Contacts of the helix formed by residues 191 - 210 (chain A) in PDB entry 2H6D
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 ALA 191 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLU* 4.9 0.2 - - - +
190A TYR* 1.3 79.0 - - - +
192A GLY* 1.3 64.5 + - - +
193A PRO* 3.5 6.3 - - + -
194A GLU* 3.3 42.8 + - + +
195A VAL* 3.5 8.7 + - - +
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A HIS* 3.0 38.1 + - - -
139A ASP* 3.9 6.1 - - - -
190A TYR* 3.5 11.2 + - - -
191A ALA* 1.3 68.1 - - - +
193A PRO* 1.3 74.4 - - - +
194A GLU 3.2 0.3 + - - -
195A VAL* 3.2 4.2 + - - +
196A ASP* 3.0 19.6 + - - +
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Residues in contact with PRO 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A HIS* 3.7 39.0 - - + +
137A HIS* 3.6 16.6 - - + +
191A ALA* 3.7 7.2 - - + -
192A GLY* 1.3 88.7 - - - +
194A GLU* 1.3 61.3 + - + +
196A ASP* 3.3 5.4 - - - +
197A ILE* 3.3 23.9 + - - +
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Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 4.0 3.7 - - - +
190A TYR* 5.9 0.2 - - - +
191A ALA* 3.3 29.4 + - + +
192A GLY 3.2 1.2 - - - -
193A PRO* 1.3 74.8 - - + +
195A VAL* 1.3 66.1 + - - +
197A ILE* 3.0 19.8 + - - +
198A TRP 3.3 4.5 + - - -
253A PRO* 3.2 36.1 - - + +
254A LEU* 5.2 6.6 - - - +
256A ARG* 3.0 28.3 + - + +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP* 4.0 18.2 - - + +
181A ALA* 3.8 11.9 - - + +
183A GLU* 3.2 29.4 - - + +
184A VAL* 3.7 21.3 - - + -
190A TYR* 3.2 32.8 - - + -
191A ALA 3.5 1.7 + - - +
192A GLY 3.2 7.5 + - - +
194A GLU* 1.3 76.3 - - - +
196A ASP* 1.3 62.8 + - - +
198A TRP* 3.2 4.7 + - - +
199A SER* 3.0 27.5 + - - +
256A ARG* 4.1 4.3 - - - +
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Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 4.2 8.6 - - + +
131A HIS* 2.7 31.6 + - + +
134A MET* 5.8 0.5 - - - +
137A HIS* 3.1 15.2 - - - -
138A ARG 4.4 0.9 - - - +
139A ASP* 3.6 7.8 - - - +
140A LEU* 2.9 38.8 + - + +
192A GLY 3.0 13.7 + - - +
193A PRO 3.3 11.2 - - - +
194A GLU 3.2 0.2 - - - -
195A VAL* 1.3 76.6 - - - +
197A ILE* 1.3 58.0 + - - +
199A SER* 3.4 6.3 + - - -
200A CYS* 2.9 34.6 + - - -
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Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 4.7 4.3 - - + -
127A VAL* 5.6 0.9 - - + -
131A HIS* 4.9 3.1 - - + -
193A PRO 3.4 15.3 - - - +
194A GLU* 3.0 12.7 + - - +
196A ASP* 1.3 78.6 - - + +
198A TRP* 1.3 57.9 + - - +
200A CYS* 3.1 4.2 + - - -
201A GLY* 2.9 24.4 + - - -
248A MET* 3.5 28.7 - - + +
256A ARG* 4.0 13.2 - - + -
257A ALA* 3.2 29.8 - - + +
258A THR* 4.6 2.2 - - - -
259A ILE* 3.6 40.4 - - + +
262A ILE* 4.2 7.6 - - + -
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Residues in contact with TRP 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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180A ALA* 3.1 41.5 - - - -
181A ALA* 3.4 26.9 - - + -
182A PRO* 3.5 20.4 - - + +
194A GLU 3.3 2.0 + - - -
195A VAL 3.2 7.5 + - - +
197A ILE* 1.3 78.0 - - - +
199A SER* 1.3 68.2 + - - +
201A GLY* 3.0 4.2 + - - -
202A VAL* 2.9 49.9 + - + +
214A PHE* 3.7 32.2 - + - -
226A ILE* 4.2 13.2 + - + +
248A MET 3.7 9.1 + - - -
249A LEU* 3.5 39.4 + - + +
256A ARG* 3.9 16.4 - - - +
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Residues in contact with SER 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 4.0 27.7 + - - -
142A PRO* 4.7 12.4 - - - +
195A VAL* 3.0 19.8 + - - +
196A ASP* 3.5 12.2 + - - -
198A TRP* 1.3 88.7 - - - +
200A CYS* 1.3 59.0 + - - +
202A VAL* 3.2 7.0 + - - +
203A ILE* 3.0 33.3 + - - +
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Residues in contact with CYS 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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120A PHE* 3.4 18.3 - - + -
123A ILE* 4.6 9.9 - - - -
124A LEU* 4.0 21.3 - - + -
127A VAL* 4.0 15.3 - - - -
140A LEU* 3.8 21.3 - - - -
196A ASP 2.9 19.5 + - - +
197A ILE* 3.5 9.4 - - - +
199A SER* 1.3 76.3 - - - +
201A GLY* 1.3 58.4 + - - +
203A ILE* 3.3 7.5 + - - +
204A LEU* 2.8 24.8 + - - +
248A MET* 3.6 13.5 - - + -
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Residues in contact with GLY 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE 2.9 12.0 + - - -
198A TRP 3.0 4.7 + - - -
200A CYS* 1.3 74.1 - - - +
202A VAL* 1.3 60.6 + - - +
204A LEU* 3.4 2.2 + - - -
205A TYR* 2.9 28.8 + - - +
245A LEU* 3.6 8.3 - - - +
248A MET* 3.3 24.1 - - - +
249A LEU* 3.9 16.0 - - - +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 4.4 9.4 - - + -
142A PRO* 5.0 7.9 - - + -
198A TRP* 2.9 52.3 + - + +
199A SER* 3.2 6.9 + - - +
201A GLY* 1.3 73.8 - - - +
203A ILE* 1.3 59.6 + - - +
205A TYR* 3.3 1.9 + - - +
206A ALA* 2.9 31.4 + - - +
212A LEU* 4.0 24.7 - - + -
213A PRO* 3.9 22.4 - - + +
249A LEU* 3.9 8.5 - - + -
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Residues in contact with ILE 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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101A LEU* 4.2 9.9 - - + -
102A PHE* 3.9 24.9 - - + -
120A PHE* 5.0 2.9 - - + -
123A ILE* 3.7 33.2 - - + -
140A LEU* 4.0 25.4 - - + -
142A PRO* 4.2 13.9 - - + -
145A VAL* 4.0 19.7 - - + -
199A SER 3.0 19.6 + - - +
200A CYS* 3.3 12.1 + - - +
202A VAL* 1.3 76.8 - - - +
204A LEU* 1.3 57.6 + - - +
206A ALA* 3.2 2.8 + - - +
207A LEU* 2.9 37.9 + - + +
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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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116A ALA* 4.7 3.6 - - + +
120A PHE* 3.9 36.6 - - + -
200A CYS 2.8 19.4 + - - +
201A GLY* 3.8 5.2 - - - +
203A ILE* 1.3 75.1 - - - +
205A TYR* 1.3 64.0 + - - +
207A LEU* 3.3 8.8 + - + +
208A LEU* 3.0 41.3 + - + +
241A VAL* 4.5 3.8 - - + -
244A LEU* 4.0 29.8 - - + -
245A LEU* 3.7 22.7 - - + -
248A MET* 4.4 3.1 - - - -
267A TRP* 3.8 20.6 - - + -
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLY 2.9 19.2 + - - +
202A VAL 3.5 4.7 - - - +
204A LEU* 1.3 75.4 - - - +
206A ALA* 1.3 52.9 + - - +
208A LEU* 3.2 3.6 + - - -
209A CYS* 2.7 63.4 + - + +
211A THR* 3.2 36.1 + - - -
212A LEU 3.8 0.8 + - - -
213A PRO* 3.5 41.0 + - + +
231A PHE* 3.8 21.1 - + - -
232A TYR* 2.6 45.8 + - - +
233A ILE* 4.5 3.8 - - + -
234A PRO* 4.2 0.5 - - - +
245A LEU* 3.8 20.8 - - + +
249A LEU* 5.0 0.9 - - + -
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Residues in contact with ALA 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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102A PHE* 3.9 26.0 - - + -
105A ILE* 3.7 15.3 - - + +
202A VAL 2.9 17.0 + - - +
203A ILE 3.6 4.7 - - - +
205A TYR* 1.3 74.5 - - - +
207A LEU* 1.3 60.0 + - - +
210A GLY* 2.8 30.0 + - - -
211A THR 3.3 20.0 - - - +
212A LEU* 4.3 7.4 - - + -
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Residues in contact with LEU 207 (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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101A LEU* 3.9 23.8 - - + -
105A ILE* 3.7 23.4 - - + +
110A ARG* 3.8 0.5 - - - -
111A VAL* 3.0 43.3 + - + +
116A ALA* 3.9 34.1 - - + +
119A LEU* 3.9 24.7 - - + -
120A PHE* 4.4 9.6 - - + +
123A ILE* 4.5 0.9 - - + -
203A ILE* 2.9 36.2 + - + +
204A LEU* 3.5 12.6 - - + +
206A ALA* 1.3 77.5 - - - +
208A LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 208 (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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110A ARG* 3.5 20.9 + - - +
111A VAL 4.6 4.5 - - - +
113A GLU* 4.3 20.2 - - + -
116A ALA* 3.6 24.7 - - + -
204A LEU* 3.0 34.5 + - + +
205A TYR* 3.8 2.9 - - - +
207A LEU* 1.3 80.9 - - - +
209A CYS* 1.3 63.3 + - - +
236A TYR* 3.6 10.9 - - - -
237A LEU* 4.0 22.9 - - + +
241A VAL* 3.6 33.2 - - + -
245A LEU* 4.4 10.3 - - + -
267A TRP* 4.4 8.5 - - + -
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Residues in contact with CYS 209 (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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110A ARG* 3.6 9.2 - - - +
205A TYR* 2.7 50.7 + - + +
208A LEU* 1.3 78.6 - - - +
210A GLY* 1.3 63.9 + - - +
211A THR* 3.3 10.6 + - - +
234A PRO* 3.6 33.4 - - + -
236A TYR* 3.5 16.2 + - - +
237A LEU* 3.8 17.0 - - - -
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Residues in contact with GLY 210 (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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105A ILE* 3.7 24.0 - - - +
106A CYS* 5.7 3.1 - - - -
109A GLY* 4.5 1.2 - - - -
110A ARG* 3.4 18.0 - - - +
206A ALA* 2.8 17.0 + - - -
209A CYS* 1.3 79.0 - - - +
211A THR* 1.3 63.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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