Contacts of the helix formed by residues 134 - 147 (chain A) in PDB entry 1QGI
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 ALA 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 4.2 21.2 + - - +
9A PRO* 5.8 1.8 - - + -
10A GLU* 5.5 4.9 - - - +
132A ASN 3.5 5.2 + - - -
133A ASP* 1.3 72.0 + - - +
135A ALA* 1.3 57.3 + - - +
137A ARG* 3.4 11.2 + - - +
138A LYS* 3.0 28.1 + - - +
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Residues in contact with ALA 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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85A TYR* 3.9 4.5 - - + -
88A ALA* 3.6 26.4 - - + +
89A LYS* 3.5 29.6 - - + +
133A ASP* 2.9 11.0 + - - +
134A ALA* 1.3 76.0 - - - +
136A TRP* 1.3 59.4 + - - +
138A LYS* 3.4 4.9 + - - +
139A ALA* 2.9 29.5 + - - +
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Residues in contact with TRP 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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47A TYR* 2.8 31.9 + - + -
48A GLY* 4.8 0.2 - - - -
61A ILE* 3.9 23.8 - - + -
81A LEU* 3.8 26.5 - - + -
82A PHE* 4.0 35.2 - + - -
85A TYR* 3.7 34.0 - + + -
127A ILE* 4.1 9.4 - - + +
130A LEU* 3.5 53.2 - - + +
133A ASP* 3.1 19.7 + - + +
135A ALA* 1.3 75.0 - - - +
137A ARG* 1.3 59.9 + - + +
139A ALA* 3.3 2.9 + - + +
140A MET* 2.8 47.2 + - + +
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Residues in contact with ARG 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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5A ASP 2.9 20.4 + - - -
6A ASN* 3.4 7.7 - - - +
7A PHE 2.8 36.8 + - - +
8A SER* 4.8 2.7 - - - -
11A THR* 4.0 6.7 - - - +
44A ILE* 4.7 14.5 - - - +
47A TYR* 3.6 47.3 - - + +
130A LEU 5.1 0.7 - - - +
131A GLN* 2.9 18.0 + - - +
132A ASN* 2.7 35.5 + - - +
133A ASP 3.0 20.2 + - - +
134A ALA* 3.6 10.5 - - - +
135A ALA 3.3 0.2 - - - -
136A TRP* 1.3 74.6 - - - +
138A LYS* 1.3 62.3 + - - +
140A MET* 3.3 1.3 + - - +
141A TRP* 3.0 31.0 + - + -
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Residues in contact with LYS 138 (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 SER* 4.7 0.9 - - - +
10A GLU* 4.5 18.2 + - + -
11A THR* 3.3 25.7 + - - +
14A PHE* 3.6 32.7 - - - +
88A ALA* 4.7 13.0 - - + -
134A ALA 3.0 16.8 + - - +
135A ALA* 3.5 9.0 - - - +
137A ARG* 1.3 76.5 - - - +
139A ALA* 1.3 57.7 + - - +
141A TRP* 3.2 3.7 + - - +
142A GLU* 2.9 74.3 + - - +
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Residues in contact with ALA 139 (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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81A LEU* 3.8 10.1 - - + +
84A ALA* 3.7 13.9 - - + +
85A TYR* 3.5 36.8 - - + +
88A ALA* 4.8 0.4 - - - +
135A ALA 2.9 19.0 + - - +
136A TRP* 3.6 5.4 - - + +
138A LYS* 1.3 76.6 - - - +
140A MET* 1.3 61.1 + - - +
142A GLU* 3.9 5.2 - - - +
143A THR* 2.8 33.4 + - - -
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Residues in contact with MET 140 (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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47A TYR* 3.4 33.4 - - + +
62A GLY* 3.5 16.6 - - - -
63A LEU* 3.6 43.3 - - + +
64A PHE* 3.5 22.8 - - + -
81A LEU* 3.7 15.7 - - + +
136A TRP* 2.8 40.5 + - + +
137A ARG* 3.4 9.9 - - - +
139A ALA* 1.3 78.3 - - - +
141A TRP* 1.3 56.3 - - - +
143A THR 3.4 0.2 + - - -
144A PHE* 2.9 29.7 + - + +
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Residues in contact with TRP 141 (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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7A PHE* 3.7 20.9 - + - -
11A THR* 3.6 29.6 - - + -
14A PHE* 4.3 6.0 - - + -
15A LEU* 3.8 22.6 - - + +
26A TRP* 3.8 29.2 - + - -
30A MET* 3.6 36.6 - - + -
43A TRP* 4.0 8.7 - + - -
47A TYR* 2.9 34.1 + + - -
63A LEU* 4.2 8.7 - - + -
137A ARG* 3.0 26.6 + - + +
138A LYS 3.9 2.2 - - - +
140A MET* 1.3 76.3 - - + +
142A GLU* 1.3 60.2 + - - +
144A PHE* 3.6 24.2 - + - +
145A TYR* 2.9 29.6 + - - +
149A ILE* 3.8 11.9 - - + -
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Residues in contact with GLU 142 (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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14A PHE* 4.1 24.0 - - + -
84A ALA* 4.3 19.0 - - + +
87A ALA* 5.8 2.1 - - - +
88A ALA* 6.3 0.4 - - - -
138A LYS* 2.9 61.6 + - - +
139A ALA* 3.9 5.7 - - - +
141A TRP* 1.3 75.6 - - - +
143A THR* 1.3 58.9 + - - +
145A TYR* 3.3 4.3 - - - +
146A ASN* 2.9 36.7 + - - +
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Residues in contact with THR 143 (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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64A PHE* 3.6 20.6 - - + -
77A ASP 4.3 3.8 - - - +
80A ASP* 4.0 12.0 + - + -
81A LEU* 3.6 36.1 - - + +
84A ALA* 3.7 10.4 - - - +
139A ALA 2.8 22.7 + - - -
140A MET 3.8 2.7 - - - -
142A GLU* 1.3 73.9 - - - +
144A PHE* 1.3 65.4 + - - +
146A ASN* 3.2 8.0 + - + +
147A VAL* 2.9 40.3 + - + +
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Residues in contact with PHE 144 (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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26A TRP* 5.3 1.3 - + - -
30A MET* 3.9 31.6 - - + -
33A ILE* 4.7 2.2 - - + -
63A LEU* 4.9 7.9 - - + -
64A PHE* 3.7 41.1 - + + -
140A MET 2.9 17.7 + - - +
141A TRP* 3.6 32.3 - + - +
143A THR* 1.3 74.9 - - - +
145A TYR* 1.3 57.7 + - - +
147A VAL* 4.8 0.7 - - - -
148A TYR* 2.9 42.1 + + + -
149A ILE* 3.1 15.6 + - + -
171A VAL* 3.9 26.7 - - + -
175A LEU* 3.9 20.2 - - + -
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Residues in contact with TYR 145 (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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14A PHE* 3.6 31.6 - + + -
15A LEU* 5.6 1.6 - - + -
18A ASN* 3.7 40.3 + - + +
19A THR* 4.4 11.9 - - + -
141A TRP 2.9 18.6 + - - +
142A GLU 3.3 4.5 - - - +
144A PHE* 1.3 76.9 - - - +
146A ASN* 1.3 77.3 + - - +
148A TYR 3.6 0.5 + - - -
149A ILE* 3.2 25.4 + - + +
150A ARG* 2.9 71.1 + - + +
153A VAL* 5.3 1.9 - - + +
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Residues in contact with ASN 146 (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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142A GLU* 2.9 25.7 + - - +
143A THR* 3.2 8.2 + - + +
145A TYR* 1.3 92.9 - - - +
147A VAL* 1.3 63.2 + - + +
150A ARG* 3.4 28.3 + - - +
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Residues in contact with VAL 147 (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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64A PHE* 4.3 6.5 - - + -
77A ASP* 3.6 39.3 - - + +
80A ASP* 5.6 2.9 - - - +
143A THR* 2.9 35.0 + - + +
144A PHE 4.2 1.3 - - - +
146A ASN* 1.3 81.7 - - + +
148A TYR* 1.3 96.4 + - + +
151A TYR* 5.4 3.1 - - - +
179A ALA* 4.6 8.1 - - - +
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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