Contacts of the helix formed by residues 50 - 60 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B THR* 6.0 4.5 - - - +
25C SER* 3.9 23.1 - - - +
26C ILE 3.7 13.2 - - - +
27C ILE* 5.1 15.7 - - + -
48F THR 4.3 2.7 - - - +
49F LEU* 1.4 87.4 - - + +
51F VAL* 1.3 66.9 + - - +
52F ASN* 3.2 15.3 - - - +
53F VAL* 2.9 33.6 + - + +
54F ALA 3.0 10.9 + - - -
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Residues in contact with VAL 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.6 23.6 + - + +
26F ILE* 3.6 25.8 - - + -
29F ASN* 3.3 22.2 + - - +
30F ALA* 3.7 37.0 - - - +
31F VAL* 4.1 10.8 - - + -
43F PHE* 3.8 3.0 - - + -
45F ASN* 3.3 16.1 + - + -
49F LEU 3.2 2.6 + - - -
50F PRO* 1.3 70.3 - - - +
52F ASN* 1.3 59.9 + - - +
54F ALA* 3.6 2.9 + - - +
55F PHE* 3.0 25.3 + - - +
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Residues in contact with ASN 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 4.4 4.4 - - - +
3C GLU* 4.5 7.3 + - - -
24C VAL* 2.8 37.5 + - - +
25C SER* 3.7 0.4 - - - -
26C ILE* 2.9 43.7 + - + +
2F LEU* 4.4 21.3 - - + +
26F ILE* 5.2 2.5 - - + -
31F VAL* 5.5 1.8 - - - -
50F PRO* 3.7 6.6 - - - +
51F VAL* 1.3 74.0 - - + +
53F VAL* 1.3 65.1 + - - +
55F PHE* 3.5 9.1 + - - +
56F GLU* 3.0 27.2 + - - +
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Residues in contact with VAL 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL 4.3 6.7 - - - +
49F LEU* 4.5 13.0 - - + -
50F PRO* 2.9 33.3 + - + +
52F ASN* 1.3 79.6 - - - +
54F ALA* 1.3 64.4 + - - +
56F GLU* 3.1 7.5 + - - +
57F LEU* 3.0 33.4 + - + +
102F CYS* 4.9 4.0 - - - -
104F MET* 4.1 30.1 - - + -
105F THR* 3.8 29.4 - - + +
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Residues in contact with ALA 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F PHE* 3.4 9.0 - - + -
45F ASN* 3.3 34.3 - - - +
47F THR* 3.3 17.0 - - + +
49F LEU* 4.4 10.7 - - + +
50F PRO 3.0 7.7 + - - +
51F VAL 3.7 8.3 - - - +
53F VAL* 1.3 76.6 - - - +
55F PHE* 1.3 57.9 + - - +
57F LEU* 4.1 2.9 - - - +
58F TRP* 3.1 30.0 + - - +
86F TRP* 4.3 3.5 - - - -
93F PRO* 6.1 0.2 - - - -
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Residues in contact with PHE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F LEU* 3.7 24.9 - - + -
5F VAL* 3.6 19.3 - - + -
6F ALA* 3.7 24.9 - - + -
9F VAL* 4.0 9.4 - - + -
31F VAL* 3.8 14.1 - - + -
42F ILE* 3.7 28.7 - - + -
43F PHE* 3.4 40.8 - + + -
51F VAL 3.0 17.5 + - - +
52F ASN* 3.5 7.2 - - - +
53F VAL 3.1 0.2 - - - -
54F ALA* 1.3 75.6 - - - +
56F GLU* 1.3 65.6 + - - +
58F TRP* 3.3 20.7 + + - +
59F ALA* 3.0 24.1 + - - +
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Residues in contact with GLU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GLU* 5.1 6.2 - - - +
1F SER* 5.4 10.0 + - - +
2F LEU* 6.0 0.5 - - - -
5F VAL* 4.1 25.6 - - + +
52F ASN 3.0 15.8 + - - +
53F VAL* 3.1 7.8 + - - +
55F PHE* 1.3 76.0 - - + +
57F LEU* 1.3 61.4 - - - +
59F ALA* 3.5 2.4 + - - +
60F LYS* 2.8 58.0 + - + +
102F CYS* 3.3 39.4 - - + +
103F THR* 4.6 1.6 + - - +
104F MET* 5.8 0.2 - - - +
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Residues in contact with LEU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU* 3.9 17.5 - - + -
53F VAL* 3.0 23.5 + - + +
54F ALA* 4.1 3.6 - - - +
56F GLU* 1.3 73.5 - - - +
58F TRP* 1.3 65.9 + - - +
60F LYS* 3.0 23.2 + - - +
61F ARG* 3.3 1.2 + - - -
84F VAL* 3.9 23.6 - - + +
86F TRP* 4.5 6.5 - - + -
93F PRO* 3.9 30.3 - - + -
95F HIS 5.7 0.9 - - - +
96F VAL 5.7 2.9 - - - +
98F THR* 4.9 5.8 - - - +
101F VAL* 4.2 13.7 - - + -
102F CYS* 4.1 16.6 - - + -
105F THR* 3.7 26.7 - - + +
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Residues in contact with TRP 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E GLU* 4.6 8.3 + - - -
268E PHE* 5.3 9.6 - - + -
9F VAL* 4.0 21.8 - - + -
13F GLY 5.0 3.6 - - - -
42F ILE 3.6 26.5 - - - -
43F PHE* 3.6 28.7 - + + -
54F ALA 3.1 20.1 + - - +
55F PHE* 3.8 21.8 - + - +
57F LEU* 1.3 75.1 - - - +
59F ALA* 1.3 72.6 + - - +
61F ARG* 2.8 71.6 + - - +
86F TRP* 3.7 37.2 - + + +
88F TYR* 5.6 2.4 - - - -
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Residues in contact with ALA 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 3.5 32.1 - - + -
9F VAL* 3.8 18.8 - - + -
14F HIS* 3.6 13.7 + - - +
15F PHE* 2.9 34.8 + - + +
55F PHE 3.0 10.7 + - - +
56F GLU 3.7 3.8 - - - +
58F TRP* 1.3 82.7 - - + +
60F LYS* 1.3 56.3 + - + +
61F ARG* 3.2 4.9 + - - +
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Residues in contact with LYS 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 4.8 2.6 - - - +
14F HIS* 5.7 0.2 - - - -
15F PHE* 3.6 49.5 - - + -
56F GLU* 2.8 45.9 + - + +
57F LEU 3.0 10.2 + - - +
59F ALA* 1.3 73.6 - - - +
61F ARG* 1.3 66.8 + - - +
62F ASN 3.6 0.2 + - - -
83F THR* 4.3 2.8 + - - -
84F VAL* 3.5 19.4 + - - +
101F VAL* 2.7 50.0 + - + +
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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