Contacts of the helix formed by residues 92 - 104 (chain D) in PDB entry 1GN6
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 THR 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D LYS 4.2 7.0 - - - +
91D PRO* 1.3 79.6 - - - +
93D GLY* 1.3 66.4 + - - +
94D GLU 3.8 1.0 + - - -
95D LEU 3.8 2.3 + - - -
96D ALA* 3.6 12.2 + - - -
191D GLN* 3.2 31.0 + - - +
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Residues in contact with GLY 93 (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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92D THR* 1.3 74.2 - - - +
94D GLU* 1.3 67.4 + - - -
96D ALA* 3.1 5.1 + - - +
97D ALA* 3.0 21.8 + - - +
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Residues in contact with GLU 94 (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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92D THR 3.8 0.6 + - - -
93D GLY* 1.3 69.6 - - - -
95D LEU* 1.3 59.1 + - - +
97D ALA* 3.1 8.5 + - - +
98D ALA* 2.7 30.5 + - - +
194D TYR* 4.2 28.4 + - + +
195D ALA* 5.0 10.6 - - - +
198D THR* 5.0 5.2 + - - -
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Residues in contact with LEU 95 (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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91D PRO* 4.0 4.3 - - + -
92D THR 3.8 2.6 + - - +
93D GLY 3.3 0.6 - - - -
94D GLU* 1.3 77.2 - - - +
96D ALA* 1.3 55.4 + - - +
98D ALA* 3.0 6.3 + - + +
99D ILE* 2.7 54.8 + - + +
128D LEU* 5.2 1.1 - - + -
137D LEU* 4.9 4.0 - - + -
156D LEU* 5.0 4.0 - - + -
187D TRP* 3.7 20.6 - - + -
190D VAL* 3.2 33.9 - - + -
191D GLN* 3.7 35.3 - - + +
194D TYR* 3.9 35.3 - - + -
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Residues in contact with ALA 96 (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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91D PRO* 3.5 36.5 - - + +
92D THR* 3.6 11.9 + - - -
93D GLY 3.1 9.7 + - - +
95D LEU* 1.3 78.3 - - - +
97D ALA* 1.3 60.2 + - - +
99D ILE* 4.1 3.2 - - - +
100D ALA* 3.2 22.9 + - - +
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Residues in contact with ALA 97 (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 GLY 3.0 10.9 + - - +
94D GLU* 3.5 11.0 - - - +
96D ALA* 1.3 77.4 - - - +
98D ALA* 1.3 65.5 + - - +
100D ALA* 3.3 5.5 + - - +
101D ASP* 3.0 27.5 + - - +
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Residues in contact with ALA 98 (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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94D GLU 2.7 19.1 + - - +
95D LEU* 3.5 5.4 - - - +
97D ALA* 1.3 73.1 - - - +
99D ILE* 1.3 58.2 + - - +
101D ASP* 3.7 5.9 - - - +
102D ALA* 2.8 30.7 + - - +
137D LEU* 4.0 9.1 - - + +
194D TYR* 3.2 40.2 - - + +
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Residues in contact with ILE 99 (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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91D PRO* 4.0 19.5 - - + -
95D LEU* 2.7 41.9 + - + +
96D ALA* 4.1 4.3 - - - +
98D ALA* 1.3 73.0 - - - +
100D ALA* 1.3 65.4 + - - +
103D PHE* 3.0 32.1 + - + +
105D SER 4.3 0.4 - - - +
106D PHE* 4.2 20.2 - - + +
109D PHE* 3.8 38.4 - - + -
128D LEU* 4.8 7.0 - - + -
137D LEU* 4.1 18.4 - - + -
187D TRP* 4.3 10.5 - - + -
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Residues in contact with ALA 100 (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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96D ALA 3.2 17.0 + - - +
97D ALA* 3.3 6.7 + - - +
99D ILE* 1.3 79.6 - - - +
101D ASP* 1.3 58.1 + - + +
104D GLY* 2.7 43.0 + - - +
105D SER* 4.0 13.0 - - - +
106D PHE 5.2 1.6 - - - +
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Residues in contact with ASP 101 (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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97D ALA 3.0 18.3 + - - +
98D ALA* 3.8 5.4 - - - +
100D ALA* 1.3 80.8 - - + +
102D ALA* 1.3 63.7 + - - +
104D GLY 4.4 1.4 + - - -
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Residues in contact with ALA 102 (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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51B ARG* 3.3 19.6 + - - -
98D ALA 2.8 16.4 + - - +
101D ASP* 1.3 83.3 + - - +
103D PHE* 1.3 68.4 + - + +
104D GLY 3.8 0.2 - - - -
136D LYS* 6.2 0.4 - - + -
137D LEU* 3.9 37.3 - - + +
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Residues in contact with PHE 103 (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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51B ARG* 3.4 39.0 + - - +
99D ILE* 3.0 21.3 + - + +
102D ALA* 1.3 85.8 - - + +
104D GLY* 1.3 61.7 + - - +
105D SER 3.3 3.7 + - - +
108D LYS* 3.4 17.5 - - - +
109D PHE* 3.7 42.8 - + + +
112D GLN* 3.9 9.4 - - - -
128D LEU* 3.8 25.1 - - + -
137D LEU* 3.8 30.7 - - + -
138D LEU* 4.4 0.9 - - + -
139D ILE* 3.6 31.0 - - + -
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Residues in contact with GLY 104 (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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100D ALA* 2.7 30.1 + - - +
101D ASP 4.4 1.8 + - - -
102D ALA 3.8 1.0 - - - -
103D PHE* 1.3 74.6 - - - +
105D SER* 1.3 60.7 - - - -
108D LYS* 3.9 11.4 - - - -
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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