Contacts of the helix formed by residues 81 - 87 (chain D) in PDB entry 3IKM
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 ARG 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D ARG 6.1 3.1 - - - +
71D HIS* 4.4 6.7 + - + +
80D SER* 1.3 70.2 - - - +
82D GLY* 1.3 69.1 + - - +
83D LEU* 2.9 3.7 + - - +
84D HIS* 3.0 57.4 + - - +
85D GLU* 4.0 20.9 + - - +
125D LEU* 2.8 33.7 - - + +
126D ARG* 3.9 16.8 - - - +
127D LEU 4.5 3.5 + - - +
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Residues in contact with GLY 82 (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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80D SER 2.2 14.7 + - - -
81D ARG* 1.3 77.9 - - - +
83D LEU* 1.3 64.9 + - - +
85D GLU* 3.0 30.0 - - - +
86D GLN* 4.2 1.7 + - - +
87D ILE* 5.2 1.4 - - - +
125D LEU* 3.5 18.4 - - - +
126D ARG 5.7 0.4 - - - -
127D LEU* 5.7 2.0 - - - -
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Residues in contact with LEU 83 (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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79D LEU* 3.1 26.5 - - + +
80D SER* 2.5 64.6 + - - +
82D GLY* 1.3 72.3 - - - +
84D HIS* 1.3 75.4 + - + +
85D GLU 2.8 2.8 + - - -
86D GLN 2.9 0.2 + - - -
87D ILE* 2.3 43.0 + - + +
88D PHE* 2.9 23.8 - - - +
89D GLY* 2.9 33.0 - - - +
125D LEU* 4.8 3.6 - - + -
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Residues in contact with HIS 84 (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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71D HIS* 4.6 21.0 + + + +
80D SER* 5.5 0.2 - - - -
81D ARG* 3.1 48.3 + - - +
83D LEU* 1.3 95.4 - - + +
85D GLU* 1.3 61.1 + - - +
86D GLN 4.4 0.5 - - - -
87D ILE 2.8 11.9 + - - +
88D PHE* 4.8 8.4 - - - -
89D GLY* 4.5 5.7 + - - -
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Residues in contact with GLU 85 (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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81D ARG* 4.2 17.9 + - - +
82D GLY* 3.0 31.8 - - - +
83D LEU 2.8 1.4 + - - -
84D HIS* 1.3 74.8 - - - +
86D GLN* 1.3 57.5 + - + +
127D LEU* 2.3 25.8 + - - +
128D PRO* 5.1 0.3 - - - +
130D LEU* 2.6 54.5 - - + +
131D TYR 5.0 5.1 - - - +
132D GLY 3.7 8.0 - - - +
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Residues in contact with GLN 86 (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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82D GLY 4.2 1.1 + - - +
83D LEU 2.9 3.0 + - - -
84D HIS 4.4 0.9 - - - -
85D GLU* 1.3 77.0 - - + +
87D ILE* 1.3 75.7 + - + +
88D PHE* 5.5 4.2 - - - -
130D LEU* 3.6 11.6 - - - +
131D TYR* 3.2 16.7 + - - +
132D GLY* 2.3 59.8 - - - +
133D ASP 4.6 5.4 - - - +
135D LEU* 3.9 34.2 - - + +
138D HIS* 3.2 16.0 + - - +
1159D LEU* 4.6 20.0 - - + +
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Residues in contact with ILE 87 (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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79D LEU* 5.7 0.9 - - + -
82D GLY 5.2 0.9 - - - +
83D LEU* 2.3 56.0 + - + +
84D HIS* 2.8 13.7 + - - +
86D GLN* 1.3 79.9 - - + +
88D PHE* 1.3 85.0 + - + +
135D LEU* 3.3 35.2 - - + -
1159D LEU* 5.5 4.9 - - + -
1162D CYS* 3.5 18.6 - - + -
1166D TYR* 2.8 50.5 - - + +
1171D ASN 4.4 2.2 - - - +
1172D ASP* 3.7 7.9 - - - +
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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