Contacts of the helix formed by residues 126 - 137 (chain A) in PDB entry 1GV5
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 ILE 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ILE* 6.4 1.3 - - + -
119A ALA* 3.5 7.0 - - - -
124A GLY 5.9 0.7 - - - -
125A ARG* 1.3 78.3 - - - +
127A GLY* 1.3 66.5 + - - +
128A LYS* 3.5 28.0 - - + +
129A GLN* 2.9 40.7 + - + +
130A CYS* 3.3 10.9 + - - -
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Residues in contact with GLY 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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115A TRP* 3.6 42.4 - - - +
116A SER* 4.4 5.9 - - - +
119A ALA* 3.4 6.0 - - - +
126A ILE* 1.3 72.8 - - - +
128A LYS* 1.3 62.0 + - - +
130A CYS* 3.2 4.3 + - - +
131A ARG* 3.0 18.7 + - - +
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Residues in contact with LYS 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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126A ILE* 3.5 26.4 - - + +
127A GLY* 1.3 73.8 - - - +
129A GLN* 1.3 68.9 + - + +
131A ARG* 3.4 36.7 + - - +
132A GLU* 3.0 35.4 + - - +
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Residues in contact with GLN 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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91A ILE* 5.9 3.2 - - - +
92A LYS 4.3 8.3 + - - +
95A TRP* 3.5 17.2 + - + +
124A GLY 3.7 5.1 + - - +
125A ARG* 3.2 32.2 - - - +
126A ILE* 2.9 46.7 + - + +
128A LYS* 1.3 83.3 - - + +
130A CYS* 1.3 63.9 + - - +
132A GLU* 3.9 4.5 - - - +
133A ARG* 3.0 24.6 + - - +
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Residues in contact with CYS 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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95A TRP* 4.1 15.0 - - + -
103A VAL* 4.6 7.2 - - + +
115A TRP* 3.8 17.4 - - + +
118A ILE* 4.4 7.9 - - + -
119A ALA* 4.0 17.9 - - - -
122A LEU* 3.5 31.9 - - - -
125A ARG* 4.2 6.1 - - - -
126A ILE 3.7 11.7 - - - -
127A GLY* 3.2 8.4 + - - +
129A GLN* 1.3 78.4 - - - +
131A ARG* 1.3 63.3 + - - +
133A ARG* 3.3 2.5 + - - +
134A TRP* 3.0 24.9 + - - +
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Residues in contact with ARG 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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115A TRP* 3.5 43.5 - - + +
127A GLY 3.0 12.6 + - - +
128A LYS* 3.6 39.3 - - - +
130A CYS* 1.3 76.9 - - - +
132A GLU* 1.3 83.4 + - - +
134A TRP* 3.3 2.3 + - - +
135A HIS* 3.0 51.2 + - + +
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Residues in contact with GLU 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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128A LYS* 3.0 24.9 + - - +
129A GLN* 4.0 4.7 - - - +
131A ARG* 1.3 110.9 + - - +
133A ARG* 1.3 61.8 + - - +
135A HIS* 4.6 5.6 - - - +
136A ASN* 2.9 58.6 + - - +
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Residues in contact with ARG 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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95A TRP* 3.6 59.1 + - + +
100A ASP* 2.8 43.2 + - - +
103A VAL* 5.2 1.1 - - + -
129A GLN 3.0 18.5 + - - +
130A CYS* 3.7 4.3 - - - +
131A ARG 3.3 0.2 - - - -
132A GLU* 1.3 75.4 - - - +
134A TRP* 1.3 58.0 + - - +
136A ASN* 5.3 0.2 - - - -
137A HIS* 3.0 52.4 + - - +
138A LEU* 3.0 32.7 + - + -
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Residues in contact with TRP 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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103A VAL* 4.5 4.7 - - + -
104A ILE* 4.6 18.6 - - + -
107A VAL* 3.9 39.3 - - + -
112A PRO* 3.7 15.2 - - + +
115A TRP* 3.6 23.3 - + + -
130A CYS 3.0 17.0 + - - +
131A ARG 3.6 0.9 - - - +
132A GLU 3.2 0.2 - - - -
133A ARG* 1.3 79.1 - - - +
135A HIS* 1.3 85.7 + + - +
138A LEU* 3.4 27.9 + - + +
139A ASN* 2.7 69.9 + - + +
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Residues in contact with HIS 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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112A PRO* 5.1 7.7 + - + -
115A TRP* 4.1 14.2 + + - -
131A ARG* 3.0 42.1 + - + +
132A GLU* 4.4 7.0 - - - +
134A TRP* 1.3 95.9 + + - +
136A ASN* 1.3 67.6 + - - +
139A ASN* 3.8 8.4 + - - +
140A PRO* 3.5 20.1 - - - +
141A GLU 4.6 1.4 + - - -
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Residues in contact with ASN 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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132A GLU* 2.9 46.3 + - - +
133A ARG* 5.3 0.2 - - - -
135A HIS* 1.3 83.8 - - - +
137A HIS* 1.3 60.9 + - + +
140A PRO* 4.2 13.0 - - - +
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Residues in contact with HIS 137 (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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100A ASP* 4.0 4.7 - - - -
133A ARG* 3.0 56.1 + - - +
135A HIS 3.7 0.2 - - - -
136A ASN* 1.3 83.1 - - + +
138A LEU* 1.3 87.0 + - + +
139A ASN 3.6 0.9 - - - -
140A PRO* 3.6 10.8 - - - +
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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