Contacts of the helix formed by residues 38 - 47 (chain C) in PDB entry 3RT0
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 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C ALA* 1.3 93.0 - - + +
39C LEU* 1.3 66.6 + - - +
40C HIS* 3.1 30.4 + - + +
41C LEU* 3.2 13.8 + - + -
42C VAL* 3.2 8.5 + - - +
131C THR* 4.4 11.3 - - + +
132C GLY* 4.7 4.9 - - - +
133C THR* 4.1 0.2 - - - +
175C GLN* 3.6 35.2 - - - +
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Residues in contact with LEU 39 (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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38C PRO* 1.3 73.5 - - - +
40C HIS* 1.3 60.5 + - - +
42C VAL* 3.3 1.5 + - - +
43C TRP* 2.7 34.1 + - + +
100C HIS* 3.7 42.8 - - + +
122C LEU* 3.7 18.4 - - + +
123C HIS* 3.6 27.4 - - - +
124C SER* 3.7 25.1 + - - +
132C GLY 4.7 2.2 + - - -
133C THR* 3.1 18.3 + - + +
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Residues in contact with HIS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PRO* 3.1 30.1 + - + +
39C LEU* 1.3 82.6 - - - +
41C LEU* 1.3 80.0 + - + +
43C TRP* 3.4 5.7 + - - +
44C SER* 2.9 30.1 + - - -
100C HIS* 6.3 0.4 - - - -
175C GLN* 5.8 1.1 + - - -
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ALA* 4.7 1.1 - - + -
38C PRO* 3.2 14.8 + - + +
40C HIS* 1.3 93.5 - - + +
42C VAL* 1.3 66.7 + - - +
44C SER* 2.7 29.4 + - - +
45C ILE* 3.4 8.6 + - + +
171C THR* 3.8 15.3 - - - +
174C LEU* 4.1 24.9 - - + +
175C GLN* 3.4 49.1 - - + +
178C SER* 5.6 2.0 - - - -
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Residues in contact with VAL 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 4.0 36.6 - - + -
37C ALA* 3.9 8.3 - - + +
38C PRO 3.2 7.0 + - - +
39C LEU 3.7 4.9 - - - +
41C LEU* 1.3 77.2 - - - +
43C TRP* 1.3 58.1 + - - +
45C ILE* 3.2 6.8 + - - +
46C VAL* 3.0 24.1 + - + +
122C LEU* 3.5 23.3 - - + -
133C THR* 3.5 28.7 - - + +
167C LEU* 4.2 17.7 - - + -
171C THR* 4.0 13.5 - - - +
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Residues in contact with TRP 43 (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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39C LEU* 2.7 28.4 + - + +
40C HIS* 3.8 5.4 - - - +
42C VAL* 1.3 70.6 - - - +
44C SER* 1.3 61.8 + - - +
46C VAL* 4.0 21.1 - - + +
47C ARG* 2.8 55.3 + - + +
95C LEU* 4.2 10.3 - - + -
96C ASP 3.4 17.9 - - - -
97C ASP* 2.9 28.7 + - - +
100C HIS* 3.4 40.5 + + - -
101C ILE 3.4 31.0 - - - -
102C LEU* 4.3 3.8 - - + -
120C ILE 5.1 0.9 - - - -
122C LEU* 3.6 26.2 - - + +
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Residues in contact with SER 44 (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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40C HIS* 2.9 16.3 + - - -
41C LEU* 2.7 33.1 + - - +
43C TRP* 1.3 76.2 - - - +
45C ILE* 1.3 63.5 + - - +
47C ARG* 3.9 11.8 - - - +
48C ARG* 3.3 24.3 - - - +
54C LYS* 5.2 1.0 - - - -
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Residues in contact with ILE 45 (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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41C LEU* 3.7 12.1 - - + +
42C VAL 3.2 6.7 + - - +
43C TRP 3.1 0.4 - - - -
44C SER* 1.3 86.7 + - - +
46C VAL* 1.3 66.9 + - - +
47C ARG 3.3 0.2 - - - -
48C ARG* 3.3 20.8 + - - +
51C GLU 5.3 0.7 - - - +
54C LYS* 4.4 30.9 - - + +
55C TYR* 3.5 35.9 - - + -
167C LEU* 3.8 13.7 - - + -
170C VAL* 4.9 6.3 - - + -
171C THR* 3.8 15.7 - - + -
174C LEU* 4.0 23.6 - - + -
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Residues in contact with VAL 46 (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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42C VAL* 3.0 21.4 + - + +
43C TRP* 4.0 23.1 - - + +
45C ILE* 1.3 76.7 - - - +
47C ARG* 1.3 62.0 + - - +
48C ARG 3.1 5.0 + - - -
49C PHE* 4.9 0.2 - - - -
55C TYR* 4.4 17.6 + - - +
102C LEU* 3.6 19.6 - - + +
120C ILE* 4.0 32.8 - - + -
122C LEU* 4.5 4.7 - - + -
167C LEU* 3.6 35.0 - - + -
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Residues in contact with ARG 47 (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 TRP* 2.8 55.7 + - + +
44C SER* 3.9 15.0 - - - +
46C VAL* 1.3 73.5 - - - +
48C ARG* 1.3 69.5 + - + +
49C PHE* 2.8 11.4 + - - +
69C LEU* 3.6 37.1 - - - +
95C LEU* 4.0 27.6 - - + +
97C ASP* 2.9 37.1 + - - -
102C LEU* 4.4 2.8 - - - +
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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