Contacts of the helix formed by residues 95 - 111 (chain C) in PDB entry 1RRP
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 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C THR 4.5 3.8 + - - -
94C SER* 1.3 101.8 + - - +
96C VAL* 1.3 84.9 + - - +
97C THR 3.1 0.2 - - - -
98C TYR* 3.0 7.2 + - + +
99C LYS* 2.9 21.4 + - - +
130C LYS* 3.8 35.6 - - + +
131C VAL* 3.3 22.0 - - + +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASP* 4.5 5.8 - - - +
94C SER* 2.6 11.7 + - - +
95C ARG* 1.3 95.3 - - - +
97C THR* 1.3 62.2 + - + +
99C LYS* 2.8 26.6 + - - +
100C ASN* 2.6 33.4 - - - +
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASP* 3.8 21.6 - - + +
19C GLY 5.5 1.8 - - - +
21C THR* 3.8 13.7 - - + -
90C PHE* 3.6 10.3 - - - +
91C ASP* 3.1 40.5 + - + -
92C VAL 3.8 4.0 + - - -
94C SER* 2.6 37.7 + - - +
96C VAL* 1.3 71.3 - - + +
98C TYR* 1.3 70.5 + - - +
100C ASN* 2.9 14.9 + - - +
101C VAL* 3.1 11.6 + - - +
104C TRP* 5.4 0.9 + - - -
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Residues in contact with TYR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 3.5 31.2 - + + -
95C ARG* 3.0 10.9 + - + +
97C THR* 1.3 80.8 + - - +
99C LYS* 1.3 69.0 + - - +
101C VAL* 2.9 30.0 + - + +
102C PRO* 3.5 5.5 - - + +
119C LEU* 5.6 1.1 - - + -
131C VAL* 3.5 26.0 - - + -
135C SER* 3.7 6.3 + - - -
136C ILE* 3.4 32.3 - - + +
137C VAL* 2.6 28.6 + - - +
138C PHE* 2.9 25.1 + - + +
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Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ARG 2.9 9.7 + - - +
96C VAL* 2.8 31.7 + - - +
98C TYR* 1.3 75.7 - - - +
100C ASN* 1.3 60.5 + - - +
102C PRO* 2.9 21.8 - - - +
103C ASN* 4.5 1.4 + - - -
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Residues in contact with ASN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASP* 3.4 30.0 + - - +
96C VAL* 2.6 37.0 - - - +
97C THR 2.9 7.3 + - - +
99C LYS* 1.3 81.8 - - - +
101C VAL* 1.3 54.6 + - - +
102C PRO 3.2 0.2 - - - -
103C ASN* 2.5 59.7 + - + +
104C TRP* 3.6 6.3 + - + +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ILE* 4.6 11.3 - - + +
89C MET 5.6 0.2 - - - -
90C PHE* 3.4 37.2 - - + -
97C THR 3.1 6.3 + - - +
98C TYR* 2.9 29.5 + - + +
100C ASN* 1.3 73.7 - - - +
102C PRO* 1.3 67.4 - - + +
103C ASN 2.8 1.9 + - - -
104C TRP* 3.0 23.2 + - + +
105C HIS* 3.2 9.2 + - - +
119C LEU* 4.1 18.6 - - + -
138C PHE* 3.4 31.2 - - + -
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Residues in contact with PRO 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C TYR* 3.5 6.5 - - + +
99C LYS 2.9 27.8 - - - +
100C ASN 3.3 0.4 - - - -
101C VAL* 1.3 86.1 - - + +
103C ASN* 1.3 62.8 + - - +
105C HIS* 3.7 4.8 + - - +
106C ARG* 3.3 18.7 + - - +
138C PHE* 3.7 40.2 - - + -
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Residues in contact with ASN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LYS 4.5 1.6 + - - -
100C ASN* 2.5 56.6 + - + +
102C PRO* 1.3 69.8 - - - +
104C TRP* 1.3 68.7 + - + +
106C ARG* 2.9 47.7 + - - +
107C ASP* 3.1 10.8 + - - +
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Residues in contact with TRP 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 3.8 30.1 - - + -
17C GLY* 3.2 25.2 - - - -
18C ASP* 3.0 49.4 + - - +
67C ALA 4.3 2.5 - - - -
68C GLY 4.1 7.0 - - - -
76C ARG* 3.7 46.7 - - - -
80C TYR* 3.8 9.6 - - - -
88C ILE* 4.2 11.0 - - + -
89C MET 5.4 0.9 + - - -
97C THR 5.4 0.8 + - - -
100C ASN* 3.8 17.2 - - + +
101C VAL* 3.0 14.9 + - + +
103C ASN* 1.3 76.8 - - + +
105C HIS* 1.3 65.8 + - - +
106C ARG 2.7 1.6 + - - -
107C ASP* 2.8 24.6 + - - +
108C LEU* 2.9 16.7 + - + +
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Residues in contact with HIS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ILE* 3.7 14.4 - - + +
101C VAL 3.2 4.3 + - - +
102C PRO 3.7 4.5 - - - +
104C TRP* 1.3 78.4 - - - +
106C ARG* 1.3 60.9 + - + +
108C LEU* 3.7 4.2 + - - +
109C VAL* 2.8 53.9 + - + +
117C ILE* 4.3 8.6 - - + +
138C PHE* 3.4 29.2 - + + -
142C LYS* 3.1 48.8 + - + +
144C LEU* 3.4 28.4 - - + +
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Residues in contact with ARG 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C PRO 3.3 8.8 + - - +
103C ASN* 2.9 38.5 + - - +
104C TRP 2.7 4.6 + - - -
105C HIS* 1.3 75.1 - - + +
107C ASP* 1.3 76.1 + - - +
108C LEU 3.0 1.9 + - - -
109C VAL* 3.0 13.4 - - + +
110C ARG* 2.9 31.5 + - + +
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Residues in contact with ASP 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ARG* 4.8 9.4 - - - +
80C TYR* 3.6 33.7 + - + +
103C ASN* 3.1 11.2 + - - +
104C TRP* 2.8 22.6 + - - +
106C ARG* 1.3 84.3 + - - +
108C LEU* 1.3 63.3 + - - +
110C ARG* 3.1 47.6 + - - +
111C VAL* 3.7 2.4 + - - +
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 4.5 6.1 - - + -
16C VAL* 4.2 17.5 - - + -
80C TYR* 3.5 33.7 - - + -
86C ALA* 4.0 23.3 - - + -
88C ILE* 3.5 39.5 - - + -
104C TRP 2.9 13.4 + - - +
105C HIS 3.7 3.8 - - - +
107C ASP* 1.3 74.4 - - - +
109C VAL* 1.3 55.1 + - - +
110C ARG 2.6 15.8 + - - -
111C VAL* 3.2 3.1 + - - +
112C CYS* 3.1 32.4 + - - +
117C ILE* 4.4 16.6 - - + -
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C HIS* 2.8 46.2 - - + +
106C ARG* 3.0 20.9 - - + +
108C LEU* 1.3 74.7 - - - +
110C ARG* 1.3 59.9 + - - +
112C CYS 3.9 7.6 - - - -
113C GLU* 4.0 16.6 - - + +
114C ASN* 4.5 21.8 - - - +
117C ILE* 4.7 6.5 - - + -
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Residues in contact with ARG 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C GLY 5.9 0.2 + - - -
76C ARG 5.0 0.8 + - - -
77C ASP* 3.0 38.2 + - - -
80C TYR* 5.3 0.4 - - - -
106C ARG* 2.9 18.1 + - + +
107C ASP* 3.1 51.2 + - - +
108C LEU 2.6 6.9 + - - -
109C VAL* 1.3 77.6 - - - +
111C VAL* 1.3 67.3 + - - +
113C GLU 5.0 1.0 + - - -
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASP* 3.5 37.7 - - - +
80C TYR* 3.2 37.2 - - + +
81C ILE* 5.2 4.9 - - + +
107C ASP 4.3 2.5 - - - +
108C LEU 3.5 4.9 - - - +
110C ARG* 1.3 90.6 - - - +
112C CYS* 1.3 77.7 + - + +
113C GLU* 4.1 3.3 - - - +
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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