Contacts of the helix formed by residues 1191 - 1205 (chain A) in PDB entry 3MPX
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 SER1191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1174A TYR* 3.4 18.6 - - - +
1189A ALA* 3.5 1.2 - - - +
1190A SER* 1.3 80.9 + - - +
1192A CYS* 1.3 58.4 + - - +
1193A ALA* 3.1 14.1 - - - -
1194A GLU* 3.3 13.5 + - - +
1195A ARG 3.0 22.5 + - - -
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Residues in contact with CYS1192 (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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1174A TYR* 3.2 19.3 - - + -
1191A SER* 1.3 72.4 - - - +
1193A ALA* 1.4 56.2 + - - +
1195A ARG* 3.2 32.0 + - - +
1196A ASP* 3.1 32.3 + - - +
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Residues in contact with ALA1193 (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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1191A SER* 3.1 8.0 - - - -
1192A CYS* 1.4 77.4 - - - +
1194A GLU* 1.4 54.2 + - - +
1195A ARG 3.3 0.2 - - - -
1196A ASP* 3.6 4.2 - - - +
1197A GLU* 2.7 35.0 + - - +
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Residues in contact with GLU1194 (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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1119A THR 4.7 6.7 - - - -
1120A LEU* 4.0 17.0 - - - -
1189A ALA* 4.0 2.9 - - + -
1190A SER* 3.2 33.7 - - - +
1191A SER* 3.3 22.2 + - - +
1193A ALA* 1.4 75.5 - - - +
1195A ARG* 1.4 61.4 + - - +
1197A GLU* 3.2 7.6 + - + +
1198A TRP* 3.2 44.1 + - + +
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Residues in contact with ARG1195 (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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1166A ARG* 3.7 20.0 - - - +
1167A PRO 5.5 1.6 + - - -
1174A TYR* 3.6 31.6 - - + +
1175A ALA 3.5 29.5 + - - +
1176A LEU* 3.9 13.6 - - + +
1189A ALA* 3.6 14.9 - - + +
1191A SER 3.0 16.0 + - - +
1192A CYS* 3.2 33.4 + - - +
1194A GLU* 1.4 76.3 - - - +
1196A ASP* 1.3 85.8 + - - +
1198A TRP* 3.8 3.0 + - - +
1199A TYR* 3.1 25.5 + - - +
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Residues in contact with ASP1196 (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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1166A ARG* 2.9 34.7 + - - +
1192A CYS* 3.1 22.8 + - - +
1193A ALA* 3.3 5.6 + - - +
1194A GLU 3.3 0.2 - - - -
1195A ARG* 1.3 97.2 + - - +
1197A GLU* 1.4 64.5 + - - +
1199A TYR* 3.7 5.8 - - - +
1200A GLY* 3.3 18.4 + - - -
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Residues in contact with GLU1197 (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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1116A LYS* 4.9 5.4 - - + -
1193A ALA 2.7 20.3 + - - +
1194A GLU* 3.2 12.1 + - + +
1196A ASP* 1.4 74.6 - - - +
1198A TRP* 1.3 64.0 + - + +
1200A GLY* 3.6 0.7 + - - -
1201A CYS* 3.3 29.4 + - - -
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Residues in contact with TRP1198 (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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1116A LYS* 3.8 25.4 - - + +
1117A GLU 3.3 29.1 + - - -
1118A GLY* 3.6 15.7 - - - -
1119A THR 5.3 0.4 + - - -
1120A LEU* 4.1 32.7 - - + +
1133A LEU* 3.6 40.8 - - + -
1135A LEU* 4.0 25.8 - - + -
1140A LEU* 5.2 0.9 - - + -
1176A LEU* 4.0 17.7 - - + -
1194A GLU* 3.2 31.3 + - + +
1195A ARG* 4.1 2.7 - - - +
1197A GLU* 1.3 79.6 - - + +
1199A TYR* 1.4 54.7 + - - +
1201A CYS* 3.2 3.9 + - - +
1202A LEU* 2.7 57.6 + - + +
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Residues in contact with TYR1199 (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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1165A SER* 4.7 19.5 - - - -
1166A ARG* 3.4 59.6 + - + -
1176A LEU* 4.4 11.9 - - + +
1195A ARG 3.1 20.8 + - - +
1196A ASP* 3.9 9.6 - - - +
1197A GLU 3.4 0.6 - - - -
1198A TRP* 1.4 75.7 - - - +
1200A GLY* 1.3 55.4 + - - +
1202A LEU* 3.4 4.9 + - + +
1203A SER* 2.8 46.7 + - - -
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Residues in contact with GLY1200 (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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1196A ASP 3.3 13.5 + - - -
1197A GLU 4.1 1.3 - - - -
1199A TYR* 1.3 80.8 - - - +
1201A CYS* 1.3 58.0 + - - +
1203A SER* 3.6 7.2 - - - -
1204A ARG* 3.0 28.6 + - - +
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Residues in contact with CYS1201 (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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1115A LEU* 5.4 4.4 - - + +
1116A LYS* 4.0 27.6 - - + -
1135A LEU* 4.3 17.2 - - + +
1197A GLU* 3.3 18.2 + - - +
1198A TRP 3.2 4.8 + - - +
1200A GLY* 1.3 74.3 - - - +
1202A LEU* 1.4 63.8 + - - +
1203A SER 3.1 1.9 + - - -
1204A ARG* 3.4 15.4 + - - +
1205A ALA* 3.7 11.1 + - - +
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Residues in contact with LEU1202 (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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11A UNX 4.4 11.2 - - - -
1135A LEU* 3.8 34.0 - - + +
1140A LEU* 4.0 16.8 - - + -
1176A LEU* 3.8 20.4 - - + -
1178A ILE* 3.8 35.4 - - + -
1198A TRP* 2.7 37.3 + - + +
1199A TYR* 3.9 4.0 - - + +
1201A CYS* 1.4 72.6 - - - +
1203A SER* 1.4 60.8 + - - +
1205A ALA* 3.9 14.3 + - - +
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Residues in contact with SER1203 (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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1199A TYR* 2.8 33.5 + - - -
1200A GLY* 3.6 9.4 - - - -
1201A CYS 3.1 0.2 - - - -
1202A LEU* 1.4 74.2 - - - +
1204A ARG* 1.4 57.8 + - - +
1205A ALA 3.0 23.7 + - - +
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Residues in contact with ARG1204 (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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1200A GLY 3.0 18.1 + - - +
1201A CYS* 3.7 9.4 - - - +
1203A SER* 1.4 72.9 - - - +
1205A ALA* 1.3 57.9 + - + +
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Residues in contact with ALA1205 (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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1115A LEU* 4.1 26.5 - - + -
1135A LEU* 5.6 4.5 - - + -
1136A MSE 5.3 0.4 - - - +
1137A ASN* 4.6 16.4 - - + +
1159A VAL* 5.2 18.4 - - + -
1201A CYS 3.7 8.4 + - - +
1202A LEU 3.9 11.0 - - - +
1203A SER 3.0 13.9 + - - +
1204A ARG* 1.3 78.4 - - + +
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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