Contacts of the helix formed by residues 111 - 121 (chain A) in PDB entry 1GEY
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A TYR* 6.2 1.3 - - - -
109A THR 3.3 5.8 + - - -
110A TYR* 1.3 74.6 - - - +
112A MET* 1.3 63.7 + - - +
113A TYR 3.2 4.2 + - - -
114A SER* 3.3 14.7 + - - -
115A VAL* 3.2 21.8 - - - +
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Residues in contact with MET 112 (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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85A ASP* 3.6 22.7 - - + +
88A ILE* 4.3 6.3 - - + +
89A GLU* 6.0 1.3 - - + +
110A TYR* 3.4 43.7 - - + +
111A GLY* 1.3 75.4 - - - +
113A TYR* 1.3 65.2 + - - +
115A VAL* 3.8 26.2 - - + -
116A SER* 3.1 45.4 + - - +
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Residues in contact with TYR 113 (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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88A ILE* 3.6 34.1 - - + -
92A ILE* 4.3 5.2 - - - +
103A ILE* 4.7 5.2 - - + +
105A TYR* 4.3 17.0 - + + -
109A THR* 3.7 26.7 - - + -
110A TYR* 3.3 32.0 - + + +
111A GLY 3.2 1.2 - - - -
112A MET* 1.3 78.9 - - - +
114A SER* 1.3 60.3 + - - +
116A SER* 4.1 2.4 - - - -
117A ALA* 3.4 19.2 + - - +
151A TYR* 3.8 52.2 - + + -
153A CYS* 3.5 15.7 - - + +
184A ASP* 2.7 36.4 + - + +
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Residues in contact with SER 114 (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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103A ILE* 5.5 0.2 - - - -
105A TYR* 3.3 38.5 + - - -
111A GLY* 3.3 12.0 + - - -
113A TYR* 1.3 77.5 - - - +
115A VAL* 1.3 65.9 + - - +
117A ALA* 3.9 1.5 - - - +
118A GLU* 2.9 31.0 + - - +
124A CYS* 3.9 18.6 - - - -
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Residues in contact with VAL 115 (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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17A LEU* 5.9 4.3 - - + -
111A GLY 3.2 21.7 + - - +
112A MET* 4.0 27.4 - - + +
113A TYR 3.3 0.6 - - - -
114A SER* 1.3 77.4 + - - +
116A SER* 1.3 56.9 + - - +
118A GLU* 3.3 13.2 + - - +
119A THR* 2.7 45.3 + - - +
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Residues in contact with SER 116 (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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85A ASP 4.8 1.0 + - - -
88A ILE* 4.1 9.1 - - - +
89A GLU* 3.4 32.3 + - - +
92A ILE* 3.9 18.4 - - - -
112A MET* 3.1 30.6 + - - +
113A TYR 4.1 0.9 - - - -
115A VAL* 1.3 76.9 - - - +
117A ALA* 1.3 59.0 + - - +
119A THR* 3.2 5.3 + - - -
120A ILE* 2.9 36.3 + - - +
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Residues in contact with ALA 117 (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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92A ILE* 3.9 13.6 - - + +
103A ILE* 4.3 8.5 - - + -
113A TYR 3.4 14.4 + - - +
114A SER 4.0 3.8 - - - +
116A SER* 1.3 78.6 - - - +
118A GLU* 1.3 58.1 + - - +
120A ILE* 4.5 2.5 - - - -
121A GLY 2.8 9.7 + - - -
122A VAL* 2.8 57.8 + - + +
124A CYS* 4.2 11.2 - - - -
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Residues in contact with GLU 118 (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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13A ASN* 2.9 28.4 + - + +
16A ASN* 5.0 2.1 - - - +
17A LEU* 3.7 33.4 + - + +
114A SER 2.9 20.8 + - - +
115A VAL* 3.7 13.7 - - - +
117A ALA* 1.3 78.6 - - - +
119A THR* 1.3 57.7 + - - +
121A GLY* 3.7 3.3 + - - +
122A VAL 4.5 3.8 - - - -
124A CYS* 5.0 4.0 - - - -
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Residues in contact with THR 119 (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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11A ARG* 3.4 10.6 + - - -
13A ASN* 3.0 16.5 + - - -
14A VAL* 4.7 6.6 - - + +
17A LEU* 3.7 26.6 - - + +
89A GLU* 5.3 7.9 - - - +
115A VAL* 2.7 30.1 + - - +
116A SER* 3.2 6.9 + - - -
118A GLU* 1.3 77.8 - - - +
120A ILE* 1.3 59.5 + - + +
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Residues in contact with ILE 120 (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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11A ARG* 3.0 21.2 + - - +
89A GLU* 4.2 18.4 - - + +
92A ILE* 3.8 26.5 - - + +
93A ARG* 3.8 33.7 - - + -
96A CYS 5.6 0.9 - - - +
98A PRO* 4.5 18.5 - - + +
116A SER 2.9 22.5 + - - +
117A ALA* 3.9 4.0 - - - +
119A THR* 1.3 80.8 - - + +
121A GLY* 1.3 56.0 + - - +
122A VAL* 4.2 18.2 - - + -
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Residues in contact with GLY 121 (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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11A ARG* 4.1 9.4 - - - -
13A ASN* 4.3 6.3 - - - -
98A PRO* 4.0 5.0 - - - +
99A GLY* 3.5 20.6 + - - -
117A ALA 2.8 5.5 + - - -
118A GLU* 3.7 6.9 + - - -
119A THR 3.4 2.4 - - - -
120A ILE* 1.3 80.5 - - - +
122A VAL* 1.3 63.7 + - - +
123A GLU 4.2 0.3 + - - -
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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