Contacts of the helix formed by residues 38 - 52 (chain B) in PDB entry 2RHG
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 ASP 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B SER 3.0 13.3 + - - +
35B ALA 3.1 8.1 + - - +
37B LYS* 1.3 77.9 - - - +
39B PRO* 1.3 69.7 - - - +
40B GLU* 2.8 35.9 + - - +
41B PHE* 3.0 23.9 + - + +
42B GLN* 3.2 12.9 + - - +
100B ARG* 3.1 32.3 + - - +
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Residues in contact with PRO 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LYS 3.2 11.9 - - - +
38B ASP* 1.3 89.0 - - - +
40B GLU* 1.3 57.4 + - + +
42B GLN* 3.3 10.6 + - + +
43B ALA* 2.9 30.9 + - - +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASP* 2.8 21.7 + - - +
39B PRO* 1.3 79.4 - - + +
41B PHE* 1.3 61.3 + - - +
43B ALA* 3.5 5.7 + - - +
44B GLN* 3.1 25.0 + - - +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA* 3.5 33.0 - - + +
36B GLN* 4.5 0.7 - - - -
38B ASP* 3.0 21.7 + - + +
40B GLU* 1.3 77.3 - - - +
42B GLN* 1.3 78.7 + - - +
44B GLN* 3.1 14.1 + - - +
45B PHE* 2.8 41.2 + + + +
93B GLY 3.9 12.1 - - - -
96B LEU* 3.6 45.5 - - + -
97B LEU* 4.0 5.4 - - + -
100B ARG* 4.2 14.1 - - + +
204B PHE* 4.0 26.9 - + - -
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA 3.1 24.0 + - - -
36B GLN* 3.1 34.9 + - - +
38B ASP 3.2 12.1 + - - +
39B PRO* 3.3 10.1 + - + +
41B PHE* 1.3 91.6 - - - +
43B ALA* 1.3 52.6 + - - +
45B PHE* 3.3 12.8 + - - +
46B ALA* 2.8 37.7 + - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PRO 2.9 17.2 + - - +
40B GLU* 3.8 7.2 - - - +
42B GLN* 1.3 76.5 - - - +
44B GLN* 1.3 57.5 + - - +
46B ALA* 3.9 5.5 - - - +
47B ASP* 3.0 29.6 + - - +
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Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLU 3.1 19.1 + - - +
41B PHE* 3.5 13.4 - - - +
43B ALA* 1.3 74.4 - - - +
45B PHE* 1.3 65.5 + - - +
47B ASP* 3.2 7.7 + - + +
48B LEU* 3.1 27.5 + - + +
96B LEU* 3.3 33.2 - - + +
99B LYS* 5.7 3.5 - - - -
126B LEU* 5.4 3.3 - - - +
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Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 2.8 29.8 + + + +
42B GLN* 3.6 13.9 - - - +
44B GLN* 1.3 75.8 - - - +
46B ALA* 1.3 62.1 + - - +
48B LEU* 3.2 3.4 + - + +
49B LEU* 3.0 43.5 + - + +
89B ASN 3.5 20.0 - - - -
92B LEU* 4.1 5.6 - - + -
93B GLY* 3.4 26.9 - - - -
96B LEU* 3.6 24.4 - - + +
203B GLU 5.2 0.7 - - - -
204B PHE* 3.6 29.2 - + - -
207B MET* 3.9 21.5 - - + -
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLN 2.8 22.0 + - - +
43B ALA* 3.9 6.1 - - - +
45B PHE* 1.3 74.8 - - - +
47B ASP* 1.3 58.9 + - - +
49B LEU* 3.8 10.9 - - - +
50B LYS* 3.0 32.6 + - - +
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Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA 3.0 19.7 + - - +
44B GLN* 3.5 9.0 - - - +
45B PHE 3.2 0.2 - - - -
46B ALA* 1.3 77.9 - - - +
48B LEU* 1.3 64.3 + - - +
50B LYS* 4.7 1.3 - - - -
51B ASN* 2.6 60.8 + - - +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLN* 3.1 15.8 + - + +
45B PHE 3.2 5.1 + - - +
47B ASP* 1.3 80.0 - - - +
49B LEU* 1.3 61.0 + - - +
52B TYR* 2.8 35.7 + - + +
53B ALA* 2.8 8.6 + - - -
92B LEU* 4.2 29.8 - - + -
96B LEU* 3.8 34.1 - - + -
125B LEU* 3.7 26.2 - - + -
126B LEU* 4.2 18.8 - - + -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.0 50.2 + - + +
46B ALA* 3.8 8.7 - - - +
48B LEU* 1.3 76.1 - - - +
50B LYS* 1.3 57.5 + - - +
53B ALA* 3.0 8.7 - - + +
54B GLY 2.9 25.6 + - - -
55B ARG* 2.9 26.4 + - + +
89B ASN* 3.5 36.6 - - + +
92B LEU* 4.2 9.4 - - + -
207B MET* 3.6 26.5 - - + -
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA 3.0 19.7 + - - +
47B ASP* 4.0 3.1 - - - +
49B LEU* 1.3 80.0 - - - +
51B ASN* 1.3 81.8 + - - +
54B GLY* 3.4 16.3 + - - -
55B ARG* 3.5 22.3 - - - +
56B PRO* 5.4 2.9 - - + -
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ASP* 2.6 46.0 + - - +
50B LYS* 1.3 97.7 + - - +
52B TYR* 1.3 59.1 + - - +
54B GLY 5.0 0.2 - - - -
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Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 2.8 31.6 + - + +
51B ASN* 1.3 75.4 - - - +
53B ALA* 1.3 63.7 + - - +
54B GLY* 3.4 1.4 - - - -
82B HIS* 3.2 49.5 + + - +
88B THR* 5.3 0.4 - - + -
92B LEU* 4.3 15.3 - - + -
121B LEU* 3.6 30.7 + - + +
125B LEU* 3.7 45.4 - - + +
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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