Contacts of the helix formed by residues 120 - 130 (chain R) in PDB entry 5C3I
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 MET 120 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107R THR* 4.8 0.2 - - - +
116R ARG* 3.8 19.3 - - - +
118R THR* 4.0 8.1 - - - +
119R ILE* 1.3 82.9 - - - +
121R PRO* 1.4 76.2 - - + +
122R LYS* 3.1 12.6 - - + +
123R ASP* 2.8 42.0 + - - +
124R ILE* 3.7 3.6 + - - +
47S SER* 3.8 16.8 - - - +
49S LEU* 4.9 8.5 - - + -
50S ILE* 3.5 8.2 - - - +
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Residues in contact with PRO 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120R MET* 1.4 101.7 - - + +
122R LYS* 1.3 60.4 + - - +
124R ILE* 3.4 6.8 + - + +
125R GLN* 3.2 29.5 + - - +
47S SER* 4.3 0.9 - - - +
49S LEU* 3.7 37.7 - - + -
50S ILE* 3.8 15.9 - - + -
53S GLU* 4.0 29.1 - - + +
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Residues in contact with LYS 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Q ALA* 4.1 10.0 - - + +
49Q GLU* 6.0 4.0 - - + -
87Q ALA 4.6 6.7 + - - -
88Q ASP* 3.7 29.7 + - - +
90Q VAL 5.7 1.2 + - - -
91Q GLY* 5.7 2.4 - - - -
92Q VAL* 4.0 17.2 + - - +
116R ARG* 5.2 6.1 - - - +
120R MET* 3.0 11.0 + - + +
121R PRO* 1.3 79.7 - - - +
123R ASP* 1.3 72.5 + - - +
125R GLN* 3.2 18.0 + - - +
126R LEU* 2.8 54.0 + - - +
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Residues in contact with ASP 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92Q VAL* 4.8 0.9 - - - +
107R THR* 3.3 26.1 + - + -
110R CYS* 3.6 27.4 - - + +
111R ALA* 4.3 1.2 - - - +
116R ARG* 2.9 35.9 + - - -
119R ILE* 3.8 3.3 - - - -
120R MET* 2.8 32.9 + - - +
122R LYS* 1.3 83.8 - - - +
124R ILE* 1.3 58.4 - - - +
126R LEU* 3.5 9.9 + - - +
127R ALA* 3.0 28.4 + - - +
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Residues in contact with ILE 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R LEU* 4.0 17.4 - - + +
104R PHE* 4.8 7.0 - - + -
107R THR* 4.2 19.5 - - + +
120R MET 4.4 6.1 - - - +
121R PRO 3.4 6.4 + - - +
123R ASP* 1.3 75.4 - - - +
125R GLN* 1.3 59.1 + - + +
127R ALA* 3.2 3.8 + - - +
128R ARG* 2.8 29.4 + - + +
50S ILE* 3.9 29.8 - - + -
53S GLU* 4.1 19.3 - - + -
54S THR* 3.9 22.4 - - + +
57S VAL* 3.8 29.6 - - + -
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Residues in contact with GLN 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q ALA* 3.3 29.8 - - + +
49Q GLU* 4.4 13.5 + - - +
121R PRO* 3.2 12.2 + - - +
122R LYS* 3.2 25.4 + - - +
124R ILE* 1.3 78.3 - - + +
126R LEU* 1.3 59.0 + - - +
128R ARG* 3.4 18.5 + - - +
129R ARG* 3.0 31.8 + - - +
53S GLU* 2.8 28.7 + - + +
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Residues in contact with LEU 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q VAL* 4.9 1.8 - - + -
48Q ALA* 3.6 18.8 - - + -
92Q VAL* 3.6 21.5 - - + +
93Q THR* 3.8 26.2 - - - +
94Q VAL* 4.0 24.8 - - + +
112Q TYR* 4.1 11.4 - - + -
110R CYS* 3.8 20.6 - - - -
122R LYS* 2.8 35.0 + - - +
123R ASP* 3.6 7.6 - - - +
124R ILE 3.2 0.2 - - - -
125R GLN* 1.3 73.9 - - - +
127R ALA* 1.3 64.6 + - - +
129R ARG* 3.0 15.9 + - + +
130R ILE* 3.2 14.6 + - - +
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Residues in contact with ALA 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Q TYR* 3.2 12.9 + - - +
103R LEU* 3.7 21.8 - - + +
106R ASP* 3.5 28.7 - - + -
107R THR* 4.4 0.9 - - - +
123R ASP 3.0 17.0 + - - +
124R ILE* 3.2 6.7 + - - +
126R LEU* 1.3 75.0 - - - +
128R ARG* 1.3 59.4 + - - +
130R ILE* 3.3 15.9 - - - +
131R ARG* 3.3 16.6 - - - -
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Residues in contact with ARG 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Q GLU* 4.8 6.7 + - - -
99R TYR* 3.6 19.7 - - - +
103R LEU* 3.9 8.0 - - + +
124R ILE* 2.8 17.4 + - - +
125R GLN* 3.5 18.1 - - - +
126R LEU 3.1 0.2 - - - -
127R ALA* 1.3 76.3 - - - +
129R ARG* 1.3 70.1 + - + +
130R ILE 3.5 0.2 - - - -
131R ARG* 3.6 4.7 + - - +
132R GLY 3.4 13.5 + - - -
133R GLU* 3.4 56.9 + - - +
57S VAL* 3.7 38.6 - - + +
60S VAL* 6.0 7.2 - - - +
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Residues in contact with ARG 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Q ILE* 5.8 0.8 - - - +
45Q VAL* 3.7 23.1 - - + +
47Q SER 4.5 3.0 + - - -
48Q ALA* 5.1 10.0 + - - +
50Q SER 5.0 0.4 - - - -
51Q GLU* 3.8 30.5 - - - +
54Q ASP* 2.7 39.0 + - - -
94Q VAL* 4.4 13.2 - - + -
96Q LEU* 4.2 7.6 - - + +
108Q ARG* 3.6 27.5 + - - +
125R GLN 3.0 23.1 - - - +
126R LEU* 3.0 9.2 + - - +
128R ARG* 1.3 81.9 - - - +
130R ILE* 1.3 56.7 + - - +
131R ARG 3.0 4.3 - - - -
132R GLY* 2.8 24.0 + - - +
133R GLU 4.1 17.9 + - - +
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Residues in contact with ILE 130 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Q VAL* 3.8 17.0 - - + +
96Q LEU* 4.0 12.5 - - + +
108Q ARG* 4.4 9.9 - - - +
110Q GLY* 3.4 40.5 - - - +
111Q TYR 3.6 4.5 - - - +
112Q TYR* 3.5 44.4 - - + +
145Q ARG* 3.7 19.7 - - + +
147Q THR* 3.7 8.1 + - - -
106R ASP* 3.7 9.6 - - - +
126R LEU 3.2 5.9 + - - +
127R ALA 3.3 19.3 - - - +
129R ARG* 1.3 76.7 - - - +
131R ARG* 1.3 61.8 + - + +
132R GLY 3.5 0.2 - - - -
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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