Contacts of the helix formed by residues 116 - 133 (chain C) in PDB entry 4GKH
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 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 4.6 9.0 + - - -
113C TYR* 2.8 29.2 + - - +
115C ASP* 1.3 78.3 - - - +
117C GLY* 1.3 65.4 + - - +
118C GLU 3.2 2.9 - - - -
119C ASN* 3.1 19.6 + - - +
120C ILE* 2.9 34.4 + - - +
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Residues in contact with GLY 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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30A ARG* 6.0 0.4 - - - -
110C LEU* 3.5 26.6 - - - +
113C TYR 3.9 1.6 + - - -
114C PRO 3.5 7.5 + - - -
115C ASP 3.2 4.0 - - - -
116C SER* 1.3 76.8 - - - +
118C GLU* 1.3 59.1 + - - +
120C ILE* 3.3 2.8 + - - +
121C VAL* 3.0 34.5 + - - +
243C LEU* 3.6 14.8 - - - -
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Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 5.9 0.5 + - - -
58A LYS* 5.5 10.3 - - - +
114C PRO 5.2 0.7 - - - +
115C ASP 3.5 19.1 - - - +
116C SER 3.2 0.2 - - - -
117C GLY* 1.3 79.4 + - - +
119C ASN* 1.3 63.1 + - - +
121C VAL* 3.4 1.0 + - - +
122C ASP* 3.0 34.5 + - - +
242C SER* 5.2 5.0 + - - -
243C LEU* 4.0 16.8 - - + +
246C ARG* 3.3 39.0 + - - +
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Residues in contact with ASN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASP 5.6 0.6 + - - -
116C SER* 3.1 21.0 + - - +
118C GLU* 1.3 80.7 - - - +
120C ILE* 1.3 62.6 + - + +
122C ASP* 3.5 9.8 + - - +
123C ALA* 3.1 23.6 + - - +
246C ARG* 5.5 1.7 + - - -
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Residues in contact with ILE 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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106C ALA* 4.5 9.2 - - + +
109C VAL* 3.9 20.4 - - + +
110C LEU* 3.8 41.1 - - + -
113C TYR* 5.4 0.2 - - + -
116C SER* 2.9 37.2 + - - +
117C GLY* 3.6 5.4 - - - +
119C ASN* 1.3 78.5 - - + +
121C VAL* 1.3 57.7 + - + +
123C ALA* 3.3 3.9 + - - +
124C LEU* 3.0 45.2 + - + +
201C LEU* 5.4 0.2 - - + -
206C PHE* 4.0 27.1 - - + -
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 6.0 0.7 - - + -
117C GLY 3.0 21.4 + - - +
118C GLU* 3.9 3.6 - - - +
120C ILE* 1.3 73.3 - - + +
122C ASP* 1.3 68.1 + - - +
124C LEU* 3.1 10.5 + - + +
125C ALA* 2.9 22.5 + - + +
236C LEU* 3.8 28.7 - - + -
243C LEU* 3.6 28.3 - - + +
246C ARG* 4.0 11.4 - - + +
247C LEU* 3.6 39.9 - - + +
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Residues in contact with ASP 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLU 3.0 18.6 + - - +
119C ASN* 3.8 9.9 - - - +
120C ILE 3.4 0.2 - - - -
121C VAL* 1.3 74.8 - - - +
123C ALA* 1.3 62.5 + - - +
125C ALA* 3.3 2.1 + - - +
126C VAL* 3.0 29.9 + - - +
246C ARG* 2.7 47.4 + - - +
250C LYS* 3.8 36.9 + - + +
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Residues in contact with ALA 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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119C ASN 3.1 18.2 + - - +
120C ILE 3.6 4.7 - - - +
121C VAL 3.2 0.2 - - - -
122C ASP* 1.3 77.1 - - - +
124C LEU* 1.3 58.0 + - - +
126C VAL* 3.4 6.3 + - - +
127C PHE* 3.0 30.1 + - - +
206C PHE* 4.1 21.8 - - + -
211C LEU* 3.6 12.3 - - + +
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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
----------------------------------------------------------
106C ALA* 4.3 2.9 - - + -
120C ILE* 3.0 32.2 + - + +
121C VAL* 3.1 16.4 + - + +
123C ALA* 1.3 75.8 - - - +
125C ALA* 1.3 57.8 + - - +
127C PHE* 3.7 1.7 - - - +
128C LEU* 2.9 30.4 + - - +
199C PHE* 4.2 4.9 - - + -
201C LEU* 3.6 28.5 - - + -
204C LEU* 3.5 42.0 - - + -
206C PHE* 4.3 8.1 - - + -
211C LEU* 4.0 14.4 - - + -
232C LEU* 4.0 23.1 - - + -
236C LEU* 5.0 1.6 - - + -
247C LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 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 VAL 2.9 15.9 + - - +
122C ASP 3.7 0.2 - - - +
124C LEU* 1.3 77.8 - - - +
126C VAL* 1.3 56.7 + - - +
128C LEU* 3.3 5.3 + - - +
129C ARG* 2.9 32.3 + - - +
247C LEU* 4.0 22.2 - - + +
250C LYS* 3.6 32.5 - - + -
251C TYR* 3.9 15.1 - - - +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ASP* 3.0 18.8 + - + +
123C ALA* 3.8 5.8 - - - +
124C LEU 3.3 0.2 - - - -
125C ALA* 1.3 74.2 - - - +
127C PHE* 1.3 65.8 - - - +
129C ARG* 3.3 8.9 + - - +
130C ARG* 3.0 31.5 + - + +
250C LYS* 4.0 23.1 - - + -
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Residues in contact with PHE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C MSE 3.4 27.5 - - + +
80C PRO* 4.0 20.0 - - + -
123C ALA 3.0 17.3 + - - +
124C LEU 3.7 2.9 - - - +
126C VAL* 1.3 77.1 - - - +
128C LEU* 1.3 62.6 + - - +
130C ARG* 3.2 35.5 + - - +
131C LEU* 3.1 21.0 + - + +
199C PHE* 4.0 10.8 - + - -
204C LEU* 3.7 27.6 - - + -
211C LEU* 3.6 24.5 - - + -
213C GLY* 4.3 8.3 - - - -
214C CYS* 4.0 31.4 - - + -
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Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU 2.9 18.3 + - - +
125C ALA* 3.7 5.8 - - - +
126C VAL 3.2 0.2 - - - -
127C PHE* 1.3 75.4 - - - +
129C ARG* 1.3 63.3 + - - +
131C LEU* 3.2 8.7 + - + +
132C HIS* 2.9 59.4 + - + +
199C PHE* 3.8 32.3 - - + -
228C ASP* 3.6 23.8 - - + +
229C LEU* 3.7 32.3 - - + +
232C LEU* 5.2 0.7 - - + -
247C LEU* 5.2 6.7 - - + -
251C TYR* 3.9 6.7 - - + -
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Residues in contact with ARG 129 (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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125C ALA 2.9 17.4 + - - +
126C VAL* 3.5 11.4 - - - +
128C LEU* 1.3 77.6 - - - +
130C ARG* 1.3 61.3 + - - +
132C HIS* 3.4 4.3 + - - +
133C SER* 3.0 24.8 + - - -
225C ARG* 3.3 25.5 - - - +
250C LYS 5.5 1.1 - - - +
251C TYR* 2.8 62.8 + - + +
252C GLY* 4.2 12.1 + - - -
253C ILE* 4.9 2.8 - - - +
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Residues in contact with ARG 130 (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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78C PHE 5.0 2.8 + - - -
79C MSE 4.0 17.8 - - + +
80C PRO* 3.8 25.9 - - - +
126C VAL* 3.0 25.5 + - + +
127C PHE* 3.3 36.7 - - - +
129C ARG* 1.3 73.9 - - + +
131C LEU* 1.3 66.3 + - - +
133C SER* 2.8 25.0 + - - -
134C ILE* 3.7 7.6 + - - +
211C LEU 5.5 3.2 + - - -
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Residues in contact with LEU 131 (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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75C LEU* 4.0 18.6 - - + -
79C MSE 3.7 29.3 - - + +
127C PHE* 3.1 8.4 + - + +
128C LEU* 3.2 16.8 + - + +
130C ARG* 1.3 79.2 - - - +
132C HIS* 1.3 61.9 + - - +
133C SER 3.2 1.6 + - - -
134C ILE* 3.2 37.8 + - + +
194C VAL* 3.7 20.9 - - + +
195C THR 4.1 0.9 - - - -
196C HIS* 3.6 41.3 - - + +
199C PHE* 4.8 5.4 - - + -
228C ASP* 4.0 8.5 - - - +
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Residues in contact with HIS 132 (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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128C LEU* 2.9 41.4 + - + +
129C ARG* 3.7 6.3 - - - +
131C LEU* 1.3 77.2 - - + +
133C SER* 1.3 60.3 + - - +
134C ILE 3.3 4.9 + - - +
193C VAL* 3.6 34.5 - - + +
194C VAL 3.1 23.1 - - - -
195C THR* 4.2 1.0 - - - +
225C ARG* 3.7 32.2 + - + +
228C ASP* 2.8 25.0 + - + -
229C LEU* 4.9 0.2 - - + -
251C TYR* 2.6 33.2 + + - +
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Residues in contact with SER 133 (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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129C ARG 3.0 14.9 + - - -
130C ARG* 2.8 20.5 + - - -
131C LEU 3.1 0.4 - - - -
132C HIS* 1.3 78.3 - - - +
134C ILE* 1.3 63.8 + - - +
135C PRO* 3.1 12.3 - - - +
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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
------------------------------------------------------------
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