Contacts of the helix formed by residues 93 - 104 (chain H) in PDB entry 1GN2
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 93 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92H THR* 1.3 81.9 - - - +
94H GLU* 1.3 57.9 + - - -
96H ALA* 3.0 19.7 + - - +
97H ALA* 3.0 15.3 + - - +
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Residues in contact with GLU 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H THR 3.6 1.0 + - - -
93H GLY* 1.3 66.1 - - - -
95H LEU* 1.3 60.2 + - - +
97H ALA* 3.4 12.9 + - - +
98H ALA* 2.9 30.9 + - - +
194H TYR* 4.2 16.7 + - + -
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Residues in contact with LEU 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H PRO* 4.2 5.8 - - + -
92H THR 3.7 1.7 + - - +
93H GLY 3.2 0.8 - - - -
94H GLU* 1.3 77.4 - - - +
96H ALA* 1.3 57.4 + - - +
98H ALA* 3.1 4.8 + - + +
99H ILE* 2.9 41.4 + - + +
128H LEU* 5.7 0.9 - - + -
137H LEU* 4.9 4.5 - - + -
156H LEU* 5.5 1.8 - - + -
187H TRP* 4.1 14.6 - - + -
190H VAL* 3.4 20.9 - - + -
191H GLN* 3.1 56.5 - - + +
194H TYR* 3.6 39.7 - - + -
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Residues in contact with ALA 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H PRO* 3.6 37.8 - - + +
92H THR* 3.9 4.2 + - - +
93H GLY 3.0 11.6 + - - +
95H LEU* 1.3 75.3 - - - +
97H ALA* 1.3 67.0 + - - +
99H ILE* 3.4 5.7 + - - +
100H ALA* 3.0 24.9 + - - +
106H PHE* 6.1 0.3 - - - +
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Residues in contact with ALA 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H GLY 3.0 12.0 + - - +
94H GLU* 4.0 19.1 - - - +
95H LEU 3.3 0.2 - - - -
96H ALA* 1.3 77.1 - - - +
98H ALA* 1.3 63.7 + - - +
100H ALA* 3.5 4.9 + - - +
101H ASP* 3.0 26.5 + - - +
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Residues in contact with ALA 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H GLU* 2.9 16.8 + - - +
95H LEU* 3.3 9.4 - - + +
97H ALA* 1.3 79.0 - - - +
99H ILE* 1.3 59.2 + - - +
101H ASP* 2.9 8.9 + - - +
102H ALA* 2.8 31.7 + - - +
137H LEU* 4.7 8.5 - - + -
194H TYR* 3.4 32.5 - - + +
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Residues in contact with ILE 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H PRO* 3.8 25.1 - - + -
95H LEU* 2.9 26.9 + - + +
96H ALA* 3.8 5.2 - - - +
98H ALA* 1.3 76.6 - - - +
100H ALA* 1.3 57.3 + - - +
103H PHE* 2.8 36.0 + - + +
106H PHE* 4.1 20.9 - - + -
109H PHE* 4.0 35.0 - - + -
128H LEU* 5.0 5.2 - - + -
137H LEU* 3.9 24.7 - - + -
187H TRP* 4.1 17.9 - - + -
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Residues in contact with ALA 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H ALA 3.0 17.6 + - - +
97H ALA* 4.1 4.7 - - - +
99H ILE* 1.3 76.3 - - - +
101H ASP* 1.3 60.5 + - - +
104H GLY* 2.9 33.9 + - - +
105H SER* 3.9 22.7 - - - +
106H PHE* 4.5 4.3 - - + +
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Residues in contact with ASP 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ALA 3.0 18.6 + - - +
98H ALA* 2.9 6.7 + - - +
100H ALA* 1.3 83.0 - - - +
102H ALA* 1.3 63.1 + - - +
104H GLY* 4.4 2.1 + - - -
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Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F GLU* 5.5 0.7 - - - +
51F ARG* 3.5 18.0 + - - -
98H ALA 2.8 14.8 + - - +
101H ASP* 1.3 83.7 - - - +
103H PHE* 1.3 69.3 + - + +
104H GLY 3.5 0.7 - - - -
136H LYS* 6.4 0.2 - - + -
137H LEU* 4.0 33.6 - - + +
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Residues in contact with PHE 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ARG* 3.4 41.2 - - - +
99H ILE* 2.8 23.6 + - + +
102H ALA* 1.3 81.6 - - + +
104H GLY* 1.3 55.6 + - - +
105H SER 2.9 10.4 + - - +
108H LYS* 3.3 19.9 - - - +
109H PHE* 3.6 39.9 - + + +
112H GLN* 3.8 8.1 - - - -
128H LEU* 3.9 17.5 - - + -
137H LEU* 3.9 35.2 - - + -
138H LEU* 4.2 1.8 - - + -
139H ILE* 3.5 38.6 - - + -
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Residues in contact with GLY 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H ALA* 2.9 23.4 + - - +
101H ASP 4.3 2.5 + - - -
102H ALA 3.5 2.0 - - - -
103H PHE* 1.3 73.5 - - - +
105H SER* 1.3 61.3 + - - +
108H LYS* 4.8 8.3 - - - -
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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
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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