Contacts of the helix formed by residues 1151 - 1157 (chain D) in PDB entry 3CMT
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 PRO1151 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1123D GLU* 3.5 16.8 - - - +
1149D LEU 3.3 10.3 - - - +
1150D THR* 1.3 87.3 - - - +
1152D LYS* 1.3 64.5 + - - +
1153D ALA 3.3 0.2 - - - -
1154D GLU* 3.1 36.1 + - + +
1155D ILE* 3.2 10.7 + - - +
1166D LEU* 3.9 27.8 - - + -
1167D ALA* 3.8 35.4 - - + +
1170D MET* 4.4 7.0 - - - -
2176D ARG* 4.9 1.6 - - - +
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Residues in contact with LYS1152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121D THR* 3.9 30.3 - - + +
1123D GLU* 2.7 27.5 + - + +
1150D THR 3.6 0.2 + - - -
1151D PRO* 1.3 71.4 - - - +
1153D ALA* 1.3 63.0 + - - +
1155D ILE* 3.3 4.3 + - + +
1156D GLU* 3.1 58.6 + - + +
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Residues in contact with ALA1153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151D PRO* 3.3 1.0 - - - +
1152D LYS* 1.3 78.8 - - - +
1154D GLU* 1.3 57.6 - - - +
1156D GLU* 3.8 7.0 - - - +
1157D GLY* 2.8 26.7 + - - -
1163D HIS* 3.7 12.4 - - + +
1166D LEU* 3.8 22.7 - - + -
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Residues in contact with GLU1154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150D THR* 3.6 12.9 - - + +
1151D PRO* 3.1 34.4 + - + +
1153D ALA* 1.3 76.9 - - - +
1155D ILE* 1.3 63.9 + - - +
1157D GLY 3.4 16.6 + - - +
1158D GLU 4.7 0.5 - - - +
1163D HIS* 3.4 33.0 + - + +
1166D LEU* 4.7 0.2 - - - +
2173D GLN* 3.2 29.1 - - + +
2176D ARG* 2.7 43.3 + - - -
2177D LYS* 3.4 12.9 - - + +
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Residues in contact with ILE1155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120D ASP* 3.2 27.6 - - + +
1121D THR* 3.9 14.6 - - + -
1150D THR* 3.7 39.3 - - + +
1151D PRO 3.2 3.2 + - - -
1152D LYS* 3.3 8.5 + - + +
1154D GLU* 1.3 79.8 - - - +
1156D GLU* 1.3 68.4 + - + +
1157D GLY 3.4 0.9 - - - +
2130D ASP* 5.3 0.2 - - - +
2134D ARG* 5.8 1.0 + - - -
2176D ARG 5.5 0.9 - - - +
2177D LYS* 3.3 33.3 + - + +
2181D ASN* 6.1 3.4 - - - +
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Residues in contact with GLU1156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152D LYS* 3.1 55.8 + - + +
1153D ALA* 4.2 5.3 + - - +
1155D ILE* 1.3 78.6 - - + +
1157D GLY* 1.3 65.7 + - - +
1158D GLU* 5.7 0.2 - - - +
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Residues in contact with GLY1157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1153D ALA 2.8 19.2 + - - -
1154D GLU 3.4 6.2 + - - +
1155D ILE 3.3 0.8 - - - -
1156D GLU* 1.3 82.0 - - - +
1158D GLU* 1.3 57.7 + - - +
1161D ASP* 3.5 9.9 - - - -
1163D HIS* 4.7 4.0 - - - -
2177D LYS* 2.7 28.6 + - - -
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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