Contacts of the helix formed by residues 74 - 83 (chain A) in PDB entry 1RPJ
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 VAL 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A SER 4.0 7.9 - - - +
71A VAL* 3.3 29.6 + - - +
73A LEU* 1.3 76.1 - - - +
75A MET* 1.3 73.2 - - + +
78A ALA* 3.0 23.7 + - - +
94A ILE* 3.9 17.2 - - + +
95A ASP 4.2 3.1 - - - +
98A ASN* 3.6 52.5 - - + +
99A LEU* 3.8 6.0 - - - +
102A ALA* 3.9 12.6 - - + -
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Residues in contact with MET 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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49A LEU* 5.0 4.0 - - + -
71A VAL 4.9 0.4 + - - -
72A ASN 5.1 0.4 + - - -
74A VAL* 1.3 83.6 - - + +
76A PRO* 1.3 70.6 - - + +
78A ALA* 3.2 5.3 + - + +
79A ARG* 3.0 49.4 + - - +
102A ALA* 3.9 26.2 - - + +
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Residues in contact with PRO 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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49A LEU* 3.4 36.8 - - + -
52A PHE* 3.5 21.7 - - + -
53A GLU* 3.6 22.7 - - + +
56A SER* 4.8 1.4 + - - -
73A LEU* 3.2 26.7 - - + +
75A MET* 1.3 92.9 - - + +
77A VAL* 1.3 54.8 + - - +
79A ARG* 3.2 14.5 - - - +
80A ALA* 2.8 29.8 + - - +
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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
----------------------------------------------------------
52A PHE* 3.5 28.3 - - + -
65A PHE* 3.6 26.9 - - + -
73A LEU* 2.9 25.7 + - + +
74A VAL 4.0 1.1 - - - +
76A PRO* 1.3 73.8 - - - +
78A ALA* 1.3 57.8 + - - +
80A ALA* 3.2 1.5 + - - -
81A TRP* 2.9 26.3 + - - +
87A LEU* 3.4 20.2 - - + +
94A ILE* 3.9 7.2 - - + -
99A LEU* 3.7 18.4 - - + -
105A ASN 4.3 0.4 - - - +
106A VAL* 4.0 19.5 - - + -
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Residues in contact with ALA 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 18.2 + - - +
75A MET* 3.2 6.5 + - + +
77A VAL* 1.3 75.1 - - - +
79A ARG* 1.3 63.7 + - - +
81A TRP* 3.2 4.2 + - - +
82A LYS* 3.0 30.4 + - - +
99A LEU* 3.7 12.8 - - + +
102A ALA* 3.4 39.3 - - + +
104A GLY* 4.0 8.4 - - - +
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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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49A LEU* 4.9 2.4 - - - +
53A GLU* 2.4 42.5 + - - +
56A SER* 5.2 4.3 - - - +
57A ASN* 6.0 0.9 - - - -
75A MET* 3.0 45.8 + - - +
76A PRO* 3.2 24.7 - - + +
78A ALA* 1.3 75.8 - - - +
80A ALA* 1.3 62.6 + - - +
82A LYS* 3.2 14.8 + - - +
83A LYS* 3.1 35.7 + - + +
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Residues in contact with ALA 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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52A PHE* 4.0 7.9 - - + -
56A SER* 3.7 20.0 - - - +
63A ILE* 4.9 0.2 - - + -
76A PRO 2.8 18.6 + - - +
77A VAL 3.6 4.5 - - - +
79A ARG* 1.3 71.7 - - - +
81A TRP* 1.3 64.7 + - - +
83A LYS* 3.1 9.8 + - - +
84A GLY 3.2 0.2 + - - -
85A ILE* 3.0 39.7 + - + +
87A LEU* 3.9 20.4 - - + -
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Residues in contact with TRP 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 12.7 + - - +
78A ALA 3.6 6.1 - - - +
80A ALA* 1.3 75.2 - - - +
82A LYS* 1.3 77.0 + - + +
84A GLY* 3.0 14.9 + - - -
85A ILE 4.2 3.6 - - - -
87A LEU* 3.5 15.3 - - + +
103A GLY 3.3 25.8 - - - -
104A GLY* 4.0 3.4 - - - -
105A ASN* 3.4 32.6 - - + +
106A VAL* 5.2 0.4 - - - -
107A GLU* 5.1 0.9 - - - -
269A VAL* 3.4 34.4 - - + +
270A ILE* 2.7 37.0 + - + +
271A PRO* 4.4 2.0 - - + -
272A LEU* 3.4 34.1 - - + -
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Residues in contact with LYS 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 ALA* 3.0 17.9 + - - +
79A ARG* 3.3 14.7 - - - +
81A TRP* 1.3 96.1 - - + +
83A LYS* 1.3 57.4 + - + +
84A GLY* 3.2 1.1 + - - -
102A ALA 3.1 21.7 + - - -
103A GLY* 3.4 21.1 - - - +
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Residues in contact with LYS 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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56A SER* 3.1 43.5 + - - -
57A ASN* 5.1 6.2 - - - +
58A LYS 4.5 4.8 + - - -
59A ASN* 5.8 1.6 - - - +
79A ARG* 3.1 24.0 + - + +
80A ALA 3.1 6.7 + - - +
82A LYS* 1.3 76.2 - - + +
84A GLY* 1.3 59.8 + - - +
85A ILE* 3.5 16.5 - - + +
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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