Contacts of the helix formed by residues 187 - 206 (chain A) in PDB entry 4MT7
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 LEU 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A HIS* 3.2 30.1 - - + +
183A ASP 3.7 8.2 + - - +
184A GLY* 3.0 16.5 + - - +
186A LEU* 1.3 77.2 - - - +
188A THR* 1.3 65.1 + - - +
189A PRO* 3.3 3.6 - - - -
190A VAL* 2.9 30.2 + - + +
191A GLN* 3.0 34.4 + - + +
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Residues in contact with THR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 3.8 17.4 - - - -
68A HIS* 4.9 14.7 - - + +
69A LEU* 5.0 1.9 - - - +
72A ILE* 4.7 4.7 - - - +
184A GLY 3.9 3.4 - - - +
185A PHE* 3.2 38.3 + - + +
187A LEU* 1.3 77.8 - - - +
189A PRO* 1.3 70.2 - - - +
191A GLN* 3.3 19.2 + - - +
192A LYS* 2.8 29.8 + - - +
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Residues in contact with PRO 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 3.2 26.5 - - + +
69A LEU* 4.5 1.3 - - + -
72A ILE* 5.7 0.2 - - + -
99A ILE* 3.7 27.8 - - + -
102A ILE* 4.4 3.6 - - + -
141A TYR* 3.2 28.7 - - + -
144A TYR* 3.9 14.8 - - + +
185A PHE 4.3 1.1 - - - +
186A LEU 3.9 13.2 - - - +
187A LEU 3.4 5.4 - - - -
188A THR* 1.3 95.5 - - - +
190A VAL* 1.3 63.7 + - - +
192A LYS* 4.2 0.2 - - + -
193A ILE* 3.1 18.4 + - - +
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TYR* 4.1 25.6 - - + -
145A CYS* 4.3 23.8 - - - -
148A HIS* 4.2 20.4 - - + +
187A LEU* 2.9 21.7 + - + +
189A PRO* 1.3 74.0 - - - +
191A GLN* 1.3 67.2 + - + +
193A ILE* 3.3 11.4 - - - +
194A CYS* 3.2 26.9 - - - -
235A LYS* 4.8 9.9 - - - +
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Residues in contact with GLN 191 (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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184A GLY 5.6 0.6 + - - -
187A LEU* 3.0 39.8 + - + +
188A THR* 3.5 24.0 - - - +
190A VAL* 1.3 77.9 - - - +
192A LYS* 1.3 56.5 + - - +
194A CYS* 3.0 9.2 + - - +
195A LYS* 2.8 56.3 + - - +
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 3.3 26.2 + - - -
62A GLU* 2.9 20.0 + - - +
65A TYR* 3.8 44.0 - - + -
141A TYR* 4.5 4.3 - - - +
188A THR 2.8 20.7 + - - +
189A PRO 4.0 3.8 - - - +
190A VAL 3.4 0.2 - - - -
191A GLN* 1.3 74.2 - - - +
193A ILE* 1.3 59.7 + - - +
195A LYS* 3.3 21.9 + - + +
196A TYR* 3.3 43.9 + - + +
199A GLN* 3.4 15.1 + - - +
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Residues in contact with ILE 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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138A PHE* 4.0 27.8 - - + +
141A TYR* 3.9 37.4 - - + -
145A CYS* 4.3 16.6 - - - -
189A PRO 3.1 16.2 + - - +
190A VAL* 3.3 17.5 - - - +
192A LYS* 1.3 76.7 - - - +
194A CYS* 1.3 67.7 + - - +
196A TYR* 4.0 14.1 + - + +
197A PRO* 3.9 7.6 - - - +
224A MET* 4.4 7.5 - - + +
227A VAL* 4.6 11.2 - - + -
228A THR* 3.1 27.8 + - + +
231A ILE* 5.2 7.4 - - + -
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Residues in contact with CYS 194 (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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190A VAL* 3.2 24.9 - - - +
191A GLN* 3.0 11.3 + - - +
193A ILE* 1.3 86.9 - - - +
195A LYS* 1.3 62.3 + - + +
196A TYR 3.3 0.7 - - - -
197A PRO* 3.3 12.1 - - - +
198A LEU* 4.5 9.3 + - - +
228A THR* 4.5 17.3 - - + +
232A ASN* 5.3 4.7 - - - -
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLN* 2.8 44.8 + - - +
192A LYS* 3.3 20.1 + - + +
194A CYS* 1.3 79.2 - - + +
196A TYR* 1.3 64.9 + - - +
198A LEU* 3.0 26.4 + - + +
199A GLN* 3.1 29.5 + - + +
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Residues in contact with TYR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 6.1 1.8 - - + -
62A GLU* 2.6 37.0 + - + -
106A GLN* 3.2 13.4 + - - -
109A PHE* 3.7 9.4 - + - -
131A PHE* 4.0 24.9 - + + -
138A PHE* 3.7 21.8 - + - -
141A TYR* 5.5 3.1 - + - -
192A LYS* 3.3 38.8 + - + +
193A ILE* 4.2 11.9 - - + +
194A CYS 3.3 0.2 - - - -
195A LYS* 1.3 75.8 - - - +
197A PRO* 1.3 71.6 - - + +
199A GLN* 3.1 20.6 + - + +
200A LEU* 2.9 26.2 + - - +
224A MET* 3.8 30.3 - - + -
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Residues in contact with PRO 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 ILE 3.9 7.9 - - - +
194A CYS 3.3 16.2 - - - +
196A TYR* 1.3 92.8 - - + +
198A LEU* 1.3 60.3 + - + +
200A LEU* 4.3 0.9 - - + -
201A ALA* 3.0 24.4 + - - +
221A LEU* 3.4 17.2 - - + +
224A MET* 4.0 28.5 - - + +
225A ARG* 3.8 28.5 + - + +
228A THR* 4.0 9.0 - - + +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A CYS 4.6 7.2 - - - +
195A LYS* 3.0 22.6 + - + +
197A PRO* 1.3 82.0 - - + +
199A GLN* 1.3 62.0 + - + +
201A ALA* 3.6 6.7 + - + +
202A GLU* 3.4 21.5 + - - +
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Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.2 1.6 - - - +
57A GLU* 3.2 26.9 + - - +
58A ILE* 3.6 34.8 - - + +
61A THR* 3.5 20.1 + - - +
131A PHE* 6.5 0.2 - - + -
192A LYS* 3.4 20.3 + - - -
195A LYS* 3.5 25.8 - - + +
196A TYR* 3.1 21.1 + - + +
198A LEU* 1.3 78.8 - - + +
200A LEU* 1.3 61.9 + - + +
202A GLU* 3.7 6.9 + - - +
203A LEU* 3.2 24.9 + - - +
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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
----------------------------------------------------------
58A ILE* 5.2 4.7 - - + -
127A ILE* 5.4 1.6 - - + -
128A GLY* 6.3 1.3 - - - -
131A PHE* 4.3 28.9 - - + -
196A TYR 2.9 14.8 + - - +
198A LEU 3.3 0.2 - - - -
199A GLN* 1.3 78.9 - - + +
201A ALA* 1.3 59.1 + - - +
203A LEU* 3.3 21.6 + - + +
204A LEU* 2.9 29.6 + - - +
217A VAL* 4.1 11.4 - - + +
220A ALA* 3.5 20.6 - - + +
221A LEU* 3.4 49.1 - - + +
224A MET* 3.9 16.6 - - + -
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Residues in contact with ALA 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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197A PRO 3.0 17.5 + - - +
198A LEU* 3.8 9.4 - - + +
200A LEU* 1.3 78.2 - - - +
202A GLU* 1.3 61.5 + - - +
204A LEU* 3.2 5.1 + - - +
205A LYS* 3.1 24.3 + - - +
221A LEU* 3.7 18.5 - - + +
225A ARG* 4.1 11.4 - - - +
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Residues in contact with GLU 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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50A MET* 5.9 0.9 - - - +
54A VAL* 3.5 23.0 - - + +
57A GLU* 5.5 4.3 - - - +
198A LEU 3.4 13.1 + - - +
199A GLN* 3.8 8.1 - - - +
201A ALA* 1.3 79.9 - - - +
203A LEU* 1.3 60.9 + - - +
205A LYS* 2.7 37.2 + - - +
206A TYR* 3.3 42.2 + - - -
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Residues in contact with LEU 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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51A ARG* 3.7 25.1 - - + +
54A VAL* 3.6 25.1 - - + +
55A ILE* 3.6 24.0 - - + -
58A ILE* 4.7 2.2 - - + -
127A ILE* 3.8 28.0 - - + -
199A GLN 3.2 15.7 + - - +
200A LEU* 3.7 12.3 - - + +
201A ALA 3.3 0.4 - - - -
202A GLU* 1.3 75.1 - - - +
204A LEU* 1.3 59.0 + - - +
206A TYR* 3.4 9.9 + - - +
207A THR* 2.5 25.5 + - - +
217A VAL* 3.7 31.0 - - + -
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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 2.9 13.4 + - - +
201A ALA* 3.2 9.2 + - - +
203A LEU* 1.3 78.0 - - - +
205A LYS* 1.3 64.3 + - - +
207A THR* 2.9 24.8 + - - +
214A TYR* 3.8 38.9 - - + +
217A VAL* 3.9 19.5 - - + +
218A ALA* 4.0 27.6 - - + +
221A LEU* 4.5 15.5 - - + -
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Residues in contact with LYS 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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47A ARG* 4.6 6.8 + - - -
201A ALA 3.1 12.4 + - - +
202A GLU* 2.7 40.7 + - - +
203A LEU 3.3 0.2 - - - -
204A LEU* 1.3 77.0 - - - +
206A TYR* 1.3 96.2 + - + +
207A THR 3.4 4.9 + - - +
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Residues in contact with TYR 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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46A ASN 5.5 0.2 - - - -
47A ARG* 3.5 45.6 + - + +
50A MET* 3.4 44.0 - - + +
51A ARG* 3.1 34.9 - - - +
54A VAL* 4.2 10.5 - - + -
202A GLU* 3.3 41.0 + - + -
203A LEU 3.4 4.7 + - - +
204A LEU 3.2 0.8 - - - -
205A LYS* 1.3 110.5 - - + +
207A THR* 1.3 59.2 + - - +
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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