Contacts of the helix formed by residues 122 - 134 (chain A) in PDB entry 1GQT
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 PRO 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A SER* 1.3 90.3 - - - +
123A ALA* 1.3 56.0 + - - +
125A VAL* 3.3 10.6 + - + +
126A GLU* 2.9 29.0 + - - +
145A PRO* 6.0 0.4 - - + -
147A GLU* 4.3 28.7 - - + +
148A SER* 3.3 9.6 - - - +
151A ALA* 4.6 16.5 - - + +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A SER* 2.9 9.4 + - - +
122A PRO* 1.3 78.3 - - - +
124A LEU* 1.3 66.6 + - + +
126A GLU* 3.3 7.1 + - - +
127A ALA* 3.2 22.0 + - - +
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Residues in contact with LEU 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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61A ILE* 5.2 5.0 - - + +
63A CYS* 3.7 22.9 - - - -
88A SER* 4.1 23.1 - - - +
90A ILE* 4.4 7.0 - - + -
119A ALA 3.5 22.4 - - - +
120A LEU* 4.3 9.6 - - + -
121A SER* 2.9 17.7 + - - +
123A ALA* 1.3 77.3 - - + +
125A VAL* 1.3 66.4 + - - +
127A ALA* 3.4 15.8 + - + +
128A GLN* 3.6 17.8 + - - +
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Residues in contact with VAL 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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10A LEU* 4.1 19.7 - - + -
61A ILE* 5.7 2.0 - - + -
120A LEU* 4.1 5.8 - - + -
121A SER 3.0 16.5 + - - +
122A PRO* 3.3 9.6 + - + +
124A LEU* 1.3 75.5 - - - +
126A GLU* 1.3 59.9 + - - +
128A GLN* 2.8 27.4 + - - +
129A ARG* 3.4 5.0 + - - -
132A ILE* 4.2 6.0 - - + +
148A SER* 3.6 28.3 - - - +
151A ALA* 4.0 6.3 - - + -
152A ALA* 3.7 34.1 - - + +
155A ILE* 4.0 13.5 - - + +
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Residues in contact with GLU 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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122A PRO 2.9 16.7 + - - +
123A ALA* 3.3 8.0 + - - +
125A VAL* 1.3 78.4 - - - +
127A ALA* 1.3 62.9 + - - +
128A GLN 3.1 1.0 + - - -
129A ARG* 3.1 61.9 + - - +
155A ILE* 4.2 6.6 - - - +
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Residues in contact with ALA 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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123A ALA 3.2 11.9 + - - +
124A LEU* 3.6 18.6 - - + +
125A VAL 3.1 0.4 - - - -
126A GLU* 1.3 75.8 - - - +
128A GLN* 1.3 70.1 + - + +
129A ARG 3.5 0.4 - - - -
130A GLU* 5.4 0.7 + - - +
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Residues in contact with GLN 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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61A ILE* 3.8 33.4 - - + -
85A THR* 6.2 0.2 - - - +
86A PRO* 3.7 26.3 + - - +
124A LEU 3.6 13.8 + - - +
125A VAL* 2.8 11.7 + - - +
127A ALA* 1.3 89.5 + - - +
129A ARG* 1.3 64.1 + - - +
130A GLU* 3.2 3.1 - - - -
131A ARG* 2.9 37.8 + - + +
132A ILE* 2.9 23.6 + - + +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A VAL 3.4 1.8 + - - -
126A GLU* 3.1 48.2 + - - +
127A ALA 3.5 1.0 - - - -
128A GLN* 1.3 75.1 - - - +
130A GLU* 1.3 60.0 + - - +
132A ILE* 3.0 4.6 + - - +
133A ALA* 2.7 40.9 + - + +
155A ILE* 3.7 44.2 - - + +
158A GLN* 3.3 29.7 + - - +
159A ASN* 4.6 4.8 - - - +
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Residues in contact with GLU 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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127A ALA 5.4 0.6 + - - +
128A GLN 3.2 1.0 - - - -
129A ARG* 1.3 87.1 - - - +
131A ARG* 1.3 64.4 + - - +
133A ALA* 3.2 7.8 + - - +
134A ASN* 3.1 49.7 + - - +
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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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8A VAL* 3.9 21.5 - - + +
59A ALA* 3.5 13.3 - - + +
61A ILE* 4.7 7.2 - - - -
83A ASP* 3.3 20.4 + - - -
85A THR* 3.3 32.5 - - - +
86A PRO* 3.6 20.7 - - - +
128A GLN* 2.9 38.7 + - + +
130A GLU* 1.3 81.2 - - - +
132A ILE* 1.3 62.1 + - + +
134A ASN* 3.5 4.4 + - - +
135A ALA* 3.3 21.0 + - - +
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Residues in contact with ILE 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 VAL* 4.6 9.9 - - + -
10A LEU* 5.3 0.4 - - + -
61A ILE* 4.3 24.7 - - + -
125A VAL* 4.2 15.9 - - + +
128A GLN 2.9 21.1 + - - +
129A ARG 3.7 4.7 - - - +
131A ARG* 1.3 76.2 - - - +
133A ALA* 1.3 61.9 + - - +
135A ALA* 3.2 10.6 + - - -
138A LEU* 4.4 11.4 - - + -
152A ALA* 4.0 28.5 - - + +
155A ILE* 3.8 9.0 - - + -
156A ALA* 3.8 36.6 - - + +
161A THR* 2.8 27.0 + - + +
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Residues in contact with ALA 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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129A ARG* 2.7 25.8 + - + +
130A GLU* 3.7 11.9 - - - +
132A ILE* 1.3 76.2 - - - +
134A ASN* 1.3 65.1 + - - +
135A ALA 4.4 0.5 - - - +
155A ILE* 4.4 1.1 - - + +
159A ASN* 3.3 52.5 - - - +
161A THR* 3.7 7.3 + - - -
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Residues in contact with ASN 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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6A SER* 4.5 6.1 - - - -
130A GLU* 3.1 37.3 + - - +
131A ARG* 4.0 4.8 - - - +
132A ILE 3.2 0.2 - - - -
133A ALA* 1.3 79.6 + - - +
135A ALA* 1.3 65.1 + - - +
136A SER* 3.8 1.2 + - - -
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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