Contacts of the helix formed by residues 46 - 58 (chain C) in PDB entry 3ORH
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 GLU 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C VAL 5.0 2.1 - - - +
42C MET* 3.3 32.8 - - + +
43C GLU 3.4 11.6 + - - +
44C ARG 3.1 0.4 - - - -
45C TRP* 1.4 104.5 - - + +
47C THR* 1.4 62.8 + - - +
48C PRO* 3.5 1.8 - - - -
49C TYR* 3.0 11.2 + - + +
50C MET* 3.0 39.5 + - + +
135C ASP* 4.9 0.9 - - - +
171C LEU* 3.5 17.8 - - + +
214C LEU* 4.6 2.7 - - - -
222C TYR* 2.6 32.7 + - - -
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Residues in contact with THR 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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42C MET* 5.3 0.8 - - - +
44C ARG* 2.6 35.8 + - - +
45C TRP 3.2 1.2 - - - -
46C GLU* 1.4 74.7 - - - +
48C PRO* 1.4 69.7 - - + +
50C MET* 3.2 1.8 + - - +
51C HIS* 3.0 50.5 + - + +
73C ILE* 3.8 22.8 - - + +
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Residues in contact with PRO 48 (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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45C TRP 3.5 14.6 - - - +
46C GLU 3.6 1.8 - - - -
47C THR* 1.4 91.9 - - + +
49C TYR* 1.3 58.5 + - - +
51C HIS* 3.3 13.9 + - + +
52C ALA 3.1 17.0 + - - -
212C MET* 3.7 20.5 - - + +
214C LEU* 3.8 23.8 - - + -
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Residues in contact with TYR 49 (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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46C GLU* 3.0 10.8 + - + +
48C PRO* 1.3 76.4 - - - +
50C MET* 1.4 83.2 + - + +
52C ALA* 3.0 14.2 + - - +
53C LEU* 3.1 23.6 + - + +
168C TYR 4.2 0.3 + - - -
169C CYS* 3.2 33.5 - - + +
171C LEU* 3.7 27.1 - - + -
174C TRP* 3.4 7.3 - - - -
212C MET* 3.8 9.8 - - - -
214C LEU* 4.0 16.9 - - + +
228C MET* 3.4 36.8 - - + -
229C ILE 2.7 24.6 + - - -
230C THR* 3.3 24.0 - - - -
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Residues in contact with MET 50 (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 MET* 3.5 24.0 - - + -
46C GLU* 3.0 36.6 + - + +
47C THR 3.7 6.3 - - - +
49C TYR* 1.4 104.8 - - + +
51C HIS* 1.4 57.6 + - - +
53C LEU* 3.4 20.8 + - + +
54C ALA* 3.0 29.3 + - - +
73C ILE* 3.7 17.7 - - + -
74C ALA* 3.9 10.7 - - - +
133C LEU* 6.0 0.2 - - - -
135C ASP* 3.5 9.9 - - - +
169C CYS* 4.2 3.1 - - - -
4002C SAH 3.4 35.2 - - - +
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Residues in contact with HIS 51 (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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47C THR* 3.0 40.3 + - + +
48C PRO* 3.4 13.0 - - + +
49C TYR 3.1 0.2 - - - -
50C MET* 1.4 74.9 - - - +
52C ALA* 1.4 59.0 + - - +
54C ALA* 3.4 1.6 + - - +
55C ALA* 2.9 31.2 + - - +
73C ILE* 4.2 14.4 + - + +
77C LYS* 3.6 49.0 + - + +
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Residues in contact with ALA 52 (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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48C PRO 3.1 4.9 + - - -
49C TYR 3.0 10.8 + - - +
51C HIS* 1.4 72.7 - - - +
53C LEU* 1.4 63.2 + - - +
55C ALA* 3.5 6.9 + - - +
56C ALA* 3.1 22.2 + - - +
210C GLU* 4.9 9.3 - - - +
212C MET* 3.7 28.5 - - + +
230C THR* 3.5 25.9 - - - +
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Residues in contact with LEU 53 (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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49C TYR* 3.1 29.7 + - + +
50C MET* 3.7 29.2 - - + +
52C ALA* 1.4 71.9 - - - +
54C ALA* 1.4 61.0 + - - +
56C ALA 3.2 1.9 + - - -
57C ALA* 2.9 27.0 + - - +
133C LEU* 3.8 26.0 - - + -
135C ASP* 4.9 0.2 - - - +
167C THR* 3.3 29.3 - - + +
168C TYR 3.8 19.3 - - - +
169C CYS* 3.6 28.9 - - + -
230C THR* 3.9 13.9 - - + -
231C PRO* 4.3 0.9 - - + -
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Residues in contact with ALA 54 (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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50C MET 3.0 17.9 + - - +
52C ALA 3.4 0.2 - - - -
53C LEU* 1.4 75.8 - - - +
55C ALA* 1.4 52.3 + - - +
57C ALA* 3.9 1.6 - - - +
58C SER* 2.7 39.3 + - - -
74C ALA* 3.4 27.1 - - - +
77C LYS* 3.5 23.8 - - + -
78C VAL* 3.8 9.3 - - + +
133C LEU* 3.7 11.4 - - - +
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Residues in contact with ALA 55 (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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51C HIS 2.9 18.5 + - - +
52C ALA* 3.7 7.4 - - - +
54C ALA* 1.4 74.1 - - - +
56C ALA* 1.3 57.3 + - - +
58C SER* 3.5 6.5 + - - -
59C SER* 3.0 31.3 + - - -
77C LYS* 4.8 9.8 - - - +
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Residues in contact with ALA 56 (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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52C ALA 3.1 14.3 + - - +
53C LEU 3.2 8.2 + - - +
55C ALA* 1.3 76.2 - - - +
57C ALA* 1.3 60.6 + - - +
59C SER* 2.7 25.9 + - - -
165C VAL* 3.7 13.6 - - + +
167C THR* 4.0 20.4 - - - +
210C GLU* 5.7 1.3 - - - +
230C THR* 4.2 4.3 - - + -
232C LEU* 3.8 29.6 - - + -
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Residues in contact with ALA 57 (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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53C LEU 2.9 16.3 + - - +
54C ALA 4.0 2.9 - - - +
56C ALA* 1.3 75.4 - - - +
58C SER* 1.3 59.8 + - - +
59C SER 3.4 0.6 + - - -
60C LYS* 4.8 2.4 + - - +
61C GLY 5.1 0.5 - - - +
64C VAL* 3.5 18.5 - - + +
78C VAL* 5.1 0.7 - - + -
130C ASP 4.8 0.3 - - - +
131C GLY* 3.3 25.3 - - - -
132C ILE 3.8 16.2 - - - +
133C LEU* 3.8 28.7 - - + +
165C VAL* 4.7 3.5 - - - +
167C THR* 3.8 4.8 - - + +
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Residues in contact with SER 58 (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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54C ALA 2.7 23.5 + - - -
55C ALA* 3.6 7.6 + - - -
57C ALA* 1.3 74.6 - - - +
59C SER* 1.4 58.5 + - - +
60C LYS 3.3 3.4 - - - -
61C GLY* 3.2 20.4 + - - -
64C VAL* 4.0 7.0 - - - -
77C LYS 5.0 0.7 + - - -
78C VAL* 4.3 18.4 - - - -
81C ALA* 3.4 33.1 - - - +
82C PRO* 5.5 1.4 - - - +
83C ILE* 3.9 10.3 - - - -
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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