Contacts of the helix formed by residues 69 - 79 (chain A) in PDB entry 4RTP
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 ARG 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ILE* 2.8 43.5 + - + +
68A MET* 1.3 85.8 - - + +
70A THR* 1.3 57.6 + - - +
71A ASP 3.6 1.3 - - - -
72A GLU* 2.9 50.8 + - + +
73A TYR* 2.9 29.3 + - - +
103A ASP* 5.5 1.2 + - - -
104A PRO* 6.2 0.4 - - - +
105A PHE* 3.6 33.2 - - + +
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Residues in contact with THR 70 (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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66A VAL* 2.6 25.1 + - + +
67A LYS 3.5 8.5 + - - -
68A MET 3.7 1.0 - - - -
69A ARG* 1.3 72.7 - - - +
71A ASP* 1.3 60.6 + - - +
73A TYR* 3.1 4.6 + - - +
74A VAL* 2.9 39.3 + - + +
148A LEU 4.9 1.6 - - - +
149A TYR* 3.6 33.4 - - + -
152A ALA* 3.2 25.8 - - + +
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG 3.6 0.2 - - - -
70A THR* 1.3 82.1 - - - +
72A GLU* 1.3 62.9 + - - +
74A VAL* 4.1 1.0 - - - +
75A GLN* 3.2 25.5 + - - +
149A TYR* 3.0 36.3 + - - +
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Residues in contact with GLU 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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69A ARG* 2.9 56.3 + - + +
70A THR 3.3 0.6 - - - -
71A ASP* 1.3 79.0 - - - +
73A TYR* 1.3 62.5 + - - +
75A GLN* 3.7 4.2 + - - +
76A ALA* 3.3 17.7 + - - +
105A PHE* 3.6 21.1 - - + -
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Residues in contact with TYR 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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7A PHE* 5.5 0.2 - - - -
62A LEU* 3.2 14.2 - - + +
65A ILE* 3.8 21.5 - - + +
66A VAL* 3.8 22.4 - - + -
69A ARG 2.9 20.0 + - - +
70A THR* 3.6 4.3 - - - +
72A GLU* 1.3 75.1 - - - +
74A VAL* 1.3 63.0 + - + +
76A ALA* 3.1 3.1 + - - +
77A ALA* 2.8 45.6 + - + +
105A PHE* 3.7 12.1 - + + -
108A ALA* 2.7 43.5 + - + -
109A VAL* 3.4 18.7 - - + -
112A LEU* 3.3 22.5 - - + +
148A LEU* 4.1 18.6 - - + -
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Residues in contact with VAL 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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66A VAL* 6.4 0.4 - - + -
70A THR* 2.9 25.4 + - + +
71A ASP 4.1 1.3 - - - +
73A TYR* 1.3 81.7 - - + +
75A GLN* 1.3 57.7 + - - +
77A ALA* 4.6 2.5 - - - +
78A ARG* 3.0 51.3 + - - +
143A PHE* 3.7 9.5 - - + -
145A GLU* 4.1 9.0 - - + -
148A LEU* 4.2 24.5 - - + -
149A TYR* 3.6 43.1 - - + +
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Residues in contact with GLN 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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71A ASP 3.2 16.0 + - - +
72A GLU* 3.9 5.2 - - - +
74A VAL* 1.3 80.7 - - - +
76A ALA* 1.3 62.1 + - - +
78A ARG* 3.7 26.4 + - - +
79A GLU* 3.8 17.7 + - - +
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Residues in contact with ALA 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 GLU 3.3 13.5 + - - +
73A TYR 3.1 4.7 + - - +
75A GLN* 1.3 76.0 - - - +
77A ALA* 1.3 65.0 + - - +
79A GLU* 3.5 23.3 - - - +
80A LEU* 3.6 10.2 - - - +
105A PHE* 3.9 23.3 - - + -
106A ARG* 5.5 3.3 + - - +
109A VAL* 3.9 9.7 - - + +
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Residues in contact with ALA 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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73A TYR* 2.8 46.0 + - + +
74A VAL 4.1 1.3 - - - +
76A ALA* 1.3 71.3 - - - +
78A ARG* 1.3 64.2 + - - +
79A GLU 3.1 0.7 - - - -
80A LEU* 3.1 14.4 + - - +
81A PHE* 3.3 17.4 - - + -
109A VAL* 3.8 19.0 - - + +
112A LEU* 4.3 7.2 - - + -
143A PHE* 3.8 15.7 - - + -
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Residues in contact with ARG 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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74A VAL* 3.0 30.5 + - - +
75A GLN* 3.9 22.7 + - - +
76A ALA 3.3 0.4 - - - -
77A ALA* 1.3 74.6 - - - +
79A GLU* 1.3 63.1 + - + +
80A LEU 3.2 0.2 - - - -
81A PHE* 3.3 19.7 + - + +
82A VAL* 4.2 4.9 - - - +
143A PHE* 3.6 25.3 - - + -
145A GLU* 3.0 41.4 + - - -
149A TYR* 5.1 1.4 + - - -
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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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75A GLN 3.8 14.6 - - - +
76A ALA* 3.5 15.3 + - - +
77A ALA 3.1 0.2 - - - -
78A ARG* 1.3 79.0 - - + +
80A LEU* 1.3 66.2 + - + +
81A PHE 3.3 0.4 + - - -
82A VAL* 3.7 20.7 - - - +
85A THR* 4.6 2.4 - - - +
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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