Contacts of the helix formed by residues 106 - 117 (chain D) in PDB entry 6GR2
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 TRP 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D LEU* 4.3 28.7 - - + -
76D LEU 5.3 0.4 - - - -
77D THR* 3.5 31.6 - - + +
82D ALA* 4.1 9.2 - - + -
83D ASP* 2.8 46.6 + - + +
85D PRO 3.2 10.6 + - - -
86D GLN* 3.5 28.3 - - - +
87D ARG* 4.4 4.7 - - - -
88D LEU* 4.9 2.0 - - + -
104D PRO* 3.3 16.7 - - + +
105D ARG* 1.3 79.3 - - - +
107D ALA* 1.3 75.4 + - + +
108D ASN 3.2 0.7 + - - -
109D TYR* 3.4 29.0 + - + +
110D VAL* 4.2 8.0 - - + +
129D VAL* 5.4 7.6 - - + -
135D LEU* 6.2 2.5 - - + -
145D LEU* 4.1 15.7 - - + +
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 4.8 5.8 - - + -
88D LEU* 3.4 33.4 - - + -
104D PRO* 3.3 12.7 + - + +
105D ARG 3.1 1.0 - - - -
106D TRP* 1.3 99.1 - - + +
108D ASN* 1.3 65.2 + - - +
109D TYR 3.2 0.4 + - - -
110D VAL* 3.3 8.8 + - - +
111D LYS* 2.9 29.2 + - + +
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Residues in contact with ASN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PRO* 3.2 9.6 - - - +
102D GLY 2.8 45.9 + - - +
104D PRO 4.2 0.3 - - - +
105D ARG* 2.9 26.3 + - - +
107D ALA* 1.3 78.1 - - - +
109D TYR* 1.3 57.4 + - + +
111D LYS* 3.8 13.7 + - - -
112D GLY* 2.8 25.3 + - - -
177D PHE* 3.3 39.5 + - + +
178D ALA* 4.7 3.5 - - - +
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Residues in contact with TYR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ARG* 4.2 10.1 - - + -
106D TRP* 3.4 23.8 - - - +
107D ALA 3.2 1.0 - - - -
108D ASN* 1.3 77.5 - - - +
110D VAL* 1.3 62.4 + - - +
112D GLY* 3.5 1.3 + - - -
113D VAL* 3.2 28.6 + - - +
142D SER* 3.6 25.7 - - - -
145D LEU* 4.0 18.8 - - + -
146D GLU* 3.1 37.4 - - + +
173D ALA* 4.2 5.6 - - - +
174D GLU* 4.2 9.0 + - + -
177D PHE* 5.4 0.9 - - - -
178D ALA* 3.5 32.3 + - + +
180D MET* 5.4 2.9 - - - +
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 3.5 35.9 - - + -
90D PHE* 4.6 2.0 - - + -
106D TRP* 4.2 12.3 - - + +
107D ALA* 3.4 20.0 - - - +
109D TYR* 1.3 71.9 - - - +
111D LYS* 1.3 67.6 + - - +
113D VAL* 3.3 2.3 + - - +
114D ILE* 2.9 43.0 + - + +
125D PHE* 5.3 1.3 - - + -
129D VAL* 6.2 2.0 - - + -
145D LEU* 4.8 11.6 - - + +
149D THR* 3.8 30.1 - - + +
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Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D LEU* 3.6 31.1 - - - +
90D PHE* 4.0 26.4 - - + +
99D LEU* 3.4 26.6 - - + +
100D GLU 3.4 27.3 + - - +
102D GLY* 3.9 12.1 - - - +
103D THR 4.7 4.0 + - - -
104D PRO 5.1 0.2 + - - -
107D ALA* 2.9 26.6 + - - +
108D ASN* 3.6 18.3 + - - +
110D VAL* 1.3 79.3 - - - +
112D GLY* 1.3 56.9 + - - +
114D ILE* 3.3 1.3 + - - -
115D GLN* 2.9 30.5 + - - +
177D PHE* 4.0 11.2 - - + -
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Residues in contact with GLY 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ASN 2.8 16.2 + - - -
110D VAL 3.2 0.2 - - - -
111D LYS* 1.3 73.4 - - - +
113D VAL* 1.3 60.5 + - - +
115D GLN* 3.2 0.9 + - - +
116D TYR* 3.0 30.7 + - - +
173D ALA* 3.4 16.4 - - - -
177D PHE* 3.4 29.6 - - - -
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D TYR 3.2 18.8 + - - +
110D VAL 3.8 3.1 - - - +
112D GLY* 1.3 75.4 - - - +
114D ILE* 1.3 59.0 + - - +
116D TYR 3.6 0.7 - - - -
117D TYR* 2.9 29.6 + - - +
146D GLU* 3.9 28.3 - - + +
149D THR* 3.9 20.9 - - + -
150D TYR* 3.9 36.3 - - + +
153D LEU* 4.1 5.4 - - + -
169D VAL* 4.5 6.1 - - + +
170D CYS* 4.5 7.2 - - - -
173D ALA* 3.8 14.4 - - + -
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Residues in contact with ILE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL* 4.3 3.1 - - + -
90D PHE* 4.1 18.6 - - + -
92D LEU* 4.0 11.2 - - + -
93D PRO* 3.9 19.9 - - + +
99D LEU* 3.9 13.5 - - + -
110D VAL* 2.9 35.8 + - + +
111D LYS* 3.6 4.5 - - - +
113D VAL* 1.3 78.3 - - - +
115D GLN* 1.3 64.2 + - - +
116D TYR 3.3 0.5 + - - -
117D TYR* 3.3 13.0 + - - +
122D LEU* 4.1 10.7 - - + +
125D PHE* 3.7 27.6 - - + -
149D THR* 4.8 2.0 - - + -
153D LEU* 3.9 26.0 - - + -
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Residues in contact with GLN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D PRO* 3.3 19.9 - - - +
94D THR 5.5 1.6 + - - -
98D SER* 3.3 22.2 + - - -
99D LEU* 2.8 31.2 + - + +
111D LYS 2.9 17.2 + - - +
112D GLY 3.2 4.7 + - - +
114D ILE* 1.3 79.6 - - - +
116D TYR* 1.3 72.4 + - + +
117D TYR 3.7 2.8 + - - +
177D PHE* 3.9 23.3 - - + -
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Residues in contact with TYR 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D GLY 3.0 24.0 + - - +
113D VAL 3.6 1.3 - - - -
115D GLN* 1.3 84.3 - - + +
117D TYR* 1.3 64.7 + - - +
118D PRO* 3.3 5.7 - - - +
169D VAL* 3.7 30.5 - - + +
172D GLN* 3.8 38.1 + - + -
173D ALA 4.1 7.9 - - - -
176D SER* 3.3 24.7 + - - -
177D PHE* 3.8 26.8 - + - -
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Residues in contact with TYR 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL 2.9 14.4 + - - +
114D ILE 3.3 12.6 + - - +
115D GLN 4.6 2.9 - - - +
116D TYR* 1.3 77.7 - - - +
118D PRO* 1.3 67.2 - - + +
119D ALA* 3.4 32.4 + - + +
122D LEU* 4.3 18.4 - - + -
150D TYR* 3.4 45.3 - + - -
153D LEU* 3.7 37.5 - - + -
154D GLN* 3.1 23.9 - - - +
157D CYS 2.8 29.2 + - - -
159D ASP* 3.7 11.0 + - + +
169D VAL* 4.6 1.6 - - - -
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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