Contacts of the helix formed by residues 100 - 119 (chain C) in PDB entry 2G4C
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 GLY 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A VAL* 5.5 0.4 - - - -
192A HIS* 5.2 3.6 - - - -
196A CYS* 5.7 0.2 - - - -
77C HIS* 3.8 13.2 - - - -
78C PHE 3.3 11.0 + - - -
80C SER* 3.8 16.1 - - - +
99C PHE* 1.3 77.3 - - - +
101C PRO* 1.3 76.5 - - - +
102C LEU 3.3 2.7 - - - -
103C GLY 3.0 10.9 + - - -
104C VAL* 3.0 8.6 + - - +
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Residues in contact with PRO 101 (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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126A PHE* 4.0 17.0 - - + -
127A PRO* 3.4 27.0 - - + +
128A VAL* 5.0 3.3 - - + -
196A CYS* 3.8 26.2 - - - -
199A LEU* 3.8 28.3 - - + -
77C HIS* 4.3 14.4 - - + +
100C GLY* 1.3 81.3 - - - +
102C LEU* 1.3 69.0 + - + +
104C VAL* 3.3 2.7 + - + +
105C GLU* 2.8 29.3 + - - +
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 6.5 0.4 - - + -
199A LEU* 4.9 8.1 - - + -
76C ARG 3.1 21.3 - - - +
77C HIS* 2.7 28.6 + - + +
78C PHE* 3.5 34.5 - - + -
101C PRO* 1.3 79.8 - - + +
103C GLY* 1.3 57.2 + - - +
105C GLU* 3.0 4.4 + - - +
106C LEU* 2.8 29.5 + - - +
380C PRO* 3.6 19.4 - - + +
381C ILE* 4.3 18.6 - - + -
414C TRP* 5.4 0.9 - - + -
435C MET* 3.9 33.2 - - + +
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Residues in contact with GLY 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C HIS 3.5 4.0 + - - -
78C PHE* 3.5 26.9 + - - +
99C PHE* 4.3 3.4 - - - -
100C GLY 3.0 4.8 + - - -
102C LEU* 1.3 78.6 - - - +
104C VAL* 1.3 56.2 + - - +
106C LEU* 2.9 3.9 + - - +
107C ARG* 2.8 31.7 + - - +
346C MET* 3.9 21.0 - - - +
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PRO* 4.0 26.2 - - + +
128A VAL* 3.8 9.9 - - - +
129A ASP* 3.1 40.4 - - + +
99C PHE* 3.4 14.3 - - + +
100C GLY 3.0 12.8 + - - +
101C PRO 3.7 6.7 - - - +
103C GLY* 1.3 76.0 - - - +
105C GLU* 1.3 57.7 + - - +
107C ARG* 4.3 8.3 - - - +
108C LYS* 2.9 31.1 + - + +
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Residues in contact with GLU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TRP* 4.9 0.7 + - - -
123A GLU* 6.0 2.5 - - - +
127A PRO* 3.5 22.5 - - + +
101C PRO 2.8 18.3 + - - +
102C LEU* 3.6 4.9 - - - +
104C VAL* 1.3 75.2 - - - +
106C LEU* 1.3 64.1 + - - +
108C LYS* 3.0 40.8 + - - +
109C ASN* 3.1 39.6 + - - +
380C PRO* 3.8 24.7 - - + +
381C ILE* 6.3 1.1 - - + -
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Residues in contact with LEU 106 (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* 4.1 9.4 - - + -
102C LEU 2.8 12.4 + - - +
103C GLY* 2.9 7.8 + - - +
105C GLU* 1.3 74.3 - - - +
107C ARG* 1.3 66.9 + - - +
109C ASN* 3.1 4.2 + - - +
110C LEU* 2.9 21.2 + - + +
346C MET* 3.3 38.8 - - + +
349C TYR* 5.4 3.6 - - + -
350C LEU* 3.9 15.7 - - + -
374C LEU* 4.0 30.3 - - + -
378C LEU* 2.8 46.0 - - + +
380C PRO* 4.2 2.9 - - + +
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Residues in contact with ARG 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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129A ASP* 2.8 43.0 + - - +
99C PHE* 3.6 15.7 - - - -
103C GLY 2.8 14.7 + - - +
104C VAL* 4.3 8.1 - - - +
106C LEU* 1.3 76.4 - - - +
108C LYS* 1.3 56.2 + - - +
110C LEU* 2.9 7.9 + - - +
111C ALA* 2.7 35.1 + - + +
213C VAL* 5.7 0.8 - - - +
235C THR* 2.9 34.0 + - + +
342C LEU* 4.4 21.3 - - + +
343C ASP* 3.0 28.0 + - - +
346C MET* 3.6 18.9 - - + +
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Residues in contact with LYS 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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115A TRP* 3.3 45.7 - - - +
127A PRO* 4.6 1.0 - - + +
104C VAL* 2.9 26.7 + - + +
105C GLU* 3.0 40.1 + - - +
107C ARG* 1.3 78.1 - - - +
109C ASN* 1.3 61.3 + - - +
111C ALA* 3.4 6.0 + - - +
112C ALA* 2.7 30.3 + - + +
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Residues in contact with ASN 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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105C GLU* 3.1 25.6 + - - +
106C LEU 3.1 6.3 + - - +
108C LYS* 1.3 76.5 - - - +
110C LEU* 1.3 58.3 + - - +
112C ALA* 2.9 10.1 + - - +
113C GLU* 2.6 39.5 + - - +
377C CYS 4.0 18.2 - - - +
378C LEU* 3.6 8.8 + - - -
379C ALA 3.1 27.1 + - - -
380C PRO* 4.2 4.6 + - - +
382C LYS* 4.4 9.4 + - - +
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Residues in contact with LEU 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 LEU* 2.9 14.3 + - + +
107C ARG* 2.9 10.9 + - - +
109C ASN* 1.3 76.7 - - - +
111C ALA* 1.3 56.4 + - - +
113C GLU* 3.3 4.1 + - - +
114C TRP* 2.9 27.7 + - - +
262C TRP* 3.6 24.1 - - + -
263C TRP* 5.1 2.9 - - + -
266C PHE* 5.4 0.2 - - + -
342C LEU* 3.6 39.9 - - + +
345C GLY* 3.7 24.2 - - - +
346C MET* 3.8 8.5 - - + +
349C TYR* 3.5 27.4 - - + +
378C LEU* 4.3 18.4 - - + +
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Residues in contact with ALA 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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107C ARG* 2.7 21.7 + - + +
108C LYS* 3.7 6.7 - - - +
110C LEU* 1.3 71.8 - - - +
112C ALA* 1.3 60.3 + - - +
114C TRP* 3.2 3.6 + - - +
115C TRP* 2.9 31.0 + - - +
211C ILE* 3.7 24.1 - - + +
342C LEU* 3.6 23.3 - - + +
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Residues in contact with ALA 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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108C LYS* 2.7 23.3 + - + +
109C ASN* 2.9 13.7 + - - +
111C ALA* 1.3 73.7 - - - +
113C GLU* 1.3 61.5 + - - +
115C TRP* 3.7 8.8 - - - +
116C THR* 3.4 20.8 - - - +
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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 ASN* 2.6 20.3 + - - +
110C LEU* 3.7 4.9 - - - +
112C ALA* 1.3 72.8 - - - +
114C TRP* 1.3 69.1 + - - +
115C TRP 3.2 0.4 + - - -
116C THR* 3.4 18.6 + - - +
117C SER* 3.2 20.8 + - - -
262C TRP* 4.0 7.2 - - + +
266C PHE* 3.1 39.2 - - + -
377C CYS* 3.9 21.3 - - - +
378C LEU* 4.7 4.7 - - + -
483C LYS* 3.9 24.2 + - - +
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Residues in contact with TRP 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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110C LEU 2.9 14.7 + - - +
111C ALA* 3.3 12.8 - - - +
113C GLU* 1.3 78.3 - - - +
115C TRP* 1.3 113.2 + + - +
117C SER* 3.0 10.3 + - - -
118C VAL* 3.1 41.2 - - + +
119C VAL* 4.0 5.2 - - + -
209C ALA* 4.2 4.7 - - + -
211C ILE* 3.7 11.9 - - + -
237C ALA* 3.7 29.5 + - + +
238C SER* 3.8 33.0 - - - -
239C LEU* 4.4 4.9 - - + -
259C ARG* 3.6 40.0 - - - +
262C TRP* 3.5 20.1 - + + -
301C GLU* 5.9 0.2 - - - -
338C VAL* 6.3 2.0 - - + -
340C GLY* 5.8 2.4 - - - +
342C LEU* 4.9 5.6 - - + -
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Residues in contact with TRP 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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105A GLU* 4.9 8.1 + - - -
108A LYS* 4.6 22.0 - - + +
111C ALA 2.9 16.0 + - - +
112C ALA* 3.7 9.4 - - - +
113C GLU 3.2 0.2 - - - -
114C TRP* 1.3 114.1 - + - +
116C THR* 1.3 59.1 + - + +
119C VAL* 2.8 56.4 + - + +
120C VAL* 3.7 19.9 - - + +
127C PRO* 4.0 26.2 - - + -
209C ALA* 3.7 26.0 - - + -
210C GLN* 4.1 9.6 - - - -
211C ILE* 4.2 15.7 - - + -
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Residues in contact with THR 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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112C ALA 3.4 18.2 - - - +
113C GLU* 3.4 18.1 + - - +
115C TRP* 1.3 76.4 - - + +
117C SER* 1.3 64.5 + - - +
118C VAL 3.3 0.9 + - - -
119C VAL 3.8 4.2 + - - -
120C VAL* 3.2 29.6 + - + -
121C PHE* 3.5 34.3 - - - -
483C LYS* 5.6 3.3 + - - -
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Residues in contact with SER 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* 3.2 9.8 + - - -
114C TRP* 3.0 10.2 + - - -
116C THR* 1.3 82.6 + - - +
118C VAL* 1.3 58.7 + - - +
121C PHE* 5.4 4.5 - - - -
122C ARG* 5.1 3.6 + - - -
258C HIS* 2.9 36.2 + - - -
259C ARG* 4.7 0.8 + - - -
262C TRP* 3.2 30.8 - - - -
265C LYS* 5.2 3.5 + - - -
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Residues in contact with VAL 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 TRP* 3.1 55.2 - - + +
115C TRP 3.3 0.2 + - - -
116C THR 4.5 0.4 - - - -
117C SER* 1.3 79.9 - - - +
119C VAL* 1.3 69.7 + - + +
121C PHE* 6.3 0.2 - - - -
122C ARG* 4.0 15.2 - - - +
125C VAL* 3.7 15.2 - - - +
239C LEU* 3.4 33.9 - - + -
255C TRP* 4.2 14.9 - - + -
258C HIS* 4.6 3.1 - - + -
259C ARG* 4.9 8.1 - - - +
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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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114C TRP* 4.0 10.3 - - + -
115C TRP* 2.8 46.5 + - + +
116C THR 3.8 0.6 + - - -
117C SER 3.8 0.6 - - - -
118C VAL* 1.3 88.8 - - + +
120C VAL* 1.3 54.1 + - - +
121C PHE 2.4 35.6 + - - +
122C ARG 4.3 0.7 - - - +
123C GLU* 4.3 5.3 - - - +
125C VAL* 3.5 33.0 - - + +
126C PHE* 4.9 2.7 - - - +
127C PRO* 5.2 1.8 - - + -
209C ALA* 3.6 24.2 - - + -
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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