Contacts of the helix formed by residues 146 - 159 (chain D) 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 LEU 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D LEU* 4.4 7.4 - - + -
144D SER 3.1 6.8 + - - -
145D PRO* 1.3 71.2 - - - +
147D GLU* 1.3 62.8 + - + +
149D VAL* 3.2 11.5 + - + -
150D MET* 2.8 31.7 + - + +
171D ARG* 3.8 41.2 - - - +
173D LEU* 4.0 10.5 - - + -
174D PRO* 3.8 28.5 - - + -
177D LEU* 3.8 30.3 - - + -
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Residues in contact with GLU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PRO* 4.0 22.6 - - + +
145D PRO* 2.9 19.5 + - - +
146D LEU* 1.3 90.0 + - + +
148D SER* 1.3 56.0 + - - +
150D MET* 3.4 7.0 + - - +
151D ALA* 3.0 27.5 + - - +
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 5.4 4.5 - - - -
120D LEU* 2.6 33.4 + - - -
121D SER* 3.0 17.2 - - - -
122D PRO* 3.1 6.0 - - - +
125D VAL* 3.8 21.5 - - - +
140D MET* 5.4 0.4 - - - -
144D SER* 5.5 0.7 - - - -
145D PRO* 2.9 12.0 + - - +
147D GLU* 1.3 74.3 - - - +
149D VAL* 1.3 67.3 + - - +
151D ALA* 3.3 4.5 + - - +
152D ALA* 3.1 26.9 + - - +
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 5.1 3.6 - - + -
140D MET* 3.5 33.7 - - + +
141D GLN 3.6 24.0 - - - +
142D LEU* 5.0 3.1 - - + -
144D SER* 4.1 20.0 - - - +
145D PRO 3.1 12.3 + - - +
146D LEU* 3.5 14.8 - - + +
148D SER* 1.3 77.3 - - - +
150D MET* 1.3 59.8 + - - +
153D ALA* 3.2 23.0 + - - +
165D LEU* 4.8 7.4 - - + -
177D LEU* 4.2 24.2 - - + -
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Residues in contact with MET 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 2.8 21.2 + - + +
147D GLU* 3.6 8.3 - - - +
149D VAL* 1.3 76.0 - - - +
151D ALA* 1.3 65.1 + - - +
153D ALA* 3.3 2.1 + - - +
154D LYS* 3.0 39.2 + - - +
174D PRO* 4.1 17.3 - - + -
176D GLU* 3.6 43.7 - - + +
177D LEU* 3.8 35.4 - - + +
180D LEU* 4.4 8.3 - - - -
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PRO* 4.6 15.9 - - + +
125D VAL* 4.1 12.8 - - + -
147D GLU 3.0 17.0 + - - +
148D SER* 3.3 6.5 + - - +
150D MET* 1.3 78.2 - - - +
152D ALA* 1.3 61.0 + - - +
154D LYS* 3.6 10.9 + - - +
155D ILE* 3.3 27.7 + - + +
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 4.2 9.4 - - + -
125D VAL* 3.7 19.3 - - + +
132D ILE* 4.1 14.0 - - + +
138D LEU* 3.5 18.1 - - + +
140D MET* 4.0 11.2 - - - -
148D SER 3.1 15.2 + - - +
151D ALA* 1.3 74.9 - - - +
153D ALA* 1.3 61.5 + - - +
154D LYS 3.2 0.2 - - - -
155D ILE* 3.2 3.5 + - - +
156D ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU* 4.1 8.7 - - - +
140D MET* 4.0 10.5 - - + -
149D VAL 3.2 19.1 + - - +
150D MET 3.8 3.8 - - - +
152D ALA* 1.3 78.2 - - - +
154D LYS* 1.3 55.8 + - - +
156D ALA* 3.4 3.9 + - - +
157D HIS* 2.8 30.8 + - - +
163D VAL* 4.1 13.0 - - + +
177D LEU* 4.1 17.0 - - + -
180D LEU* 4.1 17.2 - - + +
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Residues in contact with LYS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D MET* 3.0 32.4 + - + +
151D ALA* 3.6 9.6 - - - +
153D ALA* 1.3 77.2 - - - +
155D ILE* 1.3 63.0 + - + +
157D HIS* 3.4 3.7 + - - +
158D GLN* 3.0 37.6 + - - +
176D GLU* 3.5 32.2 + - - +
180D LEU* 3.8 21.7 - - + +
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D VAL* 4.2 20.6 - - + +
126D GLU* 4.2 9.0 - - - +
129D ARG* 3.7 71.3 - - + +
132D ILE* 4.0 14.8 - - + -
133D ALA 4.6 1.3 - - - +
151D ALA* 3.3 16.0 + - + +
152D ALA 3.2 7.4 + - - +
154D LYS* 1.3 74.1 - - + +
156D ALA* 1.3 68.1 + - - +
158D GLN* 3.3 9.7 + - - +
159D ASN* 3.0 38.4 + - - +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ILE* 3.8 11.5 - - + +
138D LEU* 4.0 7.9 - - + -
152D ALA 3.0 12.6 + - - +
153D ALA 3.5 7.9 - - - +
155D ILE* 1.3 77.9 - - - +
157D HIS* 1.3 57.6 + - - +
159D ASN 2.8 18.0 + - - -
161D THR* 3.1 45.0 + - + -
163D VAL* 3.6 20.9 - - + -
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Residues in contact with HIS 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ALA 2.8 17.5 + - - +
154D LYS* 3.7 5.4 - - - +
155D ILE 3.2 0.2 - - - -
156D ALA* 1.3 77.0 - - - +
158D GLN* 1.3 70.7 + - + +
159D ASN 3.1 1.0 + - - -
160D LYS* 3.4 11.2 + - - +
161D THR 4.8 2.9 - - - -
163D VAL* 5.1 2.9 - - - -
179D ALA 5.3 4.7 - - - -
180D LEU* 3.6 40.6 + - + +
182D ASP* 5.7 3.4 + - - -
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Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ARG* 3.5 26.5 + - - -
154D LYS* 3.0 22.8 + - + +
155D ILE* 3.4 12.0 - - - +
157D HIS* 1.3 84.8 - - + +
159D ASN* 1.3 66.0 + - - +
160D LYS* 3.6 5.6 + - - +
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Residues in contact with ASN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ASN 4.7 1.0 - - - +
160B LYS* 2.7 30.8 + - - -
129D ARG* 4.9 4.6 - - - +
133D ALA* 3.5 41.7 - - - +
155D ILE* 3.0 29.3 + - - +
156D ALA 2.8 4.9 + - - +
158D GLN* 1.3 87.9 + - - +
160D LYS* 1.3 70.2 + - - +
161D THR* 3.2 3.6 - - - +
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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
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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