Contacts of the helix formed by residues 123 - 136 (chain A) in PDB entry 3GG0
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 ASP 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A MET* 6.1 0.3 - - - +
84A TYR* 3.4 12.3 + - - -
86A ARG* 2.7 44.6 + - - +
120A PRO* 4.1 7.2 - - + +
121A VAL 3.4 1.4 - - - -
122A ASN* 1.3 78.0 - - - +
124A ARG* 1.3 71.9 + - - +
125A MET* 3.0 19.5 + - - +
126A PHE* 3.7 17.8 - - + +
127A ARG* 3.1 32.9 + - - +
298B LYS* 4.8 9.9 + - - +
353B GLY 5.0 0.2 - - - -
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Residues in contact with ARG 124 (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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77A LEU 3.5 20.0 + - - -
78A MET* 3.7 41.9 - - + +
79A ARG 5.3 0.4 - - - +
80A ASP* 4.5 11.5 + - - +
122A ASN 4.0 1.6 + - - -
123A ASP* 1.3 74.7 + - - +
125A MET* 1.3 65.3 + - - +
127A ARG* 4.1 0.9 - - - +
128A LEU* 3.3 28.4 + - - +
337A THR* 4.9 0.4 + - - -
293B ARG* 5.8 2.2 - - - +
298B LYS* 5.8 0.2 - - - +
318B GLN* 3.3 51.1 + - - +
319B PRO 4.6 13.9 - - - +
320B ASP* 4.2 18.9 + - - +
352B LEU* 2.9 29.1 + - - +
353B GLY 3.4 22.7 - - - +
354B ILE* 4.7 1.4 - - - +
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Residues in contact with MET 125 (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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4A THR* 3.7 27.8 - - + +
6A ILE* 3.7 26.5 - - + +
50A VAL* 3.7 23.6 - - + -
52A GLU* 3.5 23.1 - - - +
78A MET* 4.7 8.2 - - + +
86A ARG* 3.8 27.6 - - - +
87A PHE* 3.7 20.6 - - - -
123A ASP* 3.0 12.3 + - - +
124A ARG* 1.3 78.3 - - - +
126A PHE* 1.3 63.4 + - - +
128A LEU* 3.5 3.6 + - - +
129A LEU* 3.1 26.7 + - + +
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Residues in contact with PHE 126 (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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106A LEU* 3.6 39.9 - - + -
109A ILE* 5.4 3.4 - - + -
110A LEU* 3.7 35.7 - - + -
120A PRO* 3.3 31.6 - - + +
121A VAL* 4.0 25.6 - - + -
123A ASP* 3.4 16.1 + - + +
124A ARG 3.3 0.4 - - - -
125A MET* 1.3 80.7 - - - +
127A ARG* 1.3 63.7 + - - +
129A LEU* 3.4 14.8 + - + +
130A SER* 3.1 31.1 + - - -
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Residues in contact with ARG 127 (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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121A VAL* 3.3 37.8 + - + +
122A ASN 5.5 0.2 - - - -
123A ASP 3.1 19.7 + - - +
124A ARG 4.1 0.4 - - - +
125A MET 3.3 0.4 - - - -
126A PHE* 1.3 80.1 - - + +
128A LEU* 1.3 58.2 + - - +
130A SER* 3.4 8.6 - - - -
131A ALA* 2.9 27.4 + - - +
350B GLU* 5.2 1.1 - - - +
353B GLY* 3.4 36.1 - - - +
354B ILE 4.4 2.7 + - - -
355B THR* 3.1 45.7 + - - +
377B LEU* 4.7 6.3 - - - +
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Residues in contact with LEU 128 (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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6A ILE* 4.2 20.0 - - + -
48A PHE* 3.9 15.5 - - + -
77A LEU* 4.6 25.6 - - + +
78A MET* 4.2 20.4 - - + -
124A ARG* 3.3 20.2 + - - +
125A MET* 3.8 3.8 - - - +
126A PHE 3.3 0.6 - - - -
127A ARG* 1.3 75.9 - - - +
129A LEU* 1.3 54.6 + - - +
131A ALA* 3.0 7.5 + - + +
132A PHE* 2.8 35.3 + - - +
350B GLU 4.8 1.8 - - - +
351B ASP 3.5 26.0 - - - +
352B LEU* 3.7 18.6 - - - +
353B GLY* 3.8 6.7 - - - +
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Residues in contact with LEU 129 (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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39A ILE* 3.8 27.6 - - + -
41A LEU* 3.7 22.4 - - + +
48A PHE* 3.5 27.1 - - + -
50A VAL* 4.4 5.6 - - + -
87A PHE* 4.5 8.3 - - + -
106A LEU* 4.6 8.3 - - + -
109A ILE* 4.3 21.3 - - + -
125A MET* 3.1 25.2 + - + +
126A PHE* 3.5 19.3 - - + +
128A LEU* 1.3 74.3 - - - +
130A SER* 1.3 62.2 + - - +
132A PHE* 3.1 4.3 + - - +
133A ILE* 2.9 31.2 + - + +
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Residues in contact with SER 130 (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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106A LEU* 3.3 28.1 - - - +
126A PHE* 3.1 18.4 + - - -
127A ARG* 3.4 12.1 - - - -
129A LEU* 1.3 77.6 - - - +
131A ALA* 1.3 54.4 + - - +
133A ILE* 3.1 10.5 + - - +
134A ALA* 2.8 38.1 + - - +
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Residues in contact with ALA 131 (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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127A ARG 2.9 16.2 + - - +
128A LEU* 3.0 16.1 + - + +
130A SER* 1.3 76.2 - - - +
132A PHE* 1.3 56.6 + - - +
134A ALA* 4.3 4.0 - - - +
135A ASP* 3.1 32.7 + - - +
350B GLU* 3.9 29.6 - - + +
351B ASP* 5.5 2.0 - - - -
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Residues in contact with PHE 132 (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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8A ARG* 4.7 11.4 - - + -
41A LEU* 3.8 28.5 - - + -
43A ASN* 3.8 19.8 + - - -
46A GLN* 3.9 28.5 - - + -
47A PHE 3.9 8.1 - - - -
48A PHE* 3.5 54.3 - + + -
97A LEU* 4.0 17.5 - - + +
128A LEU 2.8 13.1 + - - +
129A LEU 3.6 7.2 - - - +
131A ALA* 1.3 73.3 - - - +
133A ILE* 1.3 60.3 + - - +
136A GLY* 3.1 42.7 + - - -
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Residues in contact with ILE 133 (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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41A LEU* 3.8 25.1 - - + -
97A LEU* 3.9 25.3 - - + +
103A ASP* 6.1 4.3 - - - +
105A ALA* 4.4 21.5 - - + -
106A LEU* 4.0 30.3 - - + +
109A ILE* 5.4 3.1 - - + -
129A LEU* 2.9 21.2 + - + +
130A SER* 3.7 6.1 - - - +
132A PHE* 1.3 78.9 - - - +
134A ALA* 1.3 61.1 + - - +
136A GLY 5.0 0.5 + - - -
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Residues in contact with ALA 134 (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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130A SER* 2.8 20.9 + - - +
131A ALA* 4.3 3.8 - - - +
133A ILE* 1.3 77.5 - - - +
135A ASP* 1.3 62.6 + - + +
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Residues in contact with ASP 135 (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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131A ALA 3.1 16.5 + - - +
132A PHE* 4.8 0.2 - - - -
134A ALA* 1.3 82.5 - - + +
136A GLY* 1.3 62.7 - - - +
137A GLY* 4.2 3.3 + - - -
138A ARG* 3.0 63.8 + - - +
347B ARG* 4.9 1.0 + - - -
350B GLU* 5.6 0.2 - - - +
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Residues in contact with GLY 136 (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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8A ARG* 4.7 8.1 + - - -
43A ASN* 4.6 5.6 - - - +
46A GLN* 2.7 25.2 + - - -
132A PHE* 3.1 41.5 + - - -
133A ILE 5.0 0.4 + - - -
134A ALA 4.1 0.4 - - - -
135A ASP* 1.3 71.7 - - - +
137A GLY* 1.3 53.5 + - - +
138A ARG* 3.1 9.6 + - - +
139A TYR 4.3 4.2 + - - -
140A CYS 4.6 0.2 + - - -
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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