Contacts of the helix formed by residues 102 - 113 (chain C) in PDB entry 3IMO
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 PRO 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C SER 3.2 9.4 - - - +
101C THR* 1.3 90.2 - - + +
103C LEU* 1.3 65.9 + - - +
104C SER* 3.7 17.9 - - - +
105C LYS* 2.9 25.0 + - + +
106C LEU 3.1 8.7 + - - -
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 3.8 45.3 - - + +
32A ILE* 4.4 8.1 - - + +
34A LEU* 6.2 0.2 - - + -
35A ALA* 4.7 2.9 - - + -
99A ASN 5.4 4.9 - - - +
101A THR 6.0 0.4 - - - +
103A LEU* 3.7 42.0 - - + -
32C ILE* 4.0 12.1 - - + -
35C ALA* 3.6 27.8 - - + -
101C THR 3.5 2.5 + - - +
102C PRO* 1.3 71.2 - - - +
104C SER* 1.3 61.8 + - - +
106C LEU* 3.5 8.4 - - + +
107C VAL* 2.9 29.6 + - + +
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Residues in contact with SER 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.3 29.4 + - - -
102C PRO* 3.1 14.2 - - - +
103C LEU* 1.3 79.5 - - - +
105C LYS* 1.3 59.9 + - - +
107C VAL* 3.5 3.9 + - - +
108C GLU* 3.0 28.9 + - - +
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C HIS* 5.6 3.6 - - - -
101C THR* 4.5 7.6 - - + -
102C PRO* 2.9 26.3 + - + +
104C SER* 1.3 81.7 + - - +
106C LEU* 1.3 58.5 - - - +
108C GLU* 3.3 29.1 + - - +
109C ILE* 2.9 53.1 + - + +
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.3 12.6 - - + -
32C ILE* 4.7 4.9 - - + -
35C ALA* 3.6 44.2 - - + +
36C LEU* 3.8 13.0 - - + +
39C ALA* 4.3 2.0 - - + -
97C PHE* 3.5 31.2 - - + -
101C THR* 4.6 5.5 - - + +
102C PRO 3.1 11.0 + - - +
103C LEU* 3.1 16.6 + - + +
105C LYS* 1.3 78.7 - - - +
107C VAL* 1.3 62.5 + - + +
109C ILE* 3.4 5.1 + - - +
110C PHE* 3.1 47.1 + - + +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A MET* 4.5 1.1 - - + -
30A GLU* 3.9 31.6 - - + +
31A GLU* 4.0 27.6 - - + +
34A LEU* 3.9 22.0 - - + -
42C TRP* 4.1 15.3 - - + -
103C LEU* 2.9 21.2 + - + +
104C SER* 3.8 5.6 - - - +
106C LEU* 1.3 76.1 - - + +
108C GLU* 1.3 58.1 + - - +
111C LYS* 2.8 47.9 + - - +
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Residues in contact with GLU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C SER 3.0 20.0 + - - +
105C LYS* 3.5 32.6 + - + +
106C LEU 3.2 0.2 - - - -
107C VAL* 1.3 78.9 - - - +
109C ILE* 1.3 63.7 + - + +
111C LYS* 3.8 6.7 - - - +
112C GLY* 3.3 16.8 + - - -
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Residues in contact with ILE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C MET* 4.7 4.3 - - - -
95C HIS* 3.5 52.9 - - + +
97C PHE* 3.7 27.4 - - + -
101C THR* 5.8 0.2 - - + -
105C LYS* 2.9 44.9 + - + +
106C LEU 3.7 3.8 - - - +
108C GLU* 1.3 79.3 - - + +
110C PHE* 1.3 75.8 + - + +
112C GLY* 3.3 8.0 + - - -
113C LEU* 3.4 19.9 + - + +
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Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 3.7 32.8 - - + -
39C ALA* 3.5 37.5 - - + -
40C ILE* 4.0 11.0 - - + -
42C TRP* 3.9 20.2 - - + -
43C ARG* 2.7 42.6 + - + +
66C ILE* 4.1 10.1 - - + -
73C PHE* 3.9 17.5 - + - -
84C MET* 4.4 3.4 - - + -
97C PHE* 4.1 10.3 - + - -
106C LEU* 3.1 31.9 + - + +
109C ILE* 1.3 82.9 - - + +
111C LYS* 1.3 55.9 + - - +
112C GLY 3.2 0.2 + - - -
113C LEU* 3.3 25.4 + - + +
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Residues in contact with LYS 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 3.3 25.0 + - - +
30A GLU* 2.9 32.1 + - - -
42C TRP* 3.9 22.5 - - + -
43C ARG* 3.5 10.9 + - - +
107C VAL* 2.8 31.9 + - - +
108C GLU* 3.8 7.4 - - - +
110C PHE* 1.3 76.7 - - - +
112C GLY* 1.3 59.1 + - - +
113C LEU* 4.1 0.7 - - - +
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Residues in contact with GLY 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLU 3.3 7.4 + - - -
109C ILE 3.3 7.6 + - - -
110C PHE 3.1 0.6 - - - -
111C LYS* 1.3 78.4 - - - +
113C LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 3.1 24.9 + - - -
66C ILE* 3.8 29.0 - - + +
67C ASN* 3.3 32.1 + - - +
69C GLU* 6.2 0.2 - - - +
71C TYR* 3.6 33.9 + - + +
84C MET* 3.7 26.2 - - + -
94C ILE* 5.4 4.3 - - + -
95C HIS* 5.5 2.9 - - - +
109C ILE* 3.4 20.6 + - + +
110C PHE* 3.3 37.0 + - + +
111C LYS 4.1 1.0 - - - +
112C GLY* 1.3 83.9 - - - +
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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