Contacts of the helix formed by residues 73 - 88 (chain A) in PDB entry 1RRM
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 THR 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A VAL* 4.7 8.7 - - + +
71A ASN 3.9 9.0 - - - +
72A PRO* 1.3 74.5 - - - +
74A ILE* 1.3 65.2 + - - +
75A THR* 3.6 7.5 + - - -
76A VAL* 3.2 28.8 + - - +
77A VAL* 3.1 24.4 + - - +
154A ILE* 3.6 4.7 - - - -
155A THR* 3.3 15.9 - - + -
157A GLU* 3.6 38.8 + - + +
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Residues in contact with ILE 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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73A THR* 1.3 75.3 - - - +
75A THR* 1.3 58.7 + - - +
77A VAL* 3.3 4.9 + - - +
78A LYS* 3.0 47.1 + - + +
118A ASP 3.8 4.3 - - - +
119A VAL* 3.7 22.4 - - + -
120A ARG* 4.0 23.1 - - + +
154A ILE* 3.9 14.4 - - + -
155A THR 3.1 11.8 + - - +
156A ASP* 3.7 36.3 - - - +
157A GLU* 5.1 1.5 - - - +
163A PHE* 3.8 13.7 - - + -
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 3.1 8.7 + - - -
74A ILE* 1.3 80.8 - - - +
76A VAL* 1.3 60.0 + - + +
78A LYS* 3.3 8.6 + - - +
79A GLU* 2.9 31.1 + - + +
157A GLU* 3.8 15.7 + - - -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 3.3 20.9 + - + +
67A GLY 3.7 20.4 - - - +
68A VAL* 3.7 14.8 - - + -
69A VAL* 4.0 22.0 - - + +
72A PRO* 5.0 1.3 - - + -
73A THR* 3.2 24.9 + - - +
75A THR* 1.3 77.0 - - + +
77A VAL* 1.3 62.0 + - - +
79A GLU* 4.5 3.6 - - - +
80A GLY* 2.9 26.3 + - - -
103A THR* 4.1 18.3 - - + +
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Residues in contact with VAL 77 (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 PRO* 5.4 0.7 - - + -
73A THR 3.1 15.0 + - - +
74A ILE* 3.5 8.7 - - - +
75A THR 3.2 0.2 - - - -
76A VAL* 1.3 76.8 - - - +
78A LYS* 1.3 58.2 + - - +
80A GLY* 3.4 1.0 + - - -
81A LEU* 2.9 29.0 + - + +
103A THR* 4.4 17.3 - - + +
106A ALA* 3.7 27.4 - - + -
107A ILE* 3.8 5.0 - - + +
110A ILE* 3.8 22.7 - - + -
119A VAL* 3.9 9.9 - - + -
154A ILE* 3.8 33.0 - - + -
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.0 40.2 + - + +
75A THR* 3.7 7.0 - - - +
77A VAL* 1.3 73.0 - - - +
79A GLU* 1.3 66.9 + - - +
81A LEU* 3.3 13.4 + - + +
82A GLY* 3.1 18.4 + - - -
117A ALA 3.5 23.3 + - - +
118A ASP* 4.3 10.0 + - - +
119A VAL* 4.2 8.7 - - + -
120A ARG* 5.8 2.8 - - - +
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Residues in contact with GLU 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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65A TYR* 2.8 35.1 + - + +
67A GLY* 4.7 5.4 - - - +
75A THR* 2.9 20.9 + - + +
76A VAL* 5.0 3.3 - - - +
78A LYS* 1.3 76.2 - - - +
80A GLY* 1.3 63.7 + - - +
82A GLY* 3.1 3.9 + - - -
83A VAL* 3.1 26.1 + - + +
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Residues in contact with GLY 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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35A LEU* 4.2 2.3 - - - +
65A TYR* 3.7 26.6 - - - -
76A VAL 2.9 17.3 + - - -
79A GLU* 1.3 77.1 - - - +
81A LEU* 1.3 62.6 + - - +
83A VAL* 3.3 2.9 + - - +
84A PHE* 2.9 23.0 + - - +
107A ILE* 3.6 17.2 - - - +
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Residues in contact with LEU 81 (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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77A VAL* 2.9 18.3 + - + +
78A LYS* 3.5 11.9 - - + +
79A GLU 3.2 0.2 - - - -
80A GLY* 1.3 75.7 - - - +
82A GLY* 1.3 58.6 + - - +
84A PHE* 3.2 3.8 + - + +
85A GLN* 2.9 56.7 + - + +
107A ILE* 3.9 34.5 - - + +
110A ILE* 3.5 29.8 - - + -
111A SER* 4.0 22.0 - - - +
117A ALA* 5.5 7.9 - - + +
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Residues in contact with GLY 82 (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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78A LYS 3.1 11.2 + - - -
79A GLU* 3.1 4.4 + - - -
81A LEU* 1.3 80.6 - - - +
83A VAL* 1.3 55.5 + - - +
85A GLN* 3.3 12.7 + - - +
86A ASN* 2.9 43.2 + - - +
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Residues in contact with VAL 83 (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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35A LEU* 3.9 20.6 - - + -
63A ALA* 6.1 0.7 - - + -
64A ILE 4.5 7.0 - - - +
65A TYR* 3.8 32.5 - - + -
79A GLU* 3.1 19.1 + - + +
80A GLY 3.6 6.5 - - - +
81A LEU 3.3 0.4 - - - -
82A GLY* 1.3 74.5 - - - +
84A PHE* 1.3 63.7 + - - +
86A ASN* 3.3 6.1 + - - +
87A SER* 2.9 28.3 + - - -
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Residues in contact with PHE 84 (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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35A LEU* 3.5 24.8 - - + +
80A GLY 2.9 11.5 + - - +
81A LEU* 3.4 7.4 - - + +
83A VAL* 1.3 77.0 - - - +
85A GLN* 1.3 70.7 + - + +
87A SER* 2.7 20.1 + - - -
88A GLY 3.7 3.5 + - - -
89A ALA* 3.6 36.9 + - + +
90A ASP* 4.6 1.3 - - - -
91A TYR 4.0 8.1 - - - -
92A LEU* 3.6 27.1 - - + -
107A ILE* 4.0 14.4 - - + -
111A SER* 3.3 31.6 - - - -
133A VAL* 3.7 28.3 - - + -
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Residues in contact with GLN 85 (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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81A LEU* 2.9 48.5 + - + +
82A GLY* 3.7 13.1 - - - +
84A PHE* 1.3 84.0 - - + +
86A ASN* 1.3 66.7 + - - +
87A SER 3.6 0.3 + - - -
88A GLY* 4.1 5.9 + - - -
111A SER* 5.0 8.8 + - - +
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Residues in contact with ASN 86 (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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82A GLY* 2.9 25.5 + - - +
83A VAL* 3.7 5.5 - - - +
84A PHE 3.2 0.2 - - - -
85A GLN* 1.3 80.9 - - - +
87A SER* 1.3 60.4 + - - +
88A GLY 3.5 0.7 - - - -
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Residues in contact with SER 87 (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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33A LYS* 2.9 28.4 + - - +
35A LEU* 4.3 6.2 - - - +
63A ALA* 4.3 23.3 - - - -
83A VAL* 2.9 16.4 + - - -
84A PHE* 2.7 21.2 + - - -
86A ASN* 1.3 78.9 - - - +
88A GLY* 1.3 59.2 + - - +
89A ALA* 3.1 20.7 + - - +
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Residues in contact with GLY 88 (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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33A LYS* 4.4 9.9 - - - +
84A PHE 3.7 4.0 + - - -
85A GLN 4.1 5.6 + - - -
86A ASN 3.5 2.6 - - - -
87A SER* 1.3 78.7 + - - +
89A ALA* 1.3 65.2 + - - +
90A ASP* 3.7 3.1 + - - +
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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