Contacts of the strand formed by residues 113 - 123 (chain M) in PDB entry 3CME
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 113 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111M ASN 4.5 0.8 + - - +
112M LEU* 1.3 84.1 - - - +
114M VAL* 1.3 67.2 + - - +
115M LEU 3.3 1.0 + - - -
133M LEU* 4.3 1.8 - - - -
134M ILE 3.0 26.5 + - - +
136M PRO* 3.6 27.2 - - + +
150M ILE* 2.9 44.1 + - + +
151M CYS* 3.1 12.9 + - - +
152M ALA 2.6 30.6 + - - -
153M ASP* 4.4 5.5 + - - +
155M GLN* 3.5 18.1 - - - +
156M ALA* 3.7 26.3 - - - +
157M ASP 4.8 1.6 - - - +
158M ARG* 4.3 3.4 - - - -
8818M CL 3.5 10.5 - - + -
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Residues in contact with VAL 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M GLU* 3.7 26.7 - - - +
106M SER* 3.5 30.9 + - - -
113M ARG* 1.3 71.4 - - - +
115M LEU* 1.3 62.9 + - - +
116M ASN 3.8 9.6 - - - +
131M VAL* 3.9 20.9 - - + -
132M ILE 3.7 4.9 - - - -
133M LEU* 4.4 4.8 - - + +
150M ILE* 3.6 1.0 - - - +
158M ARG* 2.8 29.3 + - - +
159M VAL* 3.7 14.1 - - + -
164M THR* 3.7 17.5 - - - +
8818M CL 2.9 12.2 - - + +
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Residues in contact with LEU 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4320 G 5.1 7.0 + - - +
52M GLN 3.5 25.1 - - - +
53M GLY* 3.9 13.9 - - - -
113M ARG 3.3 0.6 + - - -
114M VAL* 1.3 75.9 - - - +
116M ASN* 1.3 81.7 + - + +
132M ILE* 2.8 30.0 + - + +
134M ILE* 3.8 28.5 - - + -
147M LEU* 5.0 11.4 - - + -
149M TRP* 3.7 33.1 - - + -
150M ILE* 4.0 6.3 - - + -
158M ARG* 4.4 7.2 + - - +
164M THR* 5.3 3.1 + - - +
165M GLY 5.5 1.2 + - - -
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Residues in contact with ASN 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4310 G 3.3 40.8 + - - +
4320 G 3.7 10.5 + - - -
52M GLN* 3.3 32.0 + - + +
98M GLN* 5.4 0.5 + - - -
102M GLU* 4.3 5.3 - - - +
114M VAL* 3.7 5.9 - - - +
115M LEU* 1.3 95.9 + - + +
117M SER* 1.3 67.9 + - - +
131M VAL* 3.6 2.3 - - - +
132M ILE* 2.6 36.2 + - + +
164M THR* 5.1 6.2 - - - +
165M GLY 5.1 3.3 + - - -
166M ALA* 5.3 0.9 + - - +
169M ARG* 4.8 8.5 + - - -
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Residues in contact with SER 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M GLN* 3.2 19.2 + - - +
98M GLN* 2.6 33.0 + - - +
102M GLU* 2.5 30.0 + - - +
116M ASN* 1.3 84.8 + - - +
118M TYR* 1.3 63.6 + - - +
129M HIS* 5.1 3.4 - - - -
130M GLU 3.1 15.9 - - - -
131M VAL* 3.6 19.7 - - - -
132M ILE* 4.5 0.4 - - - +
169M ARG* 5.9 0.3 + - - -
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Residues in contact with TYR 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M PRO* 3.2 26.2 - - + +
44M THR 3.5 1.0 + - - -
45M ARG* 3.5 31.1 + - + +
48M LYS* 3.7 29.8 - - + -
49M ALA* 4.1 20.2 - - + -
52M GLN* 3.3 19.1 - - - +
62M VAL* 4.4 1.3 - - + +
98M GLN* 4.2 3.6 - - - +
117M SER* 1.3 77.7 - - - +
119M SER* 1.3 71.5 + - - +
120M VAL* 3.5 4.3 - - + -
129M HIS* 3.0 8.8 - - - -
130M GLU* 2.7 81.0 + - + +
132M ILE* 4.6 10.1 - - + -
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Residues in contact with SER 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3810 G 4.8 18.1 + - - -
45M ARG* 2.6 36.2 + - - +
98M GLN* 5.2 1.6 + - - +
118M TYR* 1.3 74.8 - - - +
120M VAL* 1.3 61.5 + - - +
121M GLY* 3.4 15.3 + - - -
128M TRP 3.6 8.2 + - - -
129M HIS* 3.8 20.9 + - - -
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Residues in contact with VAL 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M TRP* 3.7 18.8 - - + -
24M GLN* 3.1 15.9 - - - +
31M TRP* 3.3 26.8 - - + -
44M THR* 4.7 2.9 - - - -
45M ARG* 4.5 5.4 - - - -
64M ARG* 4.5 2.0 - - + -
118M TYR* 3.5 12.8 - - + -
119M SER* 1.3 78.4 - - - +
121M GLY* 1.3 56.8 + - - +
128M TRP* 2.7 41.3 + - + +
129M HIS* 3.8 3.4 - - - +
130M GLU* 3.2 39.5 - - + +
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Residues in contact with GLY 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M TRP* 3.9 7.5 - - - -
15M PRO* 6.1 3.4 - - - -
24M GLN* 4.2 7.6 - - - -
28M GLN* 4.8 0.4 - - - -
119M SER* 3.4 11.1 + - - -
120M VAL* 1.3 79.0 - - - +
122M GLN* 1.3 65.3 + - - +
127M LYS* 3.9 1.7 - - - +
128M TRP* 3.1 28.0 + - - +
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Residues in contact with GLN 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4040 G 3.5 16.5 + - - -
21310 G 4.9 2.8 + - - -
21320 C 5.7 1.6 - - - +
28M GLN* 3.7 14.1 + - - +
69M LYS* 3.1 29.1 - - - +
121M GLY* 1.3 76.8 - - - +
123M ASP* 1.3 59.5 + - - +
126M GLN 3.0 19.7 - - - +
127M LYS* 3.0 36.9 - - + +
128M TRP* 3.9 7.6 - - - -
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Residues in contact with ASP 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21320 C 4.0 15.0 - - - +
28M GLN* 3.9 5.8 - - - +
32M ARG* 3.4 31.1 + - - +
69M LYS* 3.2 18.4 + - - +
122M GLN* 1.3 79.5 + - - +
124M GLY* 1.3 64.4 + - - +
125M ARG* 2.7 20.5 + - - +
126M GLN* 2.8 34.0 + - - +
128M TRP* 3.0 24.9 - - + -
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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