Contacts of the helix formed by residues 106 - 119 (chain C) in PDB entry 6CM1
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 LYS 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C ASP* 2.7 28.8 + - - +
103C ASP* 3.0 30.2 + - - +
104C PHE 3.3 0.2 - - - -
105C GLN* 1.3 77.6 - - + +
107C LYS* 1.3 75.6 + - + +
108C TRP 3.4 2.5 - - - -
109C GLN* 3.0 20.8 + - - +
110C GLU* 3.0 15.3 + - + +
316C PX4 5.1 23.1 - - - -
323C PX4 5.7 5.7 - - - -
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Residues in contact with LYS 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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100C TYR* 5.5 7.2 - - + +
103C ASP* 2.9 51.8 + - + +
104C PHE* 4.5 2.2 + - - -
106C LYS* 1.3 81.5 - - + +
108C TRP* 1.4 56.6 + - - +
110C GLU* 3.6 30.9 + - - +
111C GLU* 3.2 31.3 + - - +
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Residues in contact with TRP 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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195B ARG* 3.1 49.0 + - + +
196B LEU* 3.8 23.6 - - + -
198B ALA* 5.3 3.1 - - + +
199B ARG* 3.5 55.5 - - + +
106C LYS 3.4 1.0 - - - -
107C LYS* 1.4 73.9 - - - +
109C GLN* 1.4 82.7 + - - +
111C GLU* 3.2 16.3 + - - +
112C MET* 2.8 60.0 + - + -
316C PX4 3.9 12.3 - - + -
330C PX4 6.5 0.7 - - + -
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Residues in contact with GLN 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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199B ARG* 5.4 3.7 + - - +
105C GLN 4.1 17.7 - - - +
106C LYS 3.0 8.5 + - - +
108C TRP* 1.4 87.9 - - + +
110C GLU* 1.3 60.8 + - - +
112C MET* 3.3 10.3 + - - +
113C GLU* 3.1 32.8 + - - +
316C PX4 3.1 88.1 + - - +
323C PX4 5.6 0.5 - - - +
330C PX4 5.0 12.8 + - - -
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Residues in contact with GLU 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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106C LYS* 3.0 14.7 + - + +
107C LYS* 3.6 37.3 + - - +
109C GLN* 1.3 76.3 - - - +
111C GLU* 1.4 62.5 + - + +
113C GLU* 3.3 15.1 - - - +
114C LEU* 2.9 25.7 + - + +
316C PX4 5.0 3.6 - - - -
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Residues in contact with GLU 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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195B ARG* 3.9 23.8 + - - +
107C LYS 3.2 17.3 + - - +
108C TRP* 3.2 18.2 + - + +
110C GLU* 1.4 77.8 - - - +
112C MET* 1.3 60.4 + - - +
114C LEU* 3.5 20.6 - - + +
115C TYR* 2.8 31.2 + - - +
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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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188B TYR* 5.3 1.6 - - - -
192B LEU* 3.7 31.4 - - + +
195B ARG* 3.5 29.8 - - + +
196B LEU* 5.9 0.2 - - + -
108C TRP* 2.8 49.9 + - + +
109C GLN* 3.3 17.2 + - - +
111C GLU* 1.3 73.1 - - - +
113C GLU* 1.4 54.5 + - - +
115C TYR* 3.5 11.1 + - - -
116C ARG* 2.9 30.5 + - - +
320C PX4 3.9 28.3 - - + -
330C PX4 6.1 1.1 - - - +
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Residues in contact with GLU 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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109C GLN* 3.1 14.4 + - - +
110C GLU* 3.3 18.6 - - + +
112C MET* 1.4 74.0 - - - +
114C LEU* 1.4 53.7 + - - +
116C ARG* 3.1 7.6 + - - +
117C GLN* 2.8 32.5 + - - +
316C PX4 3.8 26.6 - - - -
330C PX4 3.5 37.8 - - - -
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Residues in contact with LEU 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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195B ARG* 6.0 3.6 - - - +
110C GLU* 2.9 17.5 + - + +
111C GLU* 3.2 25.5 + - + +
113C GLU* 1.4 69.4 - - - +
115C TYR* 1.4 68.0 + - - +
117C GLN* 3.4 10.5 + - + +
118C LYS* 3.4 44.2 + - + +
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Residues in contact with TYR 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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187B PRO 3.8 9.0 + - - -
188B TYR* 3.5 48.0 - + - -
191B GLU* 2.5 50.8 + - + +
192B LEU* 4.5 4.7 - - + -
195B ARG* 3.4 42.4 - - - +
111C GLU 2.8 19.0 + - - +
112C MET* 3.7 12.1 - - - +
114C LEU* 1.4 73.0 - - - +
116C ARG* 1.4 58.8 + - - +
118C LYS* 3.4 14.7 + - + +
119C VAL* 3.7 10.9 + - - +
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Residues in contact with ARG 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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188B TYR* 3.4 25.8 + - - +
112C MET* 2.9 20.0 + - - +
113C GLU* 3.1 8.7 + - - +
115C TYR* 1.4 72.8 - - - +
117C GLN* 1.3 59.4 + - - +
119C VAL* 3.3 23.7 - - - +
120C GLU* 2.7 35.7 + - - +
123C LEU* 3.9 17.4 - - - +
320C PX4 2.6 58.1 + - + +
330C PX4 4.7 11.6 - - - -
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Residues in contact with GLN 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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113C GLU 2.8 19.3 + - - +
114C LEU* 3.6 11.0 - - + +
116C ARG* 1.3 69.3 - - - +
118C LYS* 1.3 68.1 + - + +
120C GLU* 3.1 40.3 + - - +
121C PRO* 4.5 2.3 - - - +
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Residues in contact with LYS 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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114C LEU* 3.4 35.9 - - + +
115C TYR* 3.4 10.7 + - + +
117C GLN* 1.3 83.3 - - + +
119C VAL* 1.3 64.7 + - - +
120C GLU 3.2 1.5 + - - -
121C PRO* 3.9 11.4 - - - +
122C TYR* 5.2 2.1 - - - +
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Residues in contact with VAL 119 (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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184B HIS* 4.7 8.5 - - + +
188B TYR* 3.8 45.5 - - + -
115C TYR 3.7 4.6 + - - +
116C ARG* 3.3 31.4 - - - +
118C LYS* 1.3 78.6 - - - +
120C GLU* 1.3 57.4 + - - +
121C PRO* 3.6 0.9 - - - -
122C TYR* 3.2 26.5 + - + +
123C LEU* 2.8 38.3 + - + +
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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