Contacts of the helix formed by residues 93 - 104 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92F THR* 1.3 83.0 - - - +
94F GLU* 1.3 58.0 + - - -
96F ALA* 3.0 19.6 + - - +
97F ALA* 3.0 14.8 + - - +
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Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F THR 3.6 0.8 + - - -
93F GLY* 1.3 66.3 - - - -
95F LEU* 1.3 60.3 + - - +
97F ALA* 3.4 13.1 + - - +
98F ALA* 2.9 31.2 + - - +
194F TYR* 4.2 17.9 + - + -
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PRO* 4.2 5.8 - - + -
92F THR 3.7 1.5 + - - +
93F GLY 3.2 0.6 - - - -
94F GLU* 1.3 78.0 - - - +
96F ALA* 1.3 58.4 + - - +
98F ALA* 3.1 5.7 + - + +
99F ILE* 2.9 41.0 + - + +
128F LEU* 5.7 1.1 - - + -
137F LEU* 5.0 4.3 - - + -
156F LEU* 5.5 1.6 - - + -
187F TRP* 4.1 15.3 - - + -
190F VAL* 3.4 20.4 - - + -
191F GLN* 3.1 56.0 - - + +
194F TYR* 3.6 39.2 - - + -
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Residues in contact with ALA 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PRO* 3.6 39.2 - - + +
92F THR* 3.9 4.2 + - - +
93F GLY 3.0 10.7 + - - +
95F LEU* 1.3 76.3 - - - +
97F ALA* 1.3 67.0 + - - +
99F ILE* 3.4 5.2 + - - +
100F ALA* 3.0 25.5 + - - +
106F PHE* 6.1 0.2 - - - +
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Residues in contact with ALA 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F GLY 3.0 13.0 + - - +
94F GLU* 4.0 19.3 - - - +
95F LEU 3.3 0.2 - - - -
96F ALA* 1.3 78.0 - - - +
98F ALA* 1.3 64.0 + - - +
100F ALA* 3.9 4.8 - - - +
101F ASP* 3.0 25.6 + - - +
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F GLU* 2.9 17.2 + - - +
95F LEU* 3.3 9.9 - - + +
97F ALA* 1.3 78.7 - - - +
99F ILE* 1.3 57.8 + - - +
101F ASP* 2.9 7.7 + - - +
102F ALA* 2.8 32.1 + - - +
137F LEU* 4.7 8.7 - - + -
194F TYR* 3.4 32.3 - - + +
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Residues in contact with ILE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PRO* 3.8 25.6 - - + -
95F LEU* 2.9 26.9 + - + +
96F ALA* 3.8 5.4 - - - +
98F ALA* 1.3 76.6 - - - +
100F ALA* 1.3 59.0 + - - +
103F PHE* 2.8 34.8 + - + +
106F PHE* 4.1 21.5 - - + -
109F PHE* 4.0 35.0 - - + -
128F LEU* 5.0 5.6 - - + -
137F LEU* 3.9 24.2 - - + +
187F TRP* 4.1 17.0 - - + -
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Residues in contact with ALA 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F ALA 3.0 17.4 + - - +
97F ALA* 4.1 4.7 - - - +
99F ILE* 1.3 76.9 - - - +
101F ASP* 1.3 60.5 + - - +
104F GLY* 2.9 33.8 + - - +
105F SER* 3.9 24.7 - - - +
106F PHE* 4.5 4.3 - - + +
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Residues in contact with ASP 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F ALA 3.0 18.4 + - - +
98F ALA* 2.9 7.1 + - - +
100F ALA* 1.3 82.0 - - - +
102F ALA* 1.3 64.4 + - - +
104F GLY* 4.4 1.9 + - - -
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F ALA 2.8 13.6 + - - +
101F ASP* 1.3 83.5 - - - +
103F PHE* 1.3 72.3 + - + +
104F GLY 3.5 0.4 - - - -
136F LYS* 6.4 0.4 - - + -
137F LEU* 4.0 33.5 - - + +
51H ARG* 3.9 12.8 + - - -
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Residues in contact with PHE 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ILE* 2.8 22.7 + - + +
102F ALA* 1.3 81.8 - - + +
104F GLY* 1.3 56.2 + - - +
105F SER 2.9 10.0 + - - +
108F LYS* 3.3 20.3 - - - +
109F PHE* 3.6 41.3 - + + +
112F GLN* 3.8 11.9 - - - -
128F LEU* 3.9 17.3 - - + -
137F LEU* 3.9 35.0 - - + -
138F LEU* 4.2 1.1 - - + -
139F ILE* 3.5 39.7 - - + -
51H ARG* 3.7 35.9 + - - +
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Residues in contact with GLY 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F ALA* 2.9 23.6 + - - +
101F ASP 4.3 2.0 + - - -
102F ALA 3.5 1.8 - - - -
103F PHE* 1.3 73.5 - - - +
105F SER* 1.3 62.5 + - - -
108F 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