Contacts of the helix formed by residues 4002 - 4022 (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 ILE4002 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4001D ALA* 1.3 85.6 - - + +
4003D ASP* 1.3 61.5 + - + +
4004D GLU 3.4 0.6 + - - -
4005D ASN* 3.9 13.4 + - - +
4006D LYS* 3.9 14.1 - - + +
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Residues in contact with ASP4003 (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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4001D ALA 4.2 4.0 + - - -
4002D ILE* 1.3 74.0 - - - +
4004D GLU* 1.3 88.6 + - - +
4005D ASN 3.3 1.1 - - - -
4006D LYS* 3.4 20.9 + - + +
4007D GLN* 3.4 26.6 + - - +
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Residues in contact with GLU4004 (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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4001D ALA* 3.2 37.1 + - - +
4002D ILE 3.4 0.8 - - - -
4003D ASP* 1.3 88.1 + - - +
4005D ASN* 1.3 64.3 + - - +
4006D LYS 3.2 0.2 - - - -
4007D GLN* 3.6 13.9 + - - +
4008D LYS* 3.3 20.1 + - - +
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Residues in contact with ASN4005 (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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4001D ALA 3.3 20.0 + - - -
4002D ILE* 3.9 9.9 + - - +
4003D ASP 3.3 0.2 - - - -
4004D GLU* 1.3 78.1 - - - +
4006D LYS* 1.3 60.9 + - + +
4008D LYS* 3.4 24.0 - - - +
4009D ALA* 3.2 22.2 + - - +
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Residues in contact with LYS4006 (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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3087D GLY 5.2 5.1 + - - -
3089D THR* 4.7 5.1 + - - -
3136D GLY 4.2 16.8 - - - +
3137D ALA* 3.7 25.9 + - + +
3139D ASP* 3.6 28.0 + - - -
4002D ILE* 3.9 12.6 - - + +
4003D ASP* 3.4 24.5 + - + +
4004D GLU 3.2 0.2 - - - -
4005D ASN* 1.3 76.1 - - + +
4007D GLN* 1.3 56.4 + - + +
4009D ALA* 3.2 7.5 + - - +
4010D LEU* 2.7 34.0 + - - +
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Residues in contact with GLN4007 (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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4003D ASP* 3.4 14.8 + - - +
4004D GLU* 4.0 15.2 - - - +
4005D ASN 3.4 0.4 - - - -
4006D LYS* 1.3 73.4 - - + +
4008D LYS* 1.3 60.6 + - - +
4010D LEU* 3.5 19.4 - - + +
4011D ALA* 2.9 33.4 + - - +
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Residues in contact with LYS4008 (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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4004D GLU 3.3 11.9 + - - +
4005D ASN* 3.4 27.4 - - - +
4007D GLN* 1.3 80.6 - - - +
4009D ALA* 1.3 60.2 + - - +
4011D ALA* 4.4 3.0 - - - +
4012D ALA* 3.4 20.1 + - - +
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Residues in contact with ALA4009 (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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3135D SER* 3.9 24.6 - - - +
3137D ALA* 4.5 2.2 - - + -
4005D ASN 3.2 9.3 + - - +
4006D LYS* 3.2 10.5 + - - +
4008D LYS* 1.3 77.6 - - + +
4010D LEU* 1.3 64.7 + - - +
4012D ALA* 3.5 7.6 - - - +
4013D ALA* 3.1 22.0 + - - +
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Residues in contact with LEU4010 (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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3089D THR* 4.6 9.2 - - + -
3115D LEU* 4.0 18.6 - - + -
3132D LEU* 5.7 0.7 - - + -
3135D SER* 5.7 0.2 - - - +
3137D ALA* 3.7 26.0 - - + +
3138D VAL* 4.5 8.5 - - + -
4006D LYS 2.7 20.8 + - - +
4007D GLN* 3.2 21.7 + - + +
4009D ALA* 1.3 69.6 - - - +
4011D ALA* 1.3 62.4 + - + +
4013D ALA* 2.9 7.1 + - + +
4014D LEU* 2.9 55.3 + - + +
4028D ARG* 6.3 1.6 - - - +
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Residues in contact with ALA4011 (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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4007D GLN 2.9 15.9 + - - +
4008D LYS* 4.4 2.9 - - - +
4010D LEU* 1.3 78.8 - - + +
4012D ALA* 1.3 57.0 + - - +
4014D LEU* 3.8 8.4 - - - +
4015D GLY* 2.9 28.8 + - - -
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Residues in contact with ALA4012 (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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4008D LYS 3.4 17.4 + - - +
4009D ALA* 3.5 10.5 - - - +
4010D LEU 3.1 0.4 - - - -
4011D ALA* 1.3 80.0 - - - +
4013D ALA* 1.3 56.3 + - - +
4015D GLY* 4.0 0.9 - - - -
4016D GLN* 3.1 27.2 + - - +
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Residues in contact with ALA4013 (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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3131D ALA* 4.5 8.5 - - + +
3132D LEU* 5.0 3.8 - - + -
3135D SER* 3.6 24.2 - - - +
4009D ALA 3.1 13.8 + - - +
4010D LEU* 2.9 9.9 + - + +
4012D ALA* 1.3 75.0 - - - +
4014D LEU* 1.3 61.9 + - + +
4016D GLN* 3.2 9.3 + - + +
4017D ILE* 2.8 43.6 + - + +
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Residues in contact with LEU4014 (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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3115D LEU* 3.8 32.3 - - + -
3132D LEU* 4.7 11.4 - - + -
4010D LEU* 2.9 53.6 + - + +
4011D ALA* 3.8 7.6 - - - +
4013D ALA* 1.3 77.0 - - + +
4015D GLY* 1.3 56.9 + - - +
4017D ILE* 3.7 7.1 - - - +
4018D GLU* 3.0 37.5 + - + +
4026D ILE* 4.4 16.8 - - + +
4027D MET* 5.8 1.3 - - - -
4028D ARG* 5.4 9.6 - - - +
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Residues in contact with GLY4015 (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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4011D ALA 2.9 16.8 + - - -
4012D ALA* 4.0 0.9 - - - -
4014D LEU* 1.3 75.1 - - - +
4016D GLN* 1.3 56.7 + - - +
4018D GLU* 3.4 5.1 + - - +
4019D LYS* 3.0 32.2 + - - +
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Residues in contact with GLN4016 (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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3131D ALA* 5.2 8.1 - - + +
3134D ARG* 5.0 12.2 - - - +
4012D ALA 3.1 19.5 + - - +
4013D ALA* 3.4 9.4 - - - +
4015D GLY* 1.3 76.1 - - - +
4017D ILE* 1.3 65.6 + - + +
4019D LYS* 3.5 11.2 + - - +
4020D GLN* 3.1 50.8 + - - +
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Residues in contact with ILE4017 (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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3128D ILE* 4.0 31.4 - - + -
3131D ALA* 4.0 25.4 - - + -
3132D LEU* 3.8 31.4 - - + -
4013D ALA* 2.8 27.7 + - + +
4014D LEU* 3.7 8.1 - - - +
4016D GLN* 1.3 74.1 - - + +
4018D GLU* 1.3 54.9 + - - +
4020D GLN* 3.1 6.2 + - - +
4021D PHE* 2.7 41.4 + - + +
4025D SER* 4.0 8.7 - - - +
4026D ILE* 3.7 25.4 - - + -
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Residues in contact with GLU4018 (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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4014D LEU* 3.0 23.3 + - - +
4015D GLY* 4.0 4.4 - - - +
4017D ILE* 1.3 75.8 - - - +
4019D LYS* 1.3 57.8 + - - +
4022D GLY* 2.9 39.5 + - - +
4023D LYS 2.9 23.0 - - - +
4024D GLY* 3.6 8.1 - - - -
4025D SER* 3.7 5.1 + - - +
4026D ILE* 2.9 34.4 - - + +
4027D MET* 5.1 0.9 - - - +
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Residues in contact with LYS4019 (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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4015D GLY 3.0 18.2 + - - +
4016D GLN* 3.9 12.3 - - - +
4018D GLU* 1.3 77.1 - - - +
4020D GLN* 1.3 63.9 + - - +
4022D GLY 4.6 1.1 + - - -
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Residues in contact with GLN4020 (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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2158D GLU* 3.7 23.5 + - - +
3127D GLU* 4.5 6.3 + - - +
4016D GLN* 3.1 43.6 + - - +
4017D ILE* 3.1 5.4 + - - +
4019D LYS* 1.3 83.1 - - + +
4021D PHE* 1.3 91.5 + - + +
4022D GLY 3.6 1.2 + - - -
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Residues in contact with PHE4021 (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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2158D GLU* 4.2 10.8 - - - -
3120D ASP* 5.3 2.8 - - - +
3124D GLN* 3.5 43.0 + - + +
3127D GLU* 3.6 33.0 - - + -
3128D ILE* 4.1 23.3 - - + -
3131D ALA* 6.3 0.7 - - + -
4017D ILE* 2.7 28.8 + - + +
4020D GLN* 1.3 103.3 - - + +
4022D GLY* 1.3 60.3 + - - +
4025D SER* 3.3 25.5 - - - +
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Residues in contact with GLY4022 (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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4018D GLU* 2.9 21.7 + - - +
4019D LYS 4.6 1.4 + - - -
4020D GLN 3.6 1.8 - - - -
4021D PHE* 1.3 79.2 - - - +
4023D LYS* 1.3 69.9 - - - +
4024D GLY 3.7 0.7 - - - -
4025D SER* 3.1 13.5 + - - -
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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