Contacts of the helix formed by residues 50 - 60 (chain B) in PDB entry 2RHB
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 PRO 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B THR 4.3 3.1 - - - +
49B LEU* 1.4 87.8 - - + +
51B VAL* 1.3 55.4 + - - +
52B ASN* 3.3 11.7 - - - +
53B VAL* 2.8 38.4 + - + +
54B ALA 3.1 10.6 + - - -
104B MET* 5.7 0.4 - - + -
25D SER* 3.7 27.4 - - - +
26D ILE 3.4 19.1 - - - +
27D ILE* 4.8 17.0 - - + -
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Residues in contact with VAL 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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26B ILE* 3.7 25.6 - - + -
29B ASN* 3.4 22.7 + - - +
30B ALA* 3.7 34.5 - - - +
31B VAL* 4.0 14.1 - - + -
43B PHE* 3.8 5.0 - - + -
45B ASN* 3.7 16.6 + - + -
49B LEU 3.4 2.6 + - - -
50B PRO* 1.3 69.4 - - - +
52B ASN* 1.3 62.9 + - - +
54B ALA 3.6 0.3 + - - -
55B PHE* 3.0 27.4 + - - +
26D ILE* 3.7 21.0 + - + +
27D ILE* 5.8 0.2 - - - -
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Residues in contact with ASN 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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2B LEU* 3.9 23.5 - - + +
26B ILE* 4.9 2.0 - - + -
31B VAL* 5.5 0.7 - - - -
50B PRO* 3.7 9.2 - - - +
51B VAL* 1.3 77.5 - - + +
53B VAL* 1.3 66.2 + - - +
55B PHE* 3.7 9.0 - - - +
56B GLU* 3.2 26.2 + - - +
2D LEU* 4.4 4.8 - - + +
3D GLU* 4.5 7.7 + - - -
24D VAL* 2.7 32.1 + - - +
25D SER* 3.8 0.9 - - - -
26D ILE* 3.0 46.7 + - + +
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Residues in contact with VAL 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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49B LEU* 4.4 14.4 - - + -
50B PRO* 2.8 32.6 + - + +
52B ASN* 1.3 76.3 - - - +
54B ALA* 1.3 65.4 + - - +
56B GLU* 3.1 8.0 + - - +
57B LEU* 3.0 27.8 + - + +
102B CYS* 4.5 8.5 - - - -
104B MET* 3.9 28.0 - - + -
105B THR* 3.6 29.4 - - + -
24D VAL 4.1 11.2 - - - +
25D SER* 4.5 2.0 - - - +
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Residues in contact with ALA 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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43B PHE* 3.8 8.2 - - + -
45B ASN* 3.3 16.2 - - - +
47B THR* 3.3 36.1 - - + +
49B LEU* 4.3 11.4 - - + +
50B PRO 3.1 8.8 + - - +
51B VAL 4.0 4.5 - - - +
53B VAL* 1.3 75.9 - - - +
55B PHE* 1.3 53.1 + - - +
57B LEU* 3.3 4.5 + - - +
58B TRP* 2.8 35.9 + - - +
86B TRP* 4.2 3.4 - - - -
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Residues in contact with PHE 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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2B LEU* 3.7 30.3 - - + -
5B VAL* 3.6 21.8 - - + -
6B ALA* 3.9 28.3 - - + -
9B VAL* 4.1 6.3 - - + -
31B VAL* 3.9 15.0 - - + -
42B ILE* 4.0 18.6 - - + -
43B PHE* 3.5 38.7 - + + -
51B VAL 3.0 18.5 + - - +
52B ASN* 3.7 6.1 - - - +
53B VAL 3.1 0.2 - - - -
54B ALA* 1.3 74.4 - - - +
56B GLU* 1.3 65.1 + - + +
58B TRP* 3.8 23.0 - + - +
59B ALA* 3.0 24.6 + - - +
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Residues in contact with GLU 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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0B MET* 4.0 16.7 - - - +
1B SER* 5.5 1.0 - - - -
2B LEU* 5.5 3.1 + - - -
5B VAL* 4.1 24.0 - - + +
52B ASN 3.2 12.3 + - - +
53B VAL* 3.1 10.8 + - - +
55B PHE* 1.3 78.6 - - + +
57B LEU* 1.3 60.5 + - - +
59B ALA* 3.6 1.9 + - - +
60B LYS* 3.1 57.8 + - + +
102B CYS* 3.3 36.0 - - + +
103B THR* 4.5 3.1 + - - +
3D GLU* 4.7 9.9 - - - +
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Residues in contact with LEU 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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49B LEU* 4.0 15.0 - - + -
53B VAL* 3.0 19.5 + - + +
54B ALA 3.7 4.9 - - - +
56B GLU* 1.3 74.1 - - - +
58B TRP* 1.3 66.5 + - - +
60B LYS* 2.9 14.4 + - - +
61B ARG* 3.2 9.0 + - - -
84B VAL* 3.9 23.4 - - + +
86B TRP* 4.3 2.2 - - - -
93B PRO* 3.8 31.6 - - + -
95B HIS 5.7 1.6 - - - +
96B VAL 5.8 2.5 - - - +
98B THR* 4.4 8.3 - - - +
101B VAL* 4.1 14.4 - - + -
102B CYS* 3.5 32.3 - - + -
105B THR* 3.7 20.4 - - + +
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Residues in contact with TRP 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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266A GLU* 4.6 7.9 + - - -
268A PHE* 5.5 8.5 - - + -
9B VAL* 4.0 22.0 - - + -
13B GLY 5.3 1.6 - - - -
42B ILE 3.6 25.4 - - - -
43B PHE* 3.6 27.1 - + + -
54B ALA 2.8 20.5 + - - +
55B PHE* 3.8 23.6 - + - +
57B LEU* 1.3 72.2 - - - +
59B ALA* 1.3 71.3 + - - +
61B ARG* 2.9 70.8 + - - +
86B TRP* 3.6 45.1 - + + +
88B TYR* 5.5 2.8 - - - -
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Residues in contact with ALA 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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5B VAL* 3.5 26.2 - - + -
9B VAL* 3.7 18.2 - - + -
14B HIS* 3.8 9.4 + - - +
15B PHE* 2.8 35.0 + - + +
55B PHE 3.0 18.2 + - - +
56B GLU 3.7 2.9 - - - +
58B TRP* 1.3 85.1 - - + +
60B LYS* 1.3 56.9 + - - +
61B ARG* 3.2 7.2 + - - +
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Residues in contact with LYS 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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0B MET* 3.5 25.9 - - - +
5B VAL* 5.1 0.7 - - - -
15B PHE* 3.8 46.2 - - + -
56B GLU* 3.1 44.4 + - + +
57B LEU 2.9 10.0 + - - +
59B ALA* 1.3 75.2 - - + +
61B ARG* 1.3 66.8 - - - +
62B ASN 3.5 0.9 + - - -
83B THR* 4.6 2.3 + - - -
84B VAL* 3.8 23.9 + - + +
101B VAL* 2.7 42.6 + - + +
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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