Contacts of the helix formed by residues 116 - 128 (chain C) in PDB entry 4CYM
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 ALA 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C GLU* 3.4 42.6 - - + +
87C ARG* 4.3 6.3 - - - +
112C SER 3.2 10.5 + - - +
113C THR 3.6 6.1 - - - +
114C PHE 3.0 1.0 - - - -
115C GLU* 1.3 73.7 - - - +
117C VAL* 1.3 63.4 + - - +
118C LEU 3.1 3.1 - - - -
119C LYS* 3.0 23.2 + - - +
120C TRP* 3.3 14.1 + - + -
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Residues in contact with VAL 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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104C VAL* 3.9 20.4 - - + +
105C VAL 4.8 2.5 - - - +
106C PHE* 3.9 23.3 - - + -
113C THR 3.4 12.8 - - - +
114C PHE* 3.1 22.9 + - + +
116C ALA* 1.3 77.5 - - - +
118C LEU* 1.3 61.2 + - - +
120C TRP* 3.5 6.7 + - - +
121C LYS* 2.8 27.5 + - - +
140C LEU* 4.4 6.7 - - + -
161C PHE* 3.7 33.7 - - + -
167C PHE* 4.3 13.0 - - + -
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Residues in contact with LEU 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 PHE* 5.6 1.3 - - + +
115C GLU* 3.7 13.4 + - - +
116C ALA 3.1 0.8 - - - -
117C VAL* 1.3 81.9 - - + +
119C LYS* 1.3 59.0 + - + +
121C LYS* 3.7 8.8 - - + +
122C SER* 2.8 33.6 + - - +
161C PHE* 3.9 28.3 - - + -
165C HIS* 3.4 44.9 - - + +
167C PHE* 5.7 0.2 - - + -
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Residues in contact with LYS 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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87C ARG* 3.4 42.3 - - - +
115C GLU 4.7 3.8 - - - +
116C ALA* 3.0 17.8 + - - +
118C LEU* 1.3 76.8 - - + +
120C TRP* 1.3 59.7 + - - +
122C SER* 3.5 6.0 + - - -
123C ASP* 2.9 29.0 + - - +
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Residues in contact with TRP 120 (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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31C ILE* 3.9 29.9 - - + +
32C GLY* 3.3 44.4 - - - -
33C GLU* 3.4 7.3 + - - +
82C ILE* 4.5 11.7 - - + -
83C ALA 3.9 11.7 - - - -
84C GLY* 3.2 26.0 - - - -
86C GLU 4.5 0.2 - - - -
87C ARG* 3.4 51.4 - - + +
92C THR* 4.7 2.0 - - + -
96C TYR* 3.4 26.0 - - - -
104C VAL* 4.4 6.3 - - + -
116C ALA* 3.3 25.2 + - + -
117C VAL* 3.7 8.5 - - - +
119C LYS* 1.3 76.4 - - - +
121C LYS* 1.3 53.5 + - - +
123C ASP* 3.1 6.4 + - - +
124C LEU* 2.7 36.0 + - - +
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Residues in contact with LYS 121 (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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31C ILE* 5.1 0.2 - - - +
104C VAL* 4.9 4.9 - - + +
117C VAL 2.8 19.5 + - - +
118C LEU* 3.7 11.0 - - + +
120C TRP* 1.3 76.4 - - - +
122C SER* 1.3 61.9 + - - +
124C LEU* 3.4 10.3 + - + +
125C ASP* 2.8 59.5 + - - +
135C PRO* 5.1 4.6 - - - +
136C ILE 5.0 4.0 + - - -
138C ALA* 3.8 19.8 - - + +
165C HIS* 3.3 25.5 + - + +
166C GLY* 3.5 22.6 + - - -
167C PHE* 3.6 31.4 - - + -
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Residues in contact with SER 122 (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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118C LEU* 2.8 22.5 + - - +
119C LYS* 3.6 7.2 - - - -
121C LYS* 1.3 69.1 - - - +
123C ASP* 1.3 57.9 + - - +
125C ASP* 5.0 2.7 - - - -
126C SER* 2.7 38.9 + - - -
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Residues in contact with ASP 123 (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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87C ARG* 4.8 8.4 - - + +
92C THR* 3.3 14.2 + - - +
96C TYR* 2.6 30.0 + - - +
119C LYS 2.9 12.6 + - - +
120C TRP* 3.3 14.9 - - + +
122C SER* 1.3 77.1 - - - +
124C LEU* 1.3 65.8 + - - +
126C SER* 3.1 18.7 - - - -
127C LYS* 3.0 42.8 + - - +
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Residues in contact with LEU 124 (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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29C LEU* 3.5 31.2 - - + -
31C ILE* 4.5 11.0 - - + -
96C TYR* 3.7 21.4 - - + -
102C ALA* 3.7 25.1 - - + -
104C VAL* 5.0 2.2 - - + -
120C TRP 2.7 19.7 + - - +
121C LYS* 3.5 17.3 - - + +
123C ASP* 1.3 71.7 - - - +
125C ASP* 1.3 67.8 + - - +
127C LYS* 2.8 19.2 + - - +
128C VAL* 3.0 21.0 + - + +
136C ILE* 4.3 20.9 - - + +
138C ALA* 4.7 6.1 - - + -
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Residues in contact with ASP 125 (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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121C LYS* 2.8 55.7 + - - +
122C SER* 4.2 2.6 - - - +
124C LEU* 1.3 83.7 - - - +
126C SER* 1.3 65.9 + - - +
127C LYS 3.1 2.3 + - - -
128C VAL 4.1 14.6 + - - +
129C HIS* 5.5 1.9 + - - -
135C PRO* 3.8 25.1 - - + +
136C ILE 4.8 3.5 + - - +
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Residues in contact with SER 126 (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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122C SER 2.7 26.0 + - - -
123C ASP* 3.1 12.3 - - - -
125C ASP* 1.3 72.8 - - - +
127C LYS* 1.3 71.3 + - - +
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Residues in contact with LYS 127 (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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90C ASN* 6.0 1.6 - - - +
92C THR* 3.1 16.2 + - - +
93C ARG* 3.9 38.0 - - + +
96C TYR* 4.0 14.0 - - + +
97C LYS* 5.6 1.9 - - - -
123C ASP* 3.0 36.8 + - - +
124C LEU 2.8 11.9 + - - +
126C SER* 1.3 89.5 - - - +
128C VAL* 1.3 64.1 + - - +
129C HIS* 4.9 6.9 + - - -
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 3.2 46.2 - - + +
97C LYS* 4.9 0.9 - - - -
98C GLU* 4.3 7.4 - - - +
99C ALA* 3.9 25.1 - - + +
124C LEU* 3.0 23.3 + - + +
125C ASP* 4.1 10.8 + - - +
126C SER 4.0 0.4 - - - -
127C LYS* 1.3 85.6 - - - +
129C HIS* 1.3 78.2 + - - +
135C PRO* 4.2 11.6 - - - +
136C ILE* 4.1 13.4 + - + +
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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