Contacts of the helix formed by residues 4071 - 4085 (chain A) 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 GLY4071 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4069A SER 3.4 2.4 - - - -
4070A SER* 1.3 80.5 - - - +
4072A LYS* 1.3 60.0 + - - +
4074A THR* 3.7 0.6 - - - -
4075A LEU* 2.9 34.5 + - - +
4225A ILE* 3.8 7.9 - - - +
4262A ILE* 4.0 14.9 - - - +
4502A ADP 3.0 25.5 + - - -
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Residues in contact with LYS4072 (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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4064A ILE* 4.3 11.9 - - + +
4065A TYR* 3.9 2.5 - - - -
4066A GLY 3.4 19.9 + - - +
4067A PRO 2.7 30.7 + - - -
4068A GLU* 4.0 1.2 - - - +
4070A SER* 3.5 8.7 - - - +
4071A GLY* 1.3 77.3 - - - +
4073A THR* 1.3 62.5 + - - +
4075A LEU* 3.8 3.1 - - - +
4076A THR* 3.0 24.8 + - - -
4192A ILE* 3.6 28.0 - - + +
4193A ASN 3.4 25.8 - - - +
4194A GLN* 5.0 5.5 - - - +
4225A ILE* 3.6 17.0 - - + -
4501A ALF 3.4 25.1 - - - -
4502A ADP 2.8 23.8 + - - +
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Residues in contact with THR4073 (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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4072A LYS* 1.3 74.5 - - - +
4074A THR* 1.3 68.1 + - - +
4076A THR* 3.1 4.3 + - - -
4077A LEU* 2.8 39.9 + - + +
4092A PHE* 4.1 14.1 - - + -
4099A LEU* 4.5 9.0 - - + -
4144A ASP* 2.9 21.3 + - - +
4192A ILE* 3.9 8.2 - - - +
4500A MG 2.2 32.0 - - - -
4502A ADP 2.7 15.5 + - - -
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Residues in contact with THR4074 (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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4071A GLY* 3.7 8.3 - - - -
4072A LYS 3.4 0.2 - - - -
4073A THR* 1.3 78.8 - - - +
4075A LEU* 1.3 63.9 + - - +
4077A LEU* 3.1 4.7 + - - +
4078A GLN* 2.9 34.9 + - + +
4103A TYR* 3.9 22.4 + - - +
4107A LEU* 3.9 20.5 - - + +
4262A ILE* 3.8 31.3 - - + +
4267A GLY* 4.8 5.8 - - - -
4268A ILE* 5.1 1.3 - - + +
4502A ADP 3.0 27.2 + - - -
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Residues in contact with LEU4075 (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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4042A THR* 4.1 6.9 - - + +
4047A LEU* 4.0 24.9 - - + -
4056A LEU* 5.7 0.9 - - + -
4064A ILE* 3.7 31.0 - - + -
4071A GLY 2.9 21.6 + - - +
4072A LYS* 3.8 3.4 - - - +
4074A THR* 1.3 72.5 - - - +
4076A THR* 1.3 63.0 + - - +
4078A GLN* 3.0 19.9 + - - +
4079A VAL* 3.0 26.7 + - + +
4223A LEU* 4.9 5.2 - - + -
4225A ILE* 4.0 14.6 - - + -
4244A VAL* 4.3 4.7 - - + -
4260A PHE* 3.9 28.5 - - + -
4262A ILE* 5.4 1.3 - - + +
4268A ILE* 4.5 11.9 - - + -
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Residues in contact with THR4076 (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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4064A ILE* 4.1 3.1 - - - +
4072A LYS 3.0 10.2 + - - -
4073A THR 3.1 11.0 - - - +
4075A LEU* 1.3 79.6 - - - +
4077A LEU* 1.3 64.0 + - - +
4079A VAL* 3.2 13.9 + - - +
4080A ILE* 3.1 21.9 + - + +
4092A PHE* 3.5 17.9 - - + -
4142A VAL* 3.3 37.5 - - + +
4190A ILE* 4.0 15.0 - - - +
4192A ILE* 3.4 22.9 - - + +
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Residues in contact with LEU4077 (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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4073A THR* 2.8 35.9 + - + +
4074A THR* 3.5 5.6 - - - +
4076A THR* 1.3 73.6 - - + +
4078A GLN* 1.3 53.0 + - - +
4080A ILE* 3.2 10.7 + - + +
4081A ALA* 2.7 34.8 + - - +
4092A PHE* 4.0 26.2 - - + -
4099A LEU* 4.0 20.0 - - + -
4103A TYR* 4.9 7.0 - - + -
4104A ALA* 4.2 23.6 - - + +
4107A LEU* 3.8 24.9 - - + -
4109A VAL* 3.5 19.1 - - + +
4114A LEU* 5.8 2.9 - - + -
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Residues in contact with GLN4078 (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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4042A THR 3.9 12.6 - - - +
4043A GLY* 4.5 7.3 - - - +
4074A THR* 2.9 24.6 + - + +
4075A LEU 3.0 7.6 + - - +
4077A LEU* 1.3 76.9 - - - +
4079A VAL* 1.3 56.8 + - - +
4081A ALA* 3.3 5.3 + - - +
4082A ALA* 3.0 28.8 + - - +
4085A ARG* 4.5 2.3 + - - +
4107A LEU* 3.0 40.9 + - - +
4266A GLU 4.5 0.9 + - - +
4267A GLY* 3.4 7.9 - - - -
4268A ILE* 2.7 52.9 + - + +
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Residues in contact with VAL4079 (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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4040A ILE* 4.5 9.2 - - + +
4041A SER 3.8 19.2 - - - +
4042A THR* 3.6 18.3 + - - +
4056A LEU* 4.5 13.5 - - + -
4075A LEU* 3.0 28.2 + - + +
4076A THR* 3.2 11.2 + - - +
4078A GLN* 1.3 71.1 - - - +
4080A ILE* 1.3 63.8 + - + +
4082A ALA* 3.3 3.6 + - - +
4083A ALA* 2.8 30.1 + - - +
4140A VAL* 4.5 12.8 - - + -
4188A LEU* 5.0 2.0 - - + -
4190A ILE* 3.9 23.3 - - + -
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Residues in contact with ILE4080 (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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4076A THR* 3.1 15.0 + - + +
4077A LEU* 3.4 14.4 - - + +
4079A VAL* 1.3 76.0 - - + +
4081A ALA* 1.3 54.3 + - - +
4083A ALA* 3.0 3.3 + - - +
4084A GLN* 2.8 48.7 + - - +
4090A CYS* 3.8 32.5 - - + -
4091A ALA 4.7 1.8 - - - +
4092A PHE* 3.9 19.1 - - + -
4109A VAL* 4.0 9.2 - - + -
4114A LEU* 3.9 17.7 - - + -
4140A VAL* 4.3 7.0 - - + -
4142A VAL* 3.4 32.1 - - + -
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Residues in contact with ALA4081 (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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4077A LEU 2.7 20.3 + - - +
4078A GLN* 3.5 8.3 - - - +
4080A ILE* 1.3 72.7 - - - +
4082A ALA* 1.3 57.0 + - - +
4084A GLN* 3.3 9.8 + - - +
4085A ARG* 2.9 44.2 + - - +
4107A LEU 3.9 11.0 - - - +
4108A GLY 3.4 31.9 - - - +
4109A VAL* 4.0 4.0 - - + +
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Residues in contact with ALA4082 (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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4040A ILE* 5.4 2.2 - - + -
4041A SER* 4.3 27.8 - - - +
4043A GLY* 5.0 5.4 - - - +
4078A GLN 3.0 17.4 + - - +
4079A VAL* 3.6 4.5 - - - +
4081A ALA* 1.3 76.0 - - - +
4083A ALA* 1.3 61.8 + - - +
4085A ARG* 3.2 35.9 - - - +
4086A GLU* 3.5 15.7 + - - +
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Residues in contact with ALA4083 (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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4040A ILE* 4.4 13.6 - - + +
4079A VAL 2.8 21.0 + - - +
4080A ILE 3.5 3.8 - - - +
4082A ALA* 1.3 70.6 - - - +
4084A GLN* 1.3 60.9 + - - +
4086A GLU* 3.0 22.9 + - - -
4088A LYS* 3.1 32.4 + - + +
4090A CYS* 4.0 4.9 - - - -
4140A VAL* 3.8 28.5 - - + -
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Residues in contact with GLN4084 (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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4080A ILE* 2.8 30.3 + - - +
4081A ALA* 3.6 4.7 - - - +
4083A ALA* 1.3 68.2 - - - +
4085A ARG* 1.3 57.3 - - - +
4086A GLU 2.9 10.8 + - - -
4087A GLY* 2.9 14.7 + - - -
4088A LYS 3.8 18.6 + - - +
4089A THR* 6.1 0.2 - - - +
4090A CYS* 4.0 11.8 - - - +
4108A GLY 5.8 0.4 - - - +
4109A VAL* 3.4 9.5 - - - +
4110A ASP* 2.7 57.2 + - + +
4113A ASN* 3.9 7.5 + - - +
4114A LEU* 3.6 24.7 - - - +
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Residues in contact with ARG4085 (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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4043A GLY* 6.4 0.2 - - - -
4078A GLN* 4.5 2.2 + - - +
4081A ALA* 2.9 24.2 + - - +
4082A ALA* 3.2 45.9 - - - +
4084A GLN* 1.3 74.6 - - - +
4086A GLU* 1.3 62.2 + - + +
4087A GLY 3.6 1.0 + - - -
4107A LEU 5.5 1.0 + - - -
4108A GLY* 4.6 7.3 + - - -
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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