Contacts of the helix formed by residues 108 - 123 (chain A) in PDB entry 2GDZ
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 LEU 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 3.0 20.8 + - + +
106A ILE 3.4 0.2 - - - -
107A ASN* 1.3 78.8 - - - +
109A VAL* 1.3 71.9 + - + +
110A SER 3.2 1.6 - - - -
111A VAL* 3.1 4.1 + - + +
112A ILE* 3.1 47.8 + - + +
153A ALA 4.9 1.6 - - - +
154A SER* 3.9 21.8 - - - +
157A GLY* 3.6 40.2 - - - +
158A ILE* 3.7 10.5 - - + +
161A PHE* 5.2 0.4 - - + -
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 6.2 0.7 - - - +
68A GLN* 4.7 10.1 - - + +
104A LEU* 3.0 15.9 + - + +
105A GLN* 3.4 41.5 - - - +
108A LEU* 1.3 78.9 - - + +
110A SER* 1.3 61.1 + - - +
112A ILE* 3.2 10.9 + - + +
113A SER* 2.9 39.6 + - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.0 40.8 + - - +
66A ALA* 3.1 15.6 + - - +
71A LEU* 4.3 3.5 - - - +
90A ASN* 4.4 2.4 - - - +
105A GLN 2.9 14.1 + - - -
106A ILE* 3.2 17.4 - - - -
108A LEU 3.2 0.8 - - - -
109A VAL* 1.3 75.5 - - - +
111A VAL* 1.3 59.4 + - - +
113A SER* 3.9 7.7 - - - -
114A GLY* 2.9 26.7 + - - -
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASN* 3.7 27.9 + - + +
92A ALA 5.0 7.0 - - - +
106A ILE 4.6 2.9 - - - +
107A ASN* 3.1 23.6 - - - +
108A LEU* 3.1 9.4 + - + +
110A SER* 1.3 76.6 - - - +
112A ILE* 1.3 60.0 + - + +
115A THR* 2.9 34.2 + - - +
135A ASN* 3.4 37.9 - - + +
136A MET 5.2 1.1 - - - +
158A ILE* 4.1 20.0 - - + -
161A PHE* 4.7 6.3 - - + -
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Residues in contact with ILE 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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108A LEU* 3.1 37.3 + - + +
109A VAL* 3.5 9.4 - - + +
111A VAL* 1.3 74.3 - - + +
113A SER* 1.3 62.3 + - - +
115A THR* 3.2 2.4 + - - -
116A TYR* 2.9 54.8 + - + +
161A PHE* 3.9 42.6 - - + -
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL 5.3 0.7 - - - -
68A GLN* 3.3 40.8 + - - +
71A LEU* 4.2 13.7 - - - -
109A VAL* 2.9 23.8 + - - +
110A SER* 4.0 6.5 - - - -
112A ILE* 1.3 77.2 - - - +
114A GLY* 1.3 63.0 + - - +
116A TYR* 3.2 9.5 + - - +
117A LEU* 3.0 28.8 + - - +
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.7 15.8 - - - +
75A PHE* 3.6 11.3 - - - -
88A LEU* 3.1 13.7 - - - +
90A ASN* 3.8 10.1 - - - -
110A SER 2.9 18.3 + - - -
113A SER* 1.3 75.2 - - - +
115A THR* 1.3 59.3 + - - +
117A LEU 3.1 0.7 + - - -
118A GLY 2.8 26.5 + - - -
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Residues in contact with THR 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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88A LEU* 4.2 3.6 - - - -
90A ASN* 3.2 17.1 + - - +
111A VAL 2.9 24.2 + - - -
112A ILE 3.6 4.7 - - - -
114A GLY* 1.3 75.5 - - - +
116A TYR* 1.3 56.1 + - + +
118A GLY* 3.1 3.3 + - - -
119A LEU* 2.9 35.7 + - + +
133A ILE* 3.5 6.6 - - + +
135A ASN* 3.3 16.1 + - - -
161A PHE* 3.6 22.9 - - + -
165A ALA* 4.9 0.4 - - + -
178A LEU* 3.4 32.3 - - + -
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Residues in contact with TYR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 2.9 34.4 + - + +
113A SER* 3.7 7.4 - - - +
114A GLY 3.2 0.2 - - - -
115A THR* 1.3 76.1 - - - +
117A LEU* 1.3 58.7 + - + +
119A LEU* 3.3 24.1 + - + +
120A ASP* 2.9 36.1 + - - +
161A PHE* 3.8 29.8 - + - -
165A ALA* 5.7 3.1 - - + -
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 5.0 1.6 - - - +
71A LEU* 3.7 31.9 - - + -
72A ARG* 3.8 43.1 - - + +
75A PHE* 3.9 21.3 - - + -
113A SER* 3.0 20.0 + - - +
114A GLY 3.6 5.4 - - - +
116A TYR* 1.3 72.9 - - + +
118A GLY* 1.3 66.1 + - - +
120A ASP* 3.0 27.9 + - + +
121A TYR* 3.1 30.9 + - + -
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Residues in contact with GLY 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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75A PHE* 3.6 13.3 - - - -
85A LEU* 4.6 3.1 - - - -
88A LEU* 3.9 9.9 - - - -
114A GLY 2.8 18.6 + - - -
115A THR 3.5 3.8 - - - -
117A LEU* 1.3 72.7 - - - +
119A LEU* 1.3 55.9 + - - +
121A TYR* 3.3 0.3 + - - -
122A MET* 2.8 50.5 + - - +
133A ILE* 4.1 2.5 - - - -
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR* 2.9 25.3 + - + +
116A TYR* 3.6 30.3 - - + +
118A GLY* 1.3 73.2 - - - +
120A ASP* 1.3 66.0 + - - +
122A MET* 5.0 0.2 - - - -
123A SER* 2.9 26.4 + - - +
126A ASN* 3.0 12.3 + - - +
133A ILE* 3.9 5.4 - - + -
165A ALA* 5.5 4.5 - - + +
169A ALA* 5.6 1.6 - - + -
172A MET* 6.1 4.7 - - - -
174A SER* 4.8 9.2 - - - +
176A VAL* 3.6 40.4 - - + -
178A LEU* 4.6 12.6 - - + -
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 2.9 23.1 + - - +
117A LEU* 3.0 28.6 + - + +
119A LEU* 1.3 76.3 - - - +
121A TYR* 1.3 67.1 + - + +
126A ASN* 3.2 34.9 + - - +
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Residues in contact with TYR 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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72A ARG 4.5 1.7 + - - -
75A PHE* 3.6 30.5 - + + -
76A ARG* 3.3 29.8 + - - +
79A VAL* 3.6 37.2 - - + -
85A LEU* 4.4 15.3 - - + -
117A LEU* 3.1 35.0 + - + +
118A GLY 4.0 2.5 - - - +
120A ASP* 1.3 83.5 - - + +
122A MET* 1.3 60.3 - - + +
123A SER 3.6 0.2 - - - -
126A ASN 5.0 0.9 - - - +
127A GLY 4.6 0.7 - - - -
128A GLY* 3.4 22.9 + - - -
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Residues in contact with MET 122 (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 LEU* 3.4 43.7 - - + +
86A ASP* 3.5 25.8 - - - +
87A ILE 4.0 0.7 - - - -
88A LEU* 4.3 8.1 - - + -
118A GLY* 2.8 29.9 + - - +
121A TYR* 1.3 74.5 - - - +
123A SER* 1.3 62.2 + - - +
128A GLY* 3.9 3.1 - - - -
129A GLU 3.5 2.5 + - - +
130A GLY* 2.7 36.2 + - - +
131A GLY* 4.0 5.8 - - - -
132A ILE 3.9 11.4 - - - +
133A ILE* 3.6 31.9 - - + -
176A VAL* 3.9 13.7 - - + -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 2.9 24.6 + - - -
121A TYR 3.6 0.4 - - - -
122A MET* 1.3 75.9 - - - +
124A LYS* 1.3 66.6 + - - +
125A GLN* 3.0 17.9 + - - +
126A ASN* 2.9 27.2 + - - +
128A GLY 3.0 13.6 + - - -
172A MET* 5.9 0.2 - - - +
174A SER* 3.3 28.5 - - - -
176A VAL* 3.9 5.6 - - - +
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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
------------------------------------------------------------
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