Contacts of the helix formed by residues 113 - 125 (chain N) 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 SER 113 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369 C 4.7 0.6 + - - -
479 A 3.3 11.6 + - - -
489 C 3.4 17.3 - - - -
78N MET* 4.2 0.2 - - - -
108N SER 4.7 1.3 - - - -
110N THR* 2.7 46.7 + - - +
111N PRO 3.2 1.5 + - - -
112N GLY* 1.3 81.7 - - - +
114N LYS* 1.3 61.9 + - - +
115N VAL* 3.2 16.8 - - - -
116N PHE* 3.0 5.7 + - - +
117N ALA* 2.9 22.5 + - - +
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Residues in contact with LYS 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489 C 2.8 41.3 + - - +
499 G 3.5 16.6 + - - +
38N LYS* 3.9 25.1 - - + +
39N SER 5.2 5.5 + - - -
40N ASN 5.7 1.8 + - - -
43N VAL* 4.6 8.7 - - + +
76N GLY* 2.9 29.5 + - - +
77N ASN 3.5 20.2 - - - +
78N MET* 3.7 17.2 - - + +
81N ALA* 3.8 10.4 - - + +
112N GLY 3.8 0.2 + - - -
113N SER* 1.3 71.8 - - - +
115N VAL* 1.3 52.9 + - - +
117N ALA* 3.0 9.1 + - - +
118N ILE* 2.7 38.8 + - - +
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Residues in contact with VAL 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489 C 5.8 0.2 - - - +
36N ALA* 4.3 15.0 - - + +
38N LYS* 4.4 13.0 - - + -
102N LEU* 4.1 8.7 - - - +
104N ILE* 4.1 26.7 - - + -
107N ASN* 3.7 34.8 - - + +
108N SER 4.5 12.8 - - - +
113N SER* 4.4 13.7 - - - -
114N LYS* 1.3 76.7 - - - +
116N PHE* 1.3 73.5 + - + +
118N ILE* 3.4 14.2 - - + +
119N GLN* 3.2 17.8 + - - +
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Residues in contact with PHE 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24130 A 3.5 47.6 - + - -
102N LEU* 3.7 19.7 - - + -
104N ILE* 4.7 1.3 - - + -
109N PRO* 3.7 23.3 - - + -
110N THR 3.1 28.3 - - - -
112N GLY 4.1 1.6 - - - -
113N SER* 3.0 10.6 + - - +
115N VAL* 1.3 85.5 - - + +
117N ALA* 1.3 68.3 + - - +
119N GLN* 2.9 14.6 + - - +
120N GLU* 2.9 20.3 + - - +
135N VAL* 3.4 34.5 - - + +
136N LEU* 3.5 23.4 - - + +
137N ALA 5.6 0.2 - - - +
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Residues in contact with ALA 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N MET* 4.0 23.3 - - + -
81N ALA* 4.5 0.4 - - + -
82N TYR* 3.8 29.7 - - + +
112N GLY 5.3 0.2 - - - -
113N SER 2.9 12.7 + - - +
114N LYS* 3.1 15.9 - - - +
116N PHE* 1.3 76.2 - - - +
118N ILE* 1.3 66.1 + - - +
120N GLU* 3.1 12.2 + - - +
121N GLY 3.0 15.1 + - - -
136N LEU* 5.5 0.7 - - - -
137N ALA* 6.5 0.2 - - - -
142N THR* 5.2 2.9 - - + +
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Residues in contact with ILE 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N LEU* 4.3 11.0 - - + -
36N ALA* 3.4 35.0 - - + -
37N ARG 4.3 4.5 - - - +
38N LYS* 6.1 0.7 - - + -
43N VAL* 3.6 25.8 - - + -
44N ARG 4.0 9.0 - - - +
45N ALA* 4.0 13.5 - - + -
81N ALA* 3.9 21.3 + - + +
85N GLY* 3.8 18.8 - - - +
114N LYS* 2.7 22.4 + - + +
115N VAL* 3.4 11.4 - - + +
117N ALA* 1.3 71.5 - - - +
119N GLN* 1.3 67.2 + - - +
121N GLY* 2.9 14.0 + - - -
122N ALA* 3.0 10.6 + - - +
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Residues in contact with GLN 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24130 A 4.9 5.8 + - - -
24140 A 5.7 0.8 + - - -
34N LEU* 4.2 12.3 - - + -
102N LEU* 3.4 36.6 - - + +
115N VAL 3.2 7.4 + - - +
116N PHE* 2.9 24.3 + - - +
118N ILE* 1.3 79.3 - - - +
120N GLU* 1.3 54.8 + - - +
122N ALA* 3.1 3.3 + - - +
123N ILE* 2.8 46.7 + - + +
129N ILE* 3.8 9.9 - - + +
130N PRO 3.3 24.4 + - - -
131N HIS* 3.5 20.4 - - - +
132N ASN 4.6 1.2 + - - -
135N VAL* 5.1 0.7 - - - +
136N LEU* 3.8 17.2 - - - +
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Residues in contact with GLU 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N TYR* 3.6 16.3 - - + -
116N PHE 2.9 12.7 + - - +
117N ALA* 3.5 10.3 - - - +
119N GLN* 1.3 74.3 - - - +
121N GLY* 1.3 52.5 + - - +
123N ILE* 3.0 11.1 + - - +
124N ASP* 2.6 54.7 + - - +
136N LEU* 4.0 27.7 - - + +
137N ALA 4.6 5.8 - - - +
139N TRP* 4.4 11.2 - - - -
142N THR* 3.6 20.8 + - - +
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Residues in contact with GLY 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N TYR* 3.5 28.8 - - - -
86N LEU* 3.0 32.6 - - - +
117N ALA 3.0 6.7 + - - -
118N ILE 2.9 7.7 + - - -
120N GLU* 1.3 77.1 - - - +
122N ALA* 1.3 56.2 + - - +
124N ASP* 3.4 0.5 + - - +
125N ALA 2.9 21.0 + - - -
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Residues in contact with ALA 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N LEU* 3.6 31.0 - - + -
85N GLY* 3.5 18.5 + - - +
89N GLY* 4.1 9.9 - - - -
118N ILE 3.0 8.5 + - - +
119N GLN 3.6 7.0 - - - +
121N GLY* 1.3 73.9 - - - +
123N ILE* 1.3 64.9 + - - +
124N ASP 3.2 0.2 - - - -
125N ALA* 3.3 7.3 + - - +
127N LEU* 3.0 30.6 + - + +
129N ILE* 3.7 7.0 - - + -
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Residues in contact with ILE 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119N GLN* 2.8 41.0 + - + +
120N GLU* 3.4 9.2 - - - +
122N ALA* 1.3 76.3 - - - +
124N ASP* 1.3 66.6 + - - +
126N GLY* 3.1 12.0 + - - -
127N LEU 3.4 18.2 + - - +
128N ASP* 5.9 0.2 - - - -
129N ILE* 3.8 19.1 - - + +
131N HIS* 3.3 56.5 - - + +
136N LEU* 5.4 2.7 - - + -
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Residues in contact with ASP 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N TYR* 2.6 30.8 + - - +
86N LEU* 4.4 5.1 - - + +
120N GLU* 2.6 39.1 + - - +
121N GLY 3.5 5.2 - - - +
123N ILE* 1.3 73.8 - - - +
125N ALA* 1.3 52.9 + - - +
126N GLY* 2.7 17.7 + - - -
139N TRP* 5.3 1.4 - - - -
176N ARG* 3.3 18.0 + - - +
180N LEU* 6.2 0.7 - - + -
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Residues in contact with ALA 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N LEU* 3.4 17.5 - - + +
89N GLY* 3.2 38.6 - - - -
90N LEU* 3.3 17.3 - - + +
93N GLN* 3.5 19.9 - - - +
121N GLY 2.9 14.8 + - - +
122N ALA 3.6 2.7 - - - +
123N ILE 3.2 0.8 - - - -
124N ASP* 1.3 74.9 - - - +
126N GLY* 1.3 57.1 + - - +
127N LEU 3.4 0.9 - - - -
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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