Contacts of the helix formed by residues 46 - 58 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL 5.0 2.4 - - - +
42A MET* 3.3 34.1 - - + +
43A GLU 3.4 13.4 + - - +
44A ARG 3.1 0.6 + - - -
45A TRP* 1.4 103.7 - - + +
47A THR* 1.3 63.0 + - - +
48A PRO* 3.5 1.8 - - - -
49A TYR* 3.0 9.6 + - + +
50A MET* 2.9 40.9 + - + +
135A ASP* 5.0 1.0 - - - +
171A LEU* 3.5 23.0 - - + +
214A LEU* 4.6 2.9 - - - -
222A TYR* 3.1 25.3 + - - -
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A MET* 5.2 0.6 - - - +
43A GLU 4.7 0.2 + - - -
44A ARG* 2.7 35.8 + - - +
45A TRP 3.2 1.4 - - - -
46A GLU* 1.3 74.3 - - - +
48A PRO* 1.4 69.4 - - + +
49A TYR 3.2 0.2 + - - -
50A MET* 3.2 2.0 + - - +
51A HIS* 3.0 54.1 + - + +
73A ILE* 3.8 23.4 - - + +
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Residues in contact with PRO 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP 3.5 14.8 - - - +
46A GLU 3.6 1.8 - - - -
47A THR* 1.4 92.9 - - + +
49A TYR* 1.3 55.6 + - - +
51A HIS* 3.4 13.1 + - + +
52A ALA* 3.2 21.1 + - - +
212A MET* 3.7 27.4 - - + +
214A LEU* 3.8 17.5 - - + -
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Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 3.0 10.8 + - + +
48A PRO* 1.3 77.2 - - - +
50A MET* 1.3 83.7 + - + +
52A ALA* 3.0 13.2 + - - +
53A LEU* 3.1 23.8 + - + +
168A TYR 4.3 0.2 + - - -
169A CYS* 3.2 34.2 - - + +
171A LEU* 3.7 24.5 - - + -
174A TRP* 3.4 7.3 - - - -
212A MET* 3.8 10.0 - - - -
214A LEU* 4.0 17.0 - - + +
228A MET* 3.4 37.0 - - + -
229A ILE 2.7 30.3 + - - -
230A THR* 3.4 18.6 - - - -
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Residues in contact with MET 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A MET* 3.5 20.0 - - + -
46A GLU* 2.9 35.9 + - + +
47A THR 3.7 6.3 - - - +
49A TYR* 1.3 105.0 - - + +
51A HIS* 1.4 58.5 + - - +
53A LEU* 3.5 21.7 + - + +
54A ALA* 3.0 29.2 + - - +
73A ILE* 3.7 17.0 - - + -
74A ALA* 3.9 9.3 - - - +
135A ASP* 3.5 9.0 - - - +
169A CYS* 4.2 3.1 - - - -
171A LEU* 5.1 0.2 - - + -
4000A SAH 3.3 42.0 - - - +
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Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.0 41.5 + - + +
48A PRO* 3.4 12.8 - - + +
49A TYR 3.1 0.4 - - - -
50A MET* 1.4 75.3 - - - +
52A ALA* 1.4 58.8 + - - +
54A ALA* 3.4 1.7 + - - +
55A ALA* 2.9 30.1 + - - +
73A ILE* 4.2 14.4 + - + +
77A LYS* 3.7 49.9 + - + +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO 3.2 11.3 + - - +
49A TYR* 3.0 9.5 + - - +
51A HIS* 1.4 72.8 - - - +
53A LEU* 1.4 63.3 + - - +
55A ALA* 3.5 6.8 + - - +
56A ALA* 3.1 21.8 + - - +
210A GLU* 4.9 9.8 - - - +
212A MET* 4.2 16.6 - - + -
230A THR* 3.5 24.2 - - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TYR* 3.1 29.9 + - + +
50A MET* 3.7 29.4 - - + +
52A ALA* 1.4 70.9 - - - +
54A ALA* 1.3 61.1 + - - +
56A ALA 3.2 1.9 + - - -
57A ALA* 2.9 26.9 + - - +
74A ALA* 5.5 0.2 - - + -
133A LEU* 3.8 26.5 - - + -
135A ASP* 4.9 0.4 - - - +
167A THR* 3.3 29.5 - - + +
168A TYR 3.8 18.6 - - - +
169A CYS* 3.7 27.8 - - - -
230A THR* 3.9 13.7 - - + -
231A PRO* 4.3 1.1 - - + -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A MET 3.0 17.7 + - - +
51A HIS 3.6 0.2 - - - +
52A ALA 3.4 0.2 - - - -
53A LEU* 1.3 74.7 - - - +
55A ALA* 1.4 51.8 + - - +
57A ALA* 3.4 0.7 + - - -
58A SER* 2.8 39.0 + - - -
74A ALA* 3.4 26.7 - - - +
77A LYS* 3.5 23.3 - - + -
78A VAL* 3.8 9.9 - - + +
133A LEU* 3.7 11.1 - - - +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A HIS 2.9 18.0 + - - +
52A ALA* 3.7 8.1 - - - +
54A ALA* 1.4 73.1 - - - +
56A ALA* 1.3 56.7 + - - +
58A SER* 3.6 6.6 + - - -
59A SER* 3.0 30.7 + - - -
77A LYS* 4.8 9.3 - - - +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 3.1 13.9 + - - +
53A LEU 3.2 8.0 + - - +
55A ALA* 1.3 75.3 - - - +
57A ALA* 1.4 59.7 + - - +
59A SER* 2.7 25.9 + - - -
165A VAL* 3.3 13.7 - - + +
167A THR* 4.0 20.2 - - - +
210A GLU* 5.6 1.6 - - - +
230A THR* 4.1 5.2 - - + -
232A LEU* 3.9 28.7 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU 2.9 18.6 + - - +
54A ALA 4.0 2.9 - - - +
56A ALA* 1.4 73.5 - - - +
58A SER* 1.4 58.7 + - - +
59A SER 3.8 0.3 + - - -
60A LYS 4.8 1.6 + - - -
61A GLY 5.1 0.3 - - - +
64A VAL* 3.5 17.6 - - + +
78A VAL* 5.1 0.9 - - + -
130A ASP 4.8 0.3 - - - -
131A GLY* 3.3 22.2 - - - -
132A ILE 3.8 13.7 - - - +
133A LEU* 3.8 29.8 - - + +
165A VAL* 4.3 6.5 - - - +
167A THR* 3.8 8.9 - - + +
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA 2.8 23.3 + - - -
55A ALA* 3.6 6.9 + - - -
57A ALA* 1.4 75.2 - - - +
59A SER* 1.3 61.2 + - - +
60A LYS 3.2 3.1 - - - -
61A GLY* 3.2 15.8 + - - -
64A VAL* 4.0 7.6 - - - -
77A LYS 5.0 0.7 + - - -
78A VAL* 4.3 18.4 - - - -
81A ALA* 3.4 33.0 - - - +
82A PRO* 5.5 1.2 - - - +
83A ILE* 3.9 11.2 - - - -
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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