Contacts of the helix formed by residues 92 - 105 (chain A) in PDB entry 2FGY
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 HIS 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ILE* 3.6 24.7 - - + -
87A PRO 3.7 11.2 + - - -
88A LEU* 4.6 1.3 - - - -
89A GLY 5.1 0.9 - - - -
90A LEU 2.8 24.5 + - - +
91A ASP* 1.3 76.0 + - - +
93A VAL* 1.3 62.7 + - + +
94A THR 3.4 2.2 - - - -
95A ARG* 3.3 19.8 + - - +
96A VAL* 2.8 46.0 + - + +
113A LEU* 4.8 6.4 + - + -
115A ASP* 3.1 17.6 + - - -
121A HIS* 3.4 8.2 + + - -
621A ZN 2.1 37.2 - - - -
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Residues in contact with VAL 93 (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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91A ASP* 3.5 26.1 + - - +
92A HIS* 1.3 79.0 - - + +
94A THR* 1.3 59.9 + - - +
96A VAL* 3.1 4.0 + - - +
97A GLN* 2.9 46.1 + - - +
110A GLU* 4.0 22.4 - - - +
113A LEU* 4.0 37.4 - - + +
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Residues in contact with THR 94 (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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91A ASP* 4.6 3.8 + - - -
92A HIS 3.4 0.2 - - - -
93A VAL* 1.3 81.2 - - - +
95A ARG* 1.3 58.1 + - - +
97A GLN* 4.0 6.7 - - + +
98A GLU* 2.9 54.8 + - + +
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Residues in contact with ARG 95 (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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82A VAL* 6.0 2.6 - - - +
85A GLY 5.5 0.8 + - - -
86A ILE* 3.9 41.7 - - + +
87A PRO* 4.1 14.5 - - - +
92A HIS* 3.3 25.6 + - - +
94A THR* 1.3 80.1 - - - +
96A VAL* 1.3 60.3 + - - +
98A GLU* 4.0 8.7 - - - +
99A LEU* 3.2 23.3 + - + +
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Residues in contact with VAL 96 (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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79A PHE* 4.4 1.2 - - + -
83A VAL* 4.5 23.6 - - + -
86A ILE* 3.7 28.0 - - + -
92A HIS* 2.8 34.4 + - + +
93A VAL* 3.7 3.4 - - - +
95A ARG* 1.3 73.0 - - - +
97A GLN* 1.3 61.2 - - - +
99A LEU* 3.3 7.0 + - - +
100A ALA* 2.8 27.9 + - - +
108A LEU* 3.7 13.9 - - + -
113A LEU* 3.6 31.9 - - + -
126A ILE* 5.1 2.2 - - + -
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Residues in contact with GLN 97 (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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93A VAL* 2.9 20.9 + - - +
94A THR* 4.0 6.7 - - + +
96A VAL* 1.3 76.5 - - - +
98A GLU* 1.3 56.7 + - + +
100A ALA* 3.4 6.3 + - - +
101A GLN* 3.0 28.2 + - - +
106A HIS 4.6 0.3 - - - +
107A THR* 3.5 27.4 + - - +
108A LEU* 2.5 32.6 + - + +
110A GLU* 3.4 31.2 + - - +
113A LEU* 3.8 21.5 - - + +
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Residues in contact with GLU 98 (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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94A THR* 2.9 42.4 + - + +
95A ARG* 4.0 6.9 - - - +
97A GLN* 1.3 75.0 - - + +
99A LEU* 1.3 59.1 + - - +
101A GLN* 3.3 7.8 + - - +
102A SER* 3.0 29.5 + - - -
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Residues in contact with LEU 99 (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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79A PHE* 3.6 25.4 - - + +
82A VAL* 3.4 38.8 - - + -
83A VAL* 4.4 7.6 - - + -
86A ILE* 5.4 5.4 - - + -
95A ARG* 3.2 19.2 + - + +
96A VAL* 3.7 4.3 - - - +
98A GLU* 1.3 73.2 - - - +
100A ALA* 1.3 60.8 + - - +
102A SER* 3.6 8.5 + - - +
103A SER* 2.8 50.1 + - - +
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Residues in contact with ALA 100 (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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79A PHE* 3.6 15.1 - - + -
96A VAL 2.8 17.8 + - - +
97A GLN* 3.6 5.6 - - - +
99A LEU* 1.3 77.2 - - - +
101A GLN* 1.3 57.5 + - - +
104A LEU* 2.8 37.8 + - + +
105A GLY 3.3 0.7 + - - -
106A HIS 3.1 18.6 - - - +
107A THR* 4.7 0.7 - - - -
108A LEU* 3.8 29.2 - - + -
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Residues in contact with GLN 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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97A GLN 3.0 17.1 + - - +
98A GLU* 3.7 8.3 - - - +
99A LEU 3.3 0.2 - - - -
100A ALA* 1.3 73.3 - - - +
102A SER* 1.3 58.9 + - - +
105A GLY* 3.0 36.8 + - - +
106A HIS* 3.2 23.6 + - - +
107A THR* 4.1 7.3 + - - +
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Residues in contact with SER 102 (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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98A GLU 3.0 17.9 + - - -
99A LEU* 3.6 11.6 + - - +
101A GLN* 1.3 78.6 - - - +
103A SER* 1.3 64.2 + - - +
105A GLY 4.6 0.8 + - - -
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Residues in contact with SER 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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75A ARG* 3.4 28.4 + - - +
79A PHE* 4.1 20.9 - - - +
99A LEU* 2.8 43.7 + - - +
102A SER* 1.3 75.1 + - - +
104A LEU* 1.3 62.7 + - - +
105A GLY 3.7 0.4 - - - -
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Residues in contact with LEU 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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72A ARG* 5.3 1.1 + - - +
75A ARG* 3.1 49.9 + - + +
76A VAL* 4.1 24.5 - - + -
79A PHE* 3.8 37.2 - - + -
100A ALA* 2.8 17.4 + - + +
103A SER* 1.3 87.0 - - - +
105A GLY* 1.3 63.1 + - - +
106A HIS* 3.3 40.6 - - + +
108A LEU* 5.2 1.3 - - + -
130A ALA* 4.1 10.3 - - + -
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Residues in contact with GLY 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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75A ARG* 5.0 1.1 - - - -
100A ALA 3.3 0.2 + - - -
101A GLN* 3.0 34.9 + - - +
102A SER 4.6 0.6 - - - -
103A SER 3.7 1.0 - - - -
104A LEU* 1.3 77.3 - - - +
106A HIS* 1.3 60.4 + - - +
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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