Contacts of the helix formed by residues 70 - 80 (chain A) in PDB entry 2RRM
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLY* 3.7 7.6 - - - -
25A ARG* 3.5 18.8 + - - +
26A ASP* 4.3 23.7 - - + +
27A ASN* 5.2 0.4 - - - +
37A ILE* 4.4 0.9 - - - -
69A VAL* 1.3 79.8 - - - +
71A HIS* 1.3 70.1 + - + +
72A ALA* 3.1 9.2 - - + +
73A PHE* 3.1 33.4 + - + +
74A ALA* 2.9 21.7 + - - +
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Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.5 26.3 - - + +
22A SER* 5.0 1.8 - - - -
23A GLY 4.3 9.4 - - - +
24A GLY* 3.3 18.5 - - - +
27A ASN* 2.6 38.4 + - - -
37A ILE* 4.3 10.5 - - + -
70A GLU* 1.3 74.8 - - + +
72A ALA* 1.3 78.4 + - + +
74A ALA* 3.3 1.1 + - - +
75A VAL* 2.8 38.8 + - + +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 3.1 9.3 - - + +
71A HIS* 1.3 95.8 + - + +
73A PHE* 1.3 62.7 + - - +
75A VAL* 3.0 11.0 - - - +
76A GLN* 2.9 29.6 + - - +
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 4.4 8.7 - - + -
69A VAL* 4.1 20.9 - - + -
70A GLU* 3.1 37.3 + - + +
72A ALA* 1.3 78.4 - - - +
74A ALA* 1.3 57.9 + - - +
76A GLN* 2.7 41.9 - - - +
77A GLN* 3.1 45.8 + - - -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 5.4 4.0 - - + -
37A ILE* 3.0 38.1 - - + -
61A VAL* 4.9 3.6 - - + +
66A MET* 3.4 27.4 - - + +
69A VAL* 4.3 0.4 - - + +
70A GLU 2.9 9.0 + - - +
71A HIS* 3.7 2.7 - - - +
73A PHE* 1.3 75.8 - - - +
75A VAL* 1.3 66.3 + - - +
77A GLN* 2.9 20.1 + - - +
78A LEU* 3.4 11.4 + - + +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 5.5 6.5 - - + -
21A ILE* 3.7 29.3 - - + +
71A HIS* 2.8 19.9 + - + +
72A ALA* 3.0 28.0 - - - +
74A ALA* 1.3 73.2 - - - +
76A GLN* 1.3 58.2 + - + +
78A LEU* 3.2 24.1 - - + +
79A ARG* 2.9 44.2 + - + +
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ALA 2.9 17.6 + - - +
73A PHE* 2.7 53.8 + - - +
75A VAL* 1.3 79.7 - - + +
77A GLN* 1.3 72.9 + - - +
79A ARG* 3.9 9.5 - - - +
80A LYS* 3.4 21.7 + - - +
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A VAL* 4.8 9.0 - - + +
62A ASN* 3.8 15.3 + - + -
64A VAL* 3.2 49.3 - - + +
66A MET* 3.8 7.2 - - + +
73A PHE* 3.1 44.4 + - - -
74A ALA* 2.9 9.0 + - - +
76A GLN* 1.3 88.2 + - - +
78A LEU* 1.3 64.4 + - - +
80A LYS* 3.3 18.5 + - - +
81A SER 3.9 0.5 + - - -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.1 36.6 + - - +
17A PHE* 3.9 20.6 - - + -
19A ILE* 5.4 1.3 - - + -
21A ILE* 3.9 19.5 - - + -
61A VAL* 3.9 27.8 - - + +
62A ASN* 4.1 4.7 - - - +
74A ALA* 3.4 6.5 + - + +
75A VAL* 3.2 31.9 - - + +
77A GLN* 1.3 76.8 - - - +
79A ARG* 1.3 70.0 + - - +
80A LYS 3.1 0.4 - - - -
81A SER* 3.0 28.2 + - - -
85A ALA* 3.7 13.8 - - + +
87A ILE* 4.5 13.0 - - + -
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.3 35.3 + - - +
17A PHE* 4.8 9.7 - - + -
75A VAL* 2.9 30.6 + - + +
76A GLN* 3.9 9.6 - - - +
77A GLN 3.3 0.2 - - - -
78A LEU* 1.3 81.2 - - + +
80A LYS* 1.3 61.4 + - - +
81A SER 3.3 0.3 + - - -
82A GLY* 4.0 5.2 + - - -
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLN 3.4 10.6 + - - +
77A GLN* 3.3 14.5 + - - +
78A LEU 3.1 0.4 - - - -
79A ARG* 1.3 77.5 - - - +
81A SER* 1.3 68.2 + - - +
82A GLY* 4.5 0.3 - - - -
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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