Contacts of the helix formed by residues 183 - 197 (chain P) in PDB entry 6MZL
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 GLN 183 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870D GLU* 3.7 15.3 - - - +
178P GLU* 3.8 14.7 + - - +
179P MET 5.9 1.2 + - - -
181P PRO 4.1 4.2 + - - +
182P LEU* 1.3 70.2 - - - +
184P PRO* 1.4 75.1 - - + +
185P LYS* 3.2 30.6 + - + +
186P HIS* 3.0 26.7 + - + +
187P MET* 3.2 11.1 + - - +
50S TYR* 3.9 29.3 + - + -
53S SER* 3.1 8.7 + - - -
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Residues in contact with PRO 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870D GLU* 3.8 16.2 - - + +
182P LEU 4.8 0.2 - - - +
183P GLN* 1.4 86.7 - - + +
185P LYS* 1.3 55.6 + - - +
187P MET* 3.6 1.5 + - + +
188P ARG* 3.0 47.9 + - - +
50S TYR* 5.0 6.1 - - + -
52S GLU* 3.7 32.1 - - + +
53S SER* 3.6 12.8 - - - +
56S ILE* 3.6 20.6 - - + -
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Residues in contact with LYS 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870D GLU* 3.5 50.1 + - + +
872D PHE* 3.6 14.4 - - + -
176P TRP* 3.8 23.1 - - + -
178P GLU* 3.4 28.8 + - - -
183P GLN* 3.3 23.0 + - + +
184P PRO* 1.3 78.0 - - - +
186P HIS* 1.3 61.8 + - + +
188P ARG* 4.1 8.2 - - - +
189P GLU* 2.6 42.1 + - - +
62Q LYS* 5.9 6.3 - - - +
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Residues in contact with HIS 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169P ALA* 3.7 10.1 - - - +
172P VAL* 4.2 6.6 - - + +
173P CYS* 3.7 26.6 - - + -
176P TRP* 3.5 29.3 - + - -
178P GLU* 2.7 32.2 + - + +
179P MET 5.0 2.0 - - - -
181P PRO 4.9 2.0 - - - -
182P LEU* 3.4 33.4 - - + +
183P GLN* 3.0 30.9 + - + +
185P LYS* 1.3 82.9 - - + +
187P MET* 1.3 60.3 + - - +
189P GLU* 3.4 4.5 - - - +
190P ALA* 2.9 29.1 + - - +
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Residues in contact with MET 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165P VAL* 3.9 15.2 - - + +
166P VAL* 3.7 23.1 - - + -
169P ALA* 3.8 15.3 - - - -
182P LEU* 3.7 28.9 - - + -
183P GLN 3.2 11.8 + - - +
184P PRO 4.3 2.0 - - - +
186P HIS* 1.3 78.6 - - - +
188P ARG* 1.3 60.9 + - + +
190P ALA* 3.1 3.3 + - - +
191P VAL* 3.0 33.3 + - - +
40S MET* 3.7 17.3 - - + -
45S ASP* 3.7 14.1 - - - +
53S SER* 4.2 17.7 - - - +
56S ILE* 5.1 8.7 - - + -
57S LEU* 3.8 19.3 - - + -
60S LEU* 5.5 2.0 - - + -
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Residues in contact with ARG 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870D GLU* 3.6 28.7 - - - +
872D PHE* 4.7 0.8 - - - -
897D ASP* 5.3 8.5 + - - +
900D SER* 4.5 18.0 + - - -
901D TYR* 5.7 6.7 - - + +
904D HIS* 3.2 36.8 + - + +
184P PRO* 3.0 36.6 + - - +
185P LYS* 4.1 1.8 - - - +
187P MET* 1.3 76.0 - - - +
189P GLU* 1.3 54.1 + - - +
191P VAL* 3.4 7.8 + - - +
192P ARG* 3.0 32.7 + - - +
195P LYS* 5.2 0.7 + - - -
128Q ILE* 6.2 4.3 - - + -
56S ILE* 3.6 40.7 - - + +
60S LEU* 6.2 1.3 - - + -
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Residues in contact with GLU 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872D PHE* 3.2 22.5 - - - -
904D HIS* 3.9 2.4 - - - -
907D GLN* 3.5 6.8 - - - +
908D GLN* 2.8 17.3 + - - +
911D GLN* 4.2 0.3 - - - +
172P VAL* 3.6 26.9 - - + -
176P TRP* 3.4 19.8 - - + -
185P LYS 2.6 23.0 + - - +
186P HIS* 3.4 4.5 - - - +
188P ARG* 1.3 72.6 - - - +
190P ALA* 1.3 57.2 + - - +
192P ARG* 2.6 38.1 + - - +
193P ARG* 2.9 34.8 + - - +
66Q LEU* 3.9 13.3 - - - +
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Residues in contact with ALA 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165P VAL 3.4 13.0 - - - +
168P GLU* 3.4 15.1 - - + +
169P ALA* 3.3 30.1 - - + +
172P VAL* 4.5 2.2 - - - -
186P HIS 2.9 15.8 + - - +
187P MET 3.1 10.0 + - - +
189P GLU* 1.3 73.8 - - - +
191P VAL* 1.3 61.3 + - - +
192P ARG 3.2 0.2 - - - -
193P ARG* 3.2 1.1 + - - -
194P LEU* 2.9 33.7 + - - +
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Residues in contact with VAL 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P PHE* 3.7 22.0 - - + -
165P VAL* 3.6 19.5 - - + -
187P MET 3.0 17.8 + - - +
188P ARG* 4.0 5.8 - - - +
190P ALA* 1.3 72.3 - - - +
192P ARG* 1.3 62.1 + - - +
194P LEU* 3.2 9.9 + - - +
195P LYS* 3.0 37.9 + - - +
200P ILE* 3.9 8.1 - - + -
127Q TRP 3.6 23.3 - - - +
60S LEU* 3.7 24.2 - - + -
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Residues in contact with ARG 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872D PHE* 3.4 11.3 - - - -
904D HIS* 2.7 79.5 + - + +
907D GLN* 2.9 29.7 + - - +
908D GLN* 3.0 22.8 - - + +
188P ARG 3.0 19.6 + - - +
189P GLU* 2.6 36.2 + - - +
191P VAL* 1.3 75.2 - - - +
193P ARG* 1.3 58.0 + - - +
195P LYS* 3.2 17.6 + - - +
196P SER* 2.9 31.0 + - - -
126Q MET* 4.3 16.6 - - + -
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Residues in contact with ARG 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908D GLN* 3.7 6.3 - - - +
911D GLN* 2.9 38.1 + - - +
915D GLU* 5.4 1.1 - - - +
168P GLU* 3.3 19.6 + - + +
171P ASP* 3.3 25.7 + - - -
172P VAL* 3.4 30.7 - - - +
175P LYS* 4.7 5.1 - - - +
189P GLU* 2.9 21.2 + - - +
190P ALA 3.2 5.3 + - - +
192P ARG* 1.3 75.5 - - - +
194P LEU* 1.3 62.8 + - - +
196P SER* 3.2 8.5 + - - -
197P LYS* 3.1 37.2 + - - +
66Q LEU* 3.5 14.8 - - - +
69Q GLU* 2.7 37.8 + - - +
70Q VAL* 4.3 5.3 - - - +
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Residues in contact with LEU 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P PHE* 5.7 0.2 - - + -
164P GLU* 3.5 51.6 - - + +
165P VAL* 3.7 20.4 - - + +
168P GLU* 4.0 20.6 - - + +
190P ALA 2.9 17.7 + - - +
191P VAL* 3.2 7.8 + - - +
193P ARG* 1.3 76.5 - - - +
195P LYS* 1.3 57.7 + - - +
197P LYS* 4.0 5.9 + - + +
199P GLN* 3.3 47.5 + - + +
200P ILE* 3.4 22.7 + - + +
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Residues in contact with LYS 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901D TYR* 3.7 10.5 + - - -
188P ARG 5.2 0.6 + - - -
191P VAL* 3.0 26.9 + - - +
192P ARG* 3.5 17.4 - - - +
194P LEU* 1.3 76.6 - - - +
196P SER* 1.3 63.8 + - - +
197P LYS 3.3 0.2 - - - -
198P GLY* 3.4 11.8 + - - -
200P ILE* 3.7 25.7 - - + +
124Q TRP* 4.5 18.7 - - + +
125Q ASN 4.8 3.1 - - - +
126Q MET* 3.4 54.5 - - + +
127Q TRP 3.2 37.1 + - - +
128Q ILE* 4.3 3.8 - - - +
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Residues in contact with SER 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908D GLN* 3.7 23.7 + - - +
911D GLN* 5.5 2.5 - - - -
912D ASN* 4.7 10.5 + - - +
915D GLU* 3.2 29.5 - - - +
192P ARG 2.9 16.6 + - - -
193P ARG* 3.2 7.3 + - - -
195P LYS* 1.3 79.1 - - - +
197P LYS* 1.3 56.3 + - - +
198P GLY 3.1 4.0 + - - -
124Q TRP* 3.8 25.1 - - - -
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Residues in contact with LYS 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911D GLN* 5.4 2.4 - - - +
915D GLU* 3.3 22.8 + - - +
168P GLU* 3.0 35.8 + - - +
193P ARG* 3.1 25.3 + - - +
194P LEU* 4.4 3.4 - - + +
195P LYS 3.3 0.8 - - - -
196P SER* 1.3 75.2 - - - +
198P GLY* 1.3 62.7 + - - +
199P GLN* 3.9 36.7 + - + +
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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