Contacts of the helix formed by residues 46 - 60 (chain B) in PDB entry 2RS9
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 SER 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B GLY 3.2 1.0 - - - -
45B SER* 1.3 79.0 - - - +
47B GLY* 1.3 60.9 + - - +
48B PHE* 3.3 8.9 + - - +
49B LEU* 3.0 37.0 + - - +
50B ILE* 3.1 19.4 + - - +
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Residues in contact with GLY 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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46B SER* 1.3 74.5 + - - +
48B PHE* 1.3 60.0 + - - +
50B ILE* 3.5 17.0 + - - +
51B LEU* 3.4 24.8 + - - +
154B MET* 4.2 10.8 - - - -
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Residues in contact with PHE 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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46B SER* 3.3 7.7 + - - +
47B GLY* 1.3 72.3 - - - +
49B LEU* 1.3 74.2 + - + +
51B LEU* 3.2 23.4 + - + +
52B LEU* 3.7 38.4 + - + +
102B TYR 3.9 2.7 - - - -
103B LEU* 3.6 29.2 - - + -
104B ASN* 3.7 3.6 - - - -
105B PHE* 3.5 35.0 - + + -
151B ALA* 3.7 31.4 - - + -
154B MET* 3.7 18.1 - - + +
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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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44B GLY* 4.0 10.8 - - - +
45B SER* 3.9 11.4 - - - +
46B SER* 3.0 36.4 + - - +
48B PHE* 1.3 84.9 - - + +
50B ILE* 1.3 61.0 + - - +
52B LEU* 3.3 18.3 + - + +
53B ARG* 3.5 15.6 + - - +
97B LEU* 4.6 4.5 - - + +
100B TYR* 3.9 29.6 - - + -
102B TYR 3.4 25.4 - - - +
103B LEU* 4.6 17.9 - - + -
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Residues in contact with ILE 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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44B GLY* 3.4 28.0 - - - +
46B SER 3.1 14.2 + - - +
47B GLY* 3.7 16.2 - - - +
48B PHE 3.3 0.2 - - - -
49B LEU* 1.3 74.4 - - - +
51B LEU* 1.3 64.8 + - + +
53B ARG* 3.3 37.1 + - - +
54B LYS* 3.5 28.7 + - + +
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Residues in contact with LEU 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 GLY 3.4 14.8 + - - +
48B PHE* 3.2 21.7 + - + +
50B ILE* 1.3 76.6 - - + +
52B LEU* 1.3 60.8 + - + +
54B LYS* 3.4 7.1 + - - +
55B THR* 2.7 38.8 + - - +
105B PHE* 5.7 1.8 - - + -
147B ALA 4.6 5.8 - - - +
150B GLN* 3.8 39.4 + - + +
151B ALA* 3.7 39.0 - - + +
154B MET* 4.0 3.6 - - + -
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Residues in contact with LEU 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 PHE* 3.7 33.4 - - + +
49B LEU* 3.6 10.8 - - + +
50B ILE 3.3 0.8 - - - -
51B LEU* 1.3 75.7 - - + +
53B ARG* 1.3 59.3 + - - +
55B THR* 3.8 4.2 - - - -
56B LEU* 2.9 33.4 + - - +
97B LEU* 3.5 22.1 - - + +
102B TYR* 3.8 39.0 - - + +
105B PHE* 3.8 35.0 - - + -
108B PHE* 3.9 23.0 - - + -
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Residues in contact with ARG 53 (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 SER* 5.2 3.4 + - - +
43B SER* 3.2 48.4 + - - +
44B GLY* 4.1 13.7 + - - +
49B LEU 3.5 14.6 - - - +
50B ILE* 3.6 27.9 - - - +
51B LEU 3.3 0.4 - - - -
52B LEU* 1.3 78.0 - - - +
54B LYS* 1.3 67.7 + - + +
56B LEU* 3.5 4.1 + - - +
57B GLU* 3.4 29.1 + - - +
94B LYS* 5.1 15.1 + - - +
97B LEU* 3.8 18.4 - - + +
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Residues in contact with LYS 54 (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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50B ILE* 3.5 23.6 + - + +
51B LEU* 3.4 8.3 + - - +
53B ARG* 1.3 82.6 - - + +
55B THR* 1.3 60.6 + - - +
57B GLU* 3.6 16.3 + - - +
58B GLN* 3.3 26.1 + - - +
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Residues in contact with THR 55 (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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51B LEU* 2.7 25.6 + - - +
52B LEU* 3.8 5.2 - - - -
54B LYS* 1.3 72.8 - - - +
56B LEU* 1.3 58.8 + - - +
58B GLN* 2.9 23.2 + - - +
59B LEU* 3.0 27.3 + - + +
105B PHE* 4.6 3.9 - - + -
108B PHE* 3.7 24.2 - - + -
143B VAL* 4.1 9.9 - - + +
144B LEU* 4.6 3.6 - - + -
147B ALA* 3.4 34.9 - - + +
150B GLN* 5.1 2.9 + - - -
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Residues in contact with LEU 56 (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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52B LEU 2.9 18.1 + - - +
53B ARG* 3.8 4.7 - - - +
55B THR* 1.3 72.4 - - - +
57B GLU* 1.3 57.6 + - + +
59B LEU* 3.4 6.6 + - + +
60B GLN* 3.1 34.1 + - + +
90B PHE* 3.8 27.4 - - + +
93B MET* 3.9 30.5 - - + -
94B LYS* 3.6 50.9 - - + +
97B LEU* 4.1 13.0 - - + -
108B PHE* 3.8 10.4 - - + -
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Residues in contact with GLU 57 (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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53B ARG* 3.4 18.0 + - - +
54B LYS* 3.7 19.9 - - - +
55B THR 3.3 0.4 - - - -
56B LEU* 1.3 76.7 - - + +
58B GLN* 1.3 59.7 + - - +
60B GLN* 3.7 12.0 - - + +
61B GLU* 3.7 25.1 + - - +
94B LYS* 5.5 9.4 - - - +
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Residues in contact with GLN 58 (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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54B LYS 3.3 15.1 + - - +
55B THR* 2.9 11.5 + - - +
57B GLU* 1.3 75.3 - - - +
59B LEU* 1.3 63.7 + - - +
60B GLN 3.3 0.2 - - - -
61B GLU* 3.1 34.0 + - - +
62B LYS* 3.6 17.8 + - - +
143B VAL* 3.6 21.0 - - + +
146B GLN* 4.7 12.0 - - - +
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Residues in contact with LEU 59 (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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55B THR* 3.0 41.4 + - + +
56B LEU* 3.4 8.7 + - + +
58B GLN* 1.3 74.6 - - - +
60B GLN* 1.3 55.3 + - - +
62B LYS* 3.1 24.9 + - + +
63B ASP 4.0 2.9 + - - -
90B PHE* 3.5 29.8 - - + -
93B MET* 6.1 0.9 - - + -
108B PHE* 4.4 6.1 - - + -
112B PHE* 3.6 27.1 - - + -
136B LEU* 4.3 0.7 - - - +
140B GLY* 3.5 40.2 - - - +
143B VAL* 3.7 14.6 - - + -
144B LEU* 4.1 14.4 - - + -
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Residues in contact with GLN 60 (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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56B LEU* 3.1 24.8 + - + +
57B GLU* 3.7 12.6 - - + +
58B GLN 3.3 0.2 - - - -
59B LEU* 1.3 74.3 - - - +
61B GLU* 1.3 59.6 + - + +
62B LYS 3.3 1.6 + - - -
63B ASP* 3.8 19.4 + - - +
66B ASN* 5.7 0.2 - - - +
69B SER* 3.5 29.7 + - - -
90B PHE* 3.3 41.4 + - + +
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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