Contacts of the helix formed by residues 100 - 119 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A HIS* 3.3 15.7 - - - -
78A PHE 2.9 12.8 + - - -
79A LEU 4.7 0.2 - - - -
80A SER* 3.9 9.1 - - - -
99A PHE* 1.3 73.9 - - - +
101A PRO* 1.3 70.5 - - - +
102A LEU 3.1 2.9 - - - -
103A GLY 2.9 1.4 + - - -
104A VAL* 2.9 29.7 + - - +
127C PRO 4.6 0.4 - - - -
128C VAL* 5.8 0.7 - - - -
192C HIS* 5.3 2.2 - - - -
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Residues in contact with PRO 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A HIS* 3.8 18.2 - - + +
100A GLY* 1.3 82.0 - - - +
102A LEU* 1.3 65.1 + - + +
104A VAL* 3.5 1.1 + - + -
105A GLU* 2.9 29.1 + - - +
126C PHE* 4.0 19.5 - - + -
127C PRO* 3.2 37.7 - - + +
128C VAL* 5.6 1.1 - - - -
192C HIS* 6.0 0.2 - - - +
196C CYS* 3.7 31.0 - - - -
199C LEU* 3.8 13.7 - - + -
208C LEU* 6.0 0.2 - - + -
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG 3.1 22.9 - - - +
77A HIS* 3.1 15.9 + - + +
78A PHE* 3.8 31.0 - - + -
100A GLY 3.1 0.6 - - - -
101A PRO* 1.3 85.3 - - + +
103A GLY* 1.3 53.3 + - - +
105A GLU* 3.1 6.0 + - + +
106A LEU* 2.7 37.2 + - - +
380A PRO* 3.8 22.8 - - + +
381A ILE* 4.5 19.5 - - + -
414A TRP* 5.8 4.3 - - + -
435A MET* 4.4 26.9 - - + +
199C LEU* 6.3 3.4 - - + -
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Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.4 26.4 + - - +
99A PHE* 4.2 5.8 - - - -
100A GLY 2.9 5.1 + - - -
102A LEU* 1.3 77.6 - - - +
104A VAL* 1.3 57.5 + - - +
106A LEU* 4.3 2.7 - - - -
107A ARG* 2.8 29.5 + - - +
346A MET* 3.3 26.8 - - - +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.1 4.9 - - + -
100A GLY 2.9 21.3 + - - +
101A PRO 3.6 7.6 - - - +
103A GLY* 1.3 77.4 - - - +
105A GLU* 1.3 57.8 + - - +
107A ARG* 3.6 13.9 + - - +
108A LYS* 2.9 43.1 + - - +
127C PRO* 3.6 27.1 - - + +
128C VAL 4.1 6.1 - - - +
129C ASP* 3.5 39.7 - - + +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PRO 2.9 19.0 + - - +
102A LEU* 3.6 7.2 - - + +
104A VAL* 1.3 74.5 - - - +
106A LEU* 1.3 65.8 + - - +
108A LYS* 3.0 30.3 + - - +
109A ASN* 3.0 40.7 + - - +
380A PRO* 4.2 24.2 - - + +
381A ILE* 6.0 2.9 - - + -
412A SER* 5.8 3.3 - - - -
115C TRP* 4.9 7.4 + - - -
127C PRO* 4.1 17.2 - - + +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 4.2 9.6 - - + -
102A LEU 2.7 20.7 + - - +
103A GLY* 3.6 4.5 - - - +
105A GLU* 1.3 73.5 - - - +
107A ARG* 1.3 60.9 + - - +
109A ASN* 3.3 2.9 + - - +
110A LEU* 3.1 23.3 + - + +
346A MET* 3.3 25.4 - - - +
349A TYR* 5.2 3.1 - - + -
350A LEU* 3.9 20.2 - - + -
374A LEU* 3.9 31.2 - - + -
378A LEU* 3.0 45.5 - - + +
380A PRO* 4.5 4.8 - - + +
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.0 12.4 - - - -
103A GLY 2.8 20.7 + - - +
104A VAL* 4.0 12.8 + - - +
106A LEU* 1.3 72.9 - - - +
108A LYS* 1.3 54.1 + - - +
110A LEU* 3.4 6.1 - - + +
111A ALA* 2.7 35.4 + - + +
213A VAL* 5.7 0.4 - - - +
235A THR* 3.0 33.1 + - - -
342A LEU* 4.4 17.5 - - + -
343A ASP* 2.7 41.1 + - - -
346A MET* 3.6 19.7 - - + -
129C ASP* 2.8 37.8 + - - +
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A VAL* 2.9 41.7 + - - +
105A GLU* 3.2 33.4 - - - +
107A ARG* 1.3 74.6 - - - +
109A ASN* 1.3 59.9 + - - +
111A ALA* 3.4 6.9 + - + +
112A ALA* 2.9 27.0 + - - +
115C TRP* 4.6 25.7 - - + +
127C PRO* 4.6 6.0 - - - +
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Residues in contact with ASN 109 (chain A).
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* 3.0 36.5 + - - +
106A LEU 3.8 4.0 - - - +
108A LYS* 1.3 72.6 - - - +
110A LEU* 1.3 54.4 + - - +
112A ALA* 2.6 30.6 + - - +
113A GLU* 2.6 22.4 + - - +
377A CYS 3.9 21.6 - - - +
378A LEU* 4.0 10.3 + - - -
379A ALA 3.6 22.8 + - - -
380A PRO* 4.3 3.6 + - - +
382A LYS* 4.4 4.7 + - - +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.1 13.8 + - + +
107A ARG* 3.4 8.7 - - + +
109A ASN* 1.3 78.3 - - - +
111A ALA* 1.3 62.7 + - - +
113A GLU* 3.3 5.1 + - - +
114A TRP* 2.9 25.1 + - - +
262A TRP* 3.2 33.7 - - + -
263A TRP* 5.2 1.6 - - + -
266A PHE* 5.4 0.4 - - + -
342A LEU* 3.9 35.7 - - + +
345A GLY* 4.1 8.3 - - - +
346A MET* 4.0 24.5 - - + +
349A TYR* 4.1 21.8 - - + -
378A LEU* 4.5 18.0 - - + +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG* 2.7 22.6 + - + +
108A LYS* 3.5 8.5 - - - +
110A LEU* 1.3 73.5 - - - +
112A ALA* 1.3 62.9 + - - +
114A TRP* 3.4 4.2 + - - +
115A TRP* 3.1 23.6 + - - +
211A ILE* 3.7 19.8 - - + +
342A LEU* 3.9 24.8 - - + +
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LYS 2.9 14.8 + - - +
109A ASN* 2.6 23.0 + - - +
111A ALA* 1.3 68.9 - - - +
113A GLU* 1.3 56.2 + - - +
115A TRP* 3.2 8.4 + - - +
116A THR* 2.7 32.3 + - - -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 2.6 15.0 + - - +
110A LEU* 3.7 10.1 - - - +
112A ALA* 1.3 72.2 - - - +
114A TRP* 1.3 67.1 + - - +
116A THR* 2.9 24.8 + - - +
117A SER* 2.9 13.3 + - - -
262A TRP* 3.9 10.1 - - + +
265A LYS* 5.6 1.5 + - - +
266A PHE* 3.1 38.4 - - + -
377A CYS* 3.7 25.4 - - - +
378A LEU* 4.6 2.7 - - + -
483A LYS* 4.3 20.8 - - - +
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Residues in contact with TRP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU 2.9 12.5 + - - +
111A ALA* 3.4 11.4 - - - +
113A GLU* 1.3 74.8 - - - +
115A TRP* 1.3 93.0 + + - +
117A SER* 3.1 8.1 + - - -
118A VAL* 3.0 46.0 + - + +
119A VAL* 4.0 4.0 - - + -
209A ALA* 3.9 15.3 - - + -
210A GLN 4.7 0.2 - - - -
211A ILE* 3.5 17.9 - - + -
237A ALA* 3.5 34.3 + - + +
238A SER 4.1 14.1 - - - -
239A LEU* 4.2 14.4 - - + -
259A ARG* 3.6 40.0 - - - +
262A TRP* 3.2 22.1 - + + -
301A GLU* 4.2 6.3 + - - -
338A VAL* 5.6 3.8 - - + -
340A GLY* 6.4 0.4 - - - -
342A LEU* 4.9 6.7 - - + -
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Residues in contact with TRP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA 3.1 8.6 + - - +
112A ALA* 3.3 12.8 - - - +
113A GLU 3.0 0.4 - - - -
114A TRP* 1.3 110.9 - + - +
116A THR* 1.3 66.9 + - - +
117A SER 3.1 0.2 + - - -
119A VAL* 3.0 53.5 + - + +
120A VAL* 3.2 24.2 + - + +
127A PRO* 3.5 28.0 - - + -
209A ALA* 3.8 24.5 - - + -
210A GLN* 4.3 4.9 - - - -
211A ILE* 3.9 17.5 - - + -
105C GLU* 4.9 0.2 - - - -
108C LYS* 3.3 32.5 - - - +
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Residues in contact with THR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA 2.7 18.8 + - - -
113A GLU* 2.9 17.4 + - - -
115A TRP* 1.3 75.4 - - - +
117A SER* 1.3 62.4 + - - +
120A VAL* 3.3 28.6 - - + +
121A PHE* 3.3 40.0 + - + -
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU 2.9 5.5 + - - -
114A TRP* 3.3 10.3 - - - -
115A TRP 3.0 0.2 - - - -
116A THR* 1.3 78.3 - - - +
118A VAL* 1.3 59.9 + - - +
121A PHE* 3.1 32.8 - - - +
122A ARG* 4.1 2.1 + - - -
258A HIS* 2.7 40.3 + - - -
259A ARG* 5.0 0.9 - - - -
262A TRP* 3.2 33.7 - - - -
265A LYS* 4.1 6.9 + - - -
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TRP* 3.0 49.8 + - + +
117A SER* 1.3 79.6 - - - +
119A VAL* 1.3 75.8 + - + +
120A VAL 3.9 0.2 - - - -
121A PHE 5.0 0.4 - - - -
122A ARG* 4.2 16.7 + - - +
125A VAL* 3.7 15.3 - - + +
239A LEU* 3.5 38.4 - - + -
255A TRP* 4.2 19.0 - - + -
258A HIS* 4.5 5.4 - - + -
259A ARG* 5.4 3.1 - - - +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TRP* 4.0 3.8 - - + -
115A TRP* 3.0 53.0 + - + +
118A VAL* 1.3 81.3 - - + +
120A VAL* 1.3 71.5 + - - +
122A ARG 4.1 0.2 - - - +
123A GLU* 3.6 20.8 + - - +
125A VAL* 3.6 30.8 - - + +
127A PRO* 4.8 6.1 - - + -
209A ALA* 3.2 31.9 - - + -
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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