU* 3.6 18.8 - - + +
202A HIS* 2.6 34.8 + - - +
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Residues in contact with MET 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.8 34.1 - - + -
44A PHE* 4.9 18.6 - - + -
93A MET* 6.4 0.7 - - + -
124A LEU* 3.6 16.6 - - + -
195A ILE* 2.7 51.2 + - + +
196A ALA* 2.8 11.4 + - - +
198A PHE* 1.3 71.5 - - - +
200A LEU* 1.3 55.7 + - + +
202A HIS* 3.1 5.8 - - - +
203A PHE* 2.7 56.4 + - + -
302A HEM 3.9 24.0 - - + -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ALA* 2.9 31.6 - - + +
197A VAL* 2.7 14.9 + - - +
199A MET* 1.3 83.3 - - + +
201A LEU* 1.3 54.5 + - + +
203A PHE* 2.9 14.9 + - + -
204A LEU* 2.5 61.5 + - + +
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A SER* 4.7 6.7 - - - -
197A VAL* 2.8 52.7 + - + +
198A PHE* 3.6 26.2 - - + +
200A LEU* 1.3 76.2 - - + +
202A HIS* 1.3 66.4 + - - +
204A LEU* 4.3 11.2 - - + -
205A MET* 2.8 44.4 + - + +
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Residues in contact with HIS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 2.7 27.6 + - - -
120A SER* 3.4 2.2 + - - +
121A GLY* 3.3 7.0 - - - -
124A LEU* 3.1 19.3 - - + +
198A PHE 2.6 22.6 + - - +
199A MET* 3.1 6.5 - - - +
201A LEU* 1.3 75.4 - - - +
203A PHE* 1.3 55.1 + + + +
205A MET* 3.3 12.4 - - - +
206A ILE* 2.5 55.8 + - + +
302A HEM 2.1 81.7 + + + -
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.5 31.9 - - + -
124A LEU* 6.1 0.2 - - + -
199A MET* 2.7 53.5 + - + +
200A LEU* 2.9 16.3 + - + +
202A HIS* 1.3 78.0 - + + +
204A LEU* 1.3 59.3 + - + +
205A MET 3.1 1.6 - - - -
206A ILE* 2.5 45.9 + - + +
302A HEM 3.5 36.6 - + + -
303A HEC 4.9 37.0 - + + +
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 2.5 53.4 + - + +
201A LEU* 3.9 11.2 - - + +
203A PHE* 1.3 73.6 - - + +
205A MET* 1.3 66.3 + - + +
206A ILE 3.8 4.5 - - - +
207A ARG* 4.0 11.6 - - - +
303A HEC 5.8 1.1 - - - -
1305N OPC 6.5 1.3 - - + -
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Residues in contact with MET 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.5 33.2 - - + -
117A THR* 3.1 36.6 - - + -
120A SER* 3.3 31.0 - - - +
201A LEU* 2.8 42.6 + - + +
202A HIS* 3.3 2.7 - - - +
204A LEU* 1.3 75.1 - - + +
206A ILE* 1.3 51.6 + - - +
207A ARG* 2.4 37.6 + - - +
208A LYS* 3.6 10.9 - - - +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ARG* 6.1 0.7 - - + -
117A THR* 4.0 16.6 - - + +
202A HIS* 2.5 51.4 - - + +
203A PHE* 2.5 25.3 + - + +
204A LEU 3.8 0.9 - - - +
205A MET* 1.3 72.4 - - - +
207A ARG* 1.3 57.2 + - - +
208A LYS* 3.4 13.2 - - + +
302A HEM 3.5 39.9 - - + +
303A HEC 4.0 41.3 - - + +
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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