Contacts of the helix formed by residues 108 - 118 (chain C) in PDB entry 4CQM
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 LEU 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B LEU* 4.4 16.4 - - + -
108B LEU* 4.0 15.5 - - + -
150B ALA* 4.1 19.7 - - + +
104C LEU* 3.4 28.5 + - + +
107C ASN* 1.3 79.7 - - - +
109C LEU* 1.3 67.5 + - - +
110C GLY 3.1 0.9 - - - -
111C SER* 3.1 14.2 + - - -
112C MET* 3.1 26.5 + - + +
150C ALA 4.5 0.4 - - - +
151C SER* 3.3 18.8 - - - +
154C GLY* 3.5 32.8 - - - +
155C LEU* 3.6 12.3 - - + +
158C PHE* 5.0 0.7 - - + -
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Residues in contact with LEU 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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97B THR* 4.7 3.1 - - + -
100B MET* 3.7 36.8 - - + -
101B VAL* 3.9 24.0 - - + -
104B LEU* 3.8 14.8 - - + -
58C ALA 4.4 11.0 - - - +
104C LEU 3.1 6.1 + - - +
105C HIS* 3.4 43.1 - - + +
108C LEU* 1.3 78.9 - - - +
110C GLY* 1.3 61.1 + - - +
112C MET* 3.2 9.4 + - + +
113C LEU* 3.0 39.0 + - + +
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Residues in contact with GLY 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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57C VAL* 3.3 30.6 - - - +
105C HIS 2.8 14.4 + - - -
106C THR 3.7 11.3 + - - -
108C LEU 3.1 1.4 - - - -
109C LEU* 1.3 77.8 - - - +
111C SER* 1.3 58.7 + - - +
113C LEU* 3.5 1.9 + - - +
114C THR* 3.2 29.9 + - - +
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Residues in contact with SER 111 (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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82C ASN* 3.6 26.5 + - - +
84C ALA 5.2 3.6 + - - -
106C THR 4.3 2.6 + - - -
107C ASN 3.6 13.2 + - - -
108C LEU 3.1 9.6 + - - -
110C GLY* 1.3 75.1 - - - +
112C MET* 1.3 62.9 + - - +
114C THR* 3.0 18.7 + - - -
115C CYS* 3.2 21.0 + - - -
132C ASN* 4.3 8.4 - - - +
152C LYS* 5.6 0.9 + - - -
155C LEU* 3.7 21.5 - - - +
158C PHE* 4.5 2.2 - - - -
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Residues in contact with MET 112 (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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92B LEU* 3.9 11.5 - - + +
100B MET* 3.6 27.4 - - + +
104B LEU* 4.1 18.8 - - + -
147B VAL* 4.0 29.4 - - + -
150B ALA* 3.8 17.9 - - + -
108C LEU* 3.1 21.9 + - + +
109C LEU* 3.2 16.6 + - - +
111C SER* 1.3 77.7 - - - +
113C LEU* 1.3 56.6 + - - +
116C LYS* 3.3 25.6 + - - +
158C PHE* 3.5 43.9 - - + -
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Residues in contact with LEU 113 (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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97B THR* 3.6 27.6 - - + +
100B MET* 3.7 21.8 - - + -
57C VAL 3.8 17.9 - - - +
58C ALA 4.7 2.9 - - - +
59C LYS 4.5 0.4 - - - -
60C GLU* 3.8 29.8 - - + +
63C VAL* 3.7 17.7 - - + +
109C LEU* 3.0 31.1 + - + +
110C GLY 4.0 3.6 - - - +
111C SER 3.3 0.2 - - - -
112C MET* 1.3 76.5 - - - +
114C THR* 1.3 60.4 + - - +
115C CYS 3.3 0.2 - - - -
116C LYS* 3.3 12.7 + - + +
117C ALA* 2.9 30.0 + - - +
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Residues in contact with THR 114 (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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8C PHE* 3.6 37.9 - - + -
57C VAL* 4.2 8.5 - - + -
63C VAL* 4.0 8.1 - - + -
67C PHE* 3.1 26.1 - - + -
80C LEU* 4.0 3.1 - - - -
82C ASN* 2.3 34.5 + - - +
110C GLY 3.2 13.7 + - - +
111C SER 3.0 8.7 + - - -
113C LEU* 1.3 76.2 - - - +
115C CYS* 1.3 59.8 + - - +
117C ALA 3.4 0.3 + - - -
118C ALA* 2.9 24.8 + - - +
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Residues in contact with CYS 115 (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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92B LEU* 4.3 1.3 - - + -
80C LEU* 4.0 5.8 - - - -
82C ASN* 3.7 11.2 - - - -
111C SER 3.2 20.9 + - - +
112C MET 4.2 3.1 - - - +
114C THR* 1.3 82.4 + - - +
116C LYS* 1.3 61.8 + - - +
118C ALA* 3.1 3.2 + - - +
119C MET* 3.0 31.2 + - - +
130C ILE* 3.7 33.2 - - + -
132C ASN* 3.7 13.2 - - - -
158C PHE* 4.3 3.4 - - + -
162C LEU* 3.7 26.0 - - + -
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Residues in contact with LYS 116 (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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92B LEU* 3.4 38.3 - - + +
93B VAL* 3.9 23.1 + - - +
95B THR 2.6 29.1 + - - +
96B LYS* 4.1 7.1 - - - +
97B THR* 4.2 13.1 + - - +
100B MET* 4.5 11.6 - - - -
112C MET 3.3 16.7 + - - +
113C LEU* 3.3 12.7 + - + +
115C CYS* 1.3 79.9 - - - +
117C ALA* 1.3 61.5 + - + +
119C MET* 3.2 20.0 + - - +
120C ARG 4.4 1.2 + - - -
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Residues in contact with ALA 117 (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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63C VAL* 4.1 7.9 - - + +
64C GLN* 5.2 6.1 - - + -
67C PHE* 3.6 37.2 - - + +
113C LEU 2.9 16.3 + - - +
114C THR 3.9 0.2 - - - +
116C LYS* 1.3 79.1 - - - +
118C ALA* 1.3 59.7 + - - +
119C MET 3.1 1.5 + - - -
120C ARG* 4.5 3.5 + - - +
121C THR* 3.7 11.4 + - - +
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Residues in contact with ALA 118 (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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67C PHE* 3.5 17.7 - - + -
77C VAL* 5.0 1.8 - - + -
80C LEU* 3.7 17.7 - - + -
114C THR 2.9 18.1 + - - +
115C CYS* 3.1 6.4 + - - +
117C ALA* 1.3 75.4 - - - +
119C MET* 1.3 62.5 + - - +
121C THR* 3.2 14.1 - - + +
122C MET* 3.2 38.7 - - + +
130C ILE* 5.1 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