Contacts of the helix formed by residues 46 - 58 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D VAL 5.0 1.6 - - - +
42D MET* 3.4 30.2 - - + +
43D GLU 3.4 12.9 + - - +
44D ARG 3.1 0.8 - - - -
45D TRP* 1.3 103.8 - - + +
47D THR* 1.4 62.9 + - - +
48D PRO* 3.5 2.2 - - - -
49D TYR* 2.9 10.7 + - + +
50D MET* 2.9 43.6 + - + +
135D ASP* 4.9 1.2 - - - +
171D LEU* 3.5 19.0 - - + +
214D LEU* 4.5 2.7 - - - -
222D TYR* 2.7 30.0 + - - -
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Residues in contact with THR 47 (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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42D MET* 5.2 0.6 - - - +
44D ARG* 2.7 37.1 + - - +
45D TRP 3.2 1.2 - - - -
46D GLU* 1.4 74.0 - - - +
48D PRO* 1.4 69.5 - - + +
50D MET* 3.2 2.1 + - - +
51D HIS* 2.9 52.0 + - + +
73D ILE* 3.7 22.4 - - + +
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Residues in contact with PRO 48 (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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45D TRP 3.5 14.1 - - - +
46D GLU 3.6 1.3 - - - -
47D THR* 1.4 93.7 - - + +
49D TYR* 1.4 55.6 + - - +
51D HIS* 3.4 13.8 + - + +
52D ALA* 3.2 23.7 + - - +
212D MET* 3.7 23.9 - - + +
214D LEU* 3.9 17.3 - - + -
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Residues in contact with TYR 49 (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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46D GLU* 2.9 10.0 + - + +
48D PRO* 1.4 76.4 - - - +
50D MET* 1.4 81.2 + - + +
51D HIS 3.2 0.2 - - - -
52D ALA* 3.0 14.0 + - - +
53D LEU* 3.1 23.8 + - + +
168D TYR 4.2 0.2 + - - -
169D CYS* 3.2 34.0 - - + +
171D LEU* 3.7 26.0 - - + -
174D TRP* 3.4 6.6 - - - -
212D MET* 3.8 10.9 - - - -
214D LEU* 4.0 16.5 - - + +
228D MET* 3.4 37.0 - - + -
229D ILE 2.7 24.5 + - - -
230D THR* 3.3 24.9 - - - -
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Residues in contact with MET 50 (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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42D MET* 3.4 25.4 - - + -
46D GLU* 2.9 36.0 + - + +
47D THR 3.7 6.7 - - - +
49D TYR* 1.4 105.0 - - + +
51D HIS* 1.4 57.0 + - - +
53D LEU* 3.5 23.7 + - + +
54D ALA* 2.9 29.5 + - - +
73D ILE* 3.7 16.2 - - + -
74D ALA* 3.9 13.1 - - - +
135D ASP* 3.5 11.7 - - - +
169D CYS* 4.2 3.4 - - - -
4003D SAH 3.5 32.1 - - - +
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Residues in contact with HIS 51 (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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47D THR* 2.9 41.2 + - + +
48D PRO* 3.4 13.0 - - + +
49D TYR 3.2 0.2 - - - -
50D MET* 1.4 74.6 - - - +
52D ALA* 1.4 57.5 + - - +
54D ALA* 3.7 0.9 - - - +
55D ALA* 2.9 30.8 + - - +
73D ILE* 4.1 15.6 + - + +
77D LYS* 3.5 51.9 + - + +
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Residues in contact with ALA 52 (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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48D PRO 3.2 11.5 + - - +
49D TYR* 3.0 10.0 + - - +
51D HIS* 1.4 73.6 - - - +
53D LEU* 1.4 64.5 + - - +
55D ALA* 3.5 7.5 + - - +
56D ALA* 3.1 22.7 + - - +
210D GLU* 4.9 9.4 - - - +
212D MET* 4.3 13.7 - - + -
230D THR* 3.5 24.8 - - + +
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Residues in contact with LEU 53 (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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49D TYR* 3.1 29.4 + - + +
50D MET* 3.7 28.9 - - + +
52D ALA* 1.4 71.7 - - - +
54D ALA* 1.3 59.8 + - - +
56D ALA 3.2 1.7 + - - -
57D ALA* 2.9 26.7 + - - +
133D LEU* 3.8 26.0 - - + -
135D ASP* 5.0 0.2 - - - +
167D THR* 3.3 30.7 - - + +
168D TYR 3.8 20.2 - - - +
169D CYS* 3.7 28.3 - - + -
230D THR* 3.8 13.9 - - + -
231D PRO* 4.3 0.9 - - + -
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Residues in contact with ALA 54 (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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50D MET 2.9 18.8 + - - +
51D HIS 3.7 2.0 - - - +
52D ALA 3.4 0.2 - - - -
53D LEU* 1.3 76.0 - - - +
55D ALA* 1.4 51.1 + - - +
57D ALA 3.4 0.7 + - - -
58D SER* 2.7 40.2 + - - -
74D ALA* 3.4 26.7 - - - +
77D LYS* 3.4 21.3 - - + -
78D VAL* 3.8 9.4 - - + +
133D LEU* 3.7 11.1 - - - +
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Residues in contact with ALA 55 (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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51D HIS 2.9 18.0 + - - +
52D ALA* 3.7 8.1 - - - +
54D ALA* 1.4 73.9 - - - +
56D ALA* 1.3 56.6 + - - +
58D SER* 3.6 6.3 + - - -
59D SER* 3.0 30.5 + - - -
77D LYS* 4.9 5.3 - - + +
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Residues in contact with ALA 56 (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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52D ALA 3.1 14.5 + - - +
53D LEU 3.2 8.7 + - - +
55D ALA* 1.3 76.6 - - - +
57D ALA* 1.4 58.6 + - - +
59D SER* 2.7 26.5 + - - -
165D VAL* 3.7 14.7 - - + +
167D THR* 4.0 19.1 - - - +
210D GLU* 5.8 1.1 - - - +
230D THR* 4.3 4.5 - - + -
232D LEU* 3.8 29.4 - - + -
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Residues in contact with ALA 57 (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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53D LEU 2.9 18.5 + - - +
54D ALA 4.0 3.1 - - - +
56D ALA* 1.4 72.5 - - - +
58D SER* 1.4 58.6 + - - +
59D SER 3.4 0.6 + - - -
60D LYS 4.8 2.1 + - - -
61D GLY 5.1 0.3 - - - +
64D VAL* 3.5 18.7 - - + +
78D VAL* 5.1 1.1 - - + -
130D ASP 4.8 0.9 - - - +
131D GLY* 3.3 25.4 + - - -
132D ILE 3.8 12.6 - - - +
133D LEU* 3.8 28.7 - - + -
165D VAL* 4.7 3.6 - - - +
167D THR* 3.8 8.9 - - + +
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Residues in contact with SER 58 (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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54D ALA 2.7 24.2 + - - -
55D ALA* 3.6 6.8 + - - -
57D ALA* 1.4 75.4 - - - +
59D SER* 1.4 56.8 + - - +
60D LYS 3.2 3.4 - - - -
61D GLY* 3.2 20.2 + - - -
64D VAL* 4.0 7.2 - - - -
77D LYS 4.9 0.9 + - - -
78D VAL* 4.3 17.3 - - - -
81D ALA* 3.4 33.4 - - - +
82D PRO* 5.5 1.7 - - - +
83D ILE* 4.0 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