Contacts of the helix formed by residues 53 - 66 (chain A) in PDB entry 1RS2
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 HIS 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A VAL* 4.6 23.0 - - + +
51A THR* 3.8 4.2 + - - +
52A VAL* 1.3 72.3 - - - +
54A TYR* 1.3 62.6 + + - +
55A GLY* 3.3 16.1 - - - -
56A GLU* 2.8 68.5 + - + +
57A VAL* 3.1 22.7 + - - +
88A TYR* 4.7 1.2 + - - -
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Residues in contact with TYR 54 (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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5A ILE* 3.3 33.2 - - + -
6A PHE 4.8 8.1 - - - -
7A LEU* 4.0 23.7 - - + +
52A VAL 3.4 7.8 + - - -
53A HIS* 1.3 69.8 - + - +
55A GLY* 1.3 59.2 + - - +
56A GLU 2.9 2.5 - - - -
57A VAL* 2.6 14.7 + - + +
58A PHE* 2.6 36.6 + - - +
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Residues in contact with GLY 55 (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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53A HIS* 3.3 16.4 + - - -
54A TYR* 1.3 82.4 - - - +
56A GLU* 1.3 58.5 + - - +
58A PHE* 3.5 8.4 + - - +
59A GLU* 2.8 35.2 + - - +
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A HIS* 2.8 41.2 + - + +
55A GLY* 1.3 74.9 - - - +
57A VAL* 1.3 66.2 + - - +
59A GLU* 2.9 21.6 + - + +
60A GLU* 3.1 17.0 + - - +
88A TYR* 3.0 35.4 + - - +
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Residues in contact with VAL 57 (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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5A ILE* 5.7 1.3 - - + -
7A LEU* 3.4 23.1 - - + -
33A VAL* 4.4 2.7 - - + -
35A LEU* 4.1 17.3 - - + -
52A VAL* 3.9 19.7 - - + -
53A HIS 3.1 18.2 - - - +
54A TYR* 2.6 21.5 + - - +
56A GLU* 1.3 74.0 - - - +
58A PHE* 1.3 59.1 + - - -
60A GLU* 3.0 12.2 + - - +
61A VAL* 3.0 25.1 + - + +
84A ILE* 4.1 23.6 - - + -
88A TYR* 4.3 9.2 + - + -
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Residues in contact with PHE 58 (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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7A LEU* 3.7 17.0 - - + +
10A MET* 3.6 28.0 - - + -
11A ARG 5.9 0.2 - - - -
12A PHE* 3.7 31.2 - + - -
54A TYR 2.6 17.0 + - - +
55A GLY* 3.6 9.0 - - - +
57A VAL* 1.3 73.1 - - - +
59A GLU* 1.3 75.4 + - - +
61A VAL* 3.7 5.2 - - - +
62A LYS* 2.8 48.1 + - + +
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Residues in contact with GLU 59 (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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55A GLY* 2.8 26.1 + - - +
56A GLU* 2.9 12.2 + - + +
58A PHE* 1.3 90.1 - - - +
60A GLU* 1.3 70.0 + - + +
62A LYS* 3.8 20.9 + - - +
63A SER* 3.1 25.8 + - - -
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Residues in contact with GLU 60 (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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56A GLU* 3.4 16.7 - - - +
57A VAL* 3.0 11.3 + - - +
59A GLU* 1.3 78.1 - - - +
61A VAL* 1.3 67.1 + - - +
63A SER* 3.4 7.4 + - - -
64A ILE* 3.3 26.3 + - + +
80A ILE* 5.7 0.7 - - + -
83A ARG* 3.3 39.9 + - + +
84A ILE* 4.7 10.1 - - + -
87A GLN* 2.8 28.3 + - - +
88A TYR* 4.4 12.7 + - + +
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Residues in contact with VAL 61 (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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10A MET* 3.9 19.5 - - + -
12A PHE* 3.7 23.1 - - + -
31A VAL* 4.1 4.7 - - + -
33A VAL* 4.2 13.2 - - + -
57A VAL* 3.0 25.0 + - + +
58A PHE* 3.7 9.2 - - - +
60A GLU* 1.3 75.9 - - - +
62A LYS* 1.3 63.0 + - - +
64A ILE* 3.1 5.0 + - - +
65A MET* 2.9 24.0 + - + +
80A ILE* 3.9 40.6 - - + -
84A ILE* 4.4 1.8 - - + -
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Residues in contact with LYS 62 (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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12A PHE* 3.8 21.7 - - + -
58A PHE* 2.8 35.7 + - + +
59A GLU* 3.8 21.0 + - - +
61A VAL* 1.3 76.0 - - - +
63A SER* 1.3 60.6 + - - +
64A ILE 2.9 0.5 + - - -
65A MET 3.0 0.7 + - - -
66A GLU* 2.7 61.7 + - + +
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Residues in contact with SER 63 (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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59A GLU 3.1 14.5 + - - -
60A GLU* 3.4 9.2 + - - -
61A VAL 3.4 0.2 - - - -
62A LYS* 1.3 83.4 - - - +
64A ILE* 1.3 60.6 + - - +
66A GLU* 4.2 2.2 - - - -
67A GLY* 3.6 17.5 + - - -
83A ARG* 3.6 18.7 + - - -
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Residues in contact with ILE 64 (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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16A HIS* 4.2 10.0 - - - -
60A GLU 3.3 13.4 + - - +
61A VAL 3.1 7.1 + - - +
62A LYS 3.0 0.6 - - - -
63A SER* 1.3 79.1 + - - +
65A MET* 1.3 65.5 + - - +
66A GLU 3.3 0.2 - - - -
67A GLY* 3.3 11.5 + - - -
68A LYS 4.8 0.5 - - - +
76A LEU* 4.0 22.0 - - + +
79A ARG* 3.3 52.0 - - + +
80A ILE* 3.5 27.1 - - + -
83A ARG* 4.0 31.0 - - + +
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Residues in contact with MET 65 (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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12A PHE* 3.4 37.8 - - + +
14A GLY* 4.0 10.7 - - - -
16A HIS* 2.9 24.9 + - + -
29A PHE* 3.3 42.1 - - + -
31A VAL* 3.5 21.1 - - + -
61A VAL* 2.9 24.9 + - + +
62A LYS 3.9 0.7 - - - +
64A ILE* 1.3 76.4 - - - +
66A GLU* 1.3 60.6 + - - +
67A GLY 3.3 0.6 + - - +
76A LEU* 4.3 15.5 - - + -
80A ILE* 4.0 15.5 - - + -
98A ILE* 4.1 15.9 - - + -
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Residues in contact with GLU 66 (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 5.0 0.3 - - - +
12A PHE* 3.1 38.4 - - + +
13A TYR 4.1 17.6 + - - +
14A GLY* 5.4 1.1 - - - -
62A LYS* 2.7 42.4 + - + +
63A SER* 4.2 4.0 - - - -
65A MET* 1.3 74.6 - - - +
67A GLY* 1.3 60.9 + - - +
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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