Contacts of the helix formed by residues 146 - 159 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 4.8 9.6 - - + -
144B SER 3.3 5.2 + - - +
145B PRO* 1.3 71.3 - - - +
147B GLU* 1.3 73.6 + - - +
148B SER 3.1 0.2 + - - -
149B VAL* 3.2 6.8 + - + +
150B MET* 3.0 26.8 + - + +
171B ARG* 3.9 35.0 - - - +
173B LEU* 4.1 24.7 - - + -
174B PRO* 4.1 22.9 - - + -
177B LEU* 4.2 15.9 - - + -
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 3.9 24.2 - - + +
145B PRO* 3.5 20.0 - - - +
146B LEU* 1.3 88.1 + - - +
148B SER* 1.3 57.3 + - - +
150B MET* 3.6 5.8 + - - +
151B ALA* 3.1 25.8 + - - +
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 5.5 2.5 - - - -
120B LEU* 2.5 36.6 + - - -
121B SER* 3.3 13.7 - - - -
122B PRO* 3.5 6.4 - - - +
125B VAL* 3.8 23.5 - - - +
144B SER* 5.4 1.3 - - - -
145B PRO* 2.9 17.7 + - - +
147B GLU* 1.3 74.7 - - - +
149B VAL* 1.3 62.4 + - - +
151B ALA* 3.2 1.6 + - - +
152B ALA* 2.9 30.3 + - - +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 5.0 3.6 - - + -
140B MET* 3.4 34.0 - - + +
141B GLN 3.7 20.2 - - - +
142B LEU* 4.8 5.6 - - + -
144B SER* 4.2 19.1 - - - +
145B PRO 3.8 10.5 - - - +
146B LEU* 3.2 10.9 + - + +
148B SER* 1.3 77.3 - - - +
150B MET* 1.3 57.6 + - - +
152B ALA 3.4 0.5 + - - -
153B ALA* 2.9 26.7 + - - +
165B LEU* 4.6 13.2 - - + -
177B LEU* 3.9 25.1 - - + -
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.0 21.1 + - + +
147B GLU* 3.8 7.6 - - - +
149B VAL* 1.3 76.4 - - - +
151B ALA* 1.3 65.6 + - - +
153B ALA* 3.3 4.6 + - - +
154B LYS* 3.0 55.8 + - + +
174B PRO* 4.2 12.3 - - + -
176B GLU* 3.9 23.6 - - + +
177B LEU* 3.9 46.0 - - + +
180B LEU* 4.2 4.0 - - - -
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 4.4 19.1 - - + +
125B VAL* 4.1 13.2 - - + -
126B GLU* 5.0 9.9 - - - +
147B GLU 3.1 18.4 + - - +
148B SER* 3.2 4.0 + - - +
150B MET* 1.3 76.6 - - - +
152B ALA* 1.3 64.0 + - - +
154B LYS* 3.4 7.1 + - - +
155B ILE* 3.2 26.6 + - + +
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.1 11.4 - - + -
125B VAL* 3.7 18.7 - - + +
132B ILE* 4.1 9.3 - - + +
138B LEU* 3.6 11.4 - - + +
140B MET* 3.6 23.1 - - - -
148B SER 2.9 17.8 + - - +
151B ALA* 1.3 78.3 - - - +
153B ALA* 1.3 56.1 + - - +
155B ILE* 3.2 3.9 + - - +
156B ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 4.4 3.4 - - - -
140B MET* 4.1 11.6 - - + +
149B VAL 2.9 18.4 + - - +
150B MET 3.3 4.9 + - - +
152B ALA* 1.3 74.5 - - - +
154B LYS* 1.3 58.3 + - - +
156B ALA* 3.3 3.4 + - - +
157B HIS* 2.8 32.2 + - - +
163B VAL* 4.1 10.8 - - + +
177B LEU* 3.7 24.0 - - + -
180B LEU* 3.9 17.6 - - + +
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Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B MET* 3.0 43.5 + - + +
151B ALA* 3.9 6.7 - - - +
152B ALA 3.2 0.2 - - - -
153B ALA* 1.3 74.1 - - - +
155B ILE* 1.3 65.8 + - + +
157B HIS* 3.8 3.6 - - - +
158B GLN* 3.1 31.7 + - + +
176B GLU* 2.4 33.7 + - - -
180B LEU* 3.3 22.7 - - + -
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL* 4.1 21.8 - - + +
126B GLU* 3.8 16.2 - - - +
129B ARG* 3.3 62.4 - - + +
132B ILE* 3.6 24.9 - - + -
133B ALA 4.3 0.9 - - - +
151B ALA 3.2 15.8 + - - +
152B ALA 3.7 6.3 - - - +
154B LYS* 1.3 79.0 - - + +
156B ALA* 1.3 64.9 + - - +
158B GLN* 3.3 1.9 + - - -
159B ASN* 3.1 38.6 + - - +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ILE* 3.8 7.8 - - + +
138B LEU* 3.8 14.4 - - + -
152B ALA 2.9 16.9 + - - +
153B ALA 3.7 0.2 - - - +
155B ILE* 1.3 78.0 - - - +
157B HIS* 1.3 56.9 + - - +
159B ASN* 2.9 2.0 + - - -
160B LYS 2.8 9.0 + - - -
161B THR* 2.7 51.4 + - + -
163B VAL* 3.6 23.1 - - + -
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Residues in contact with HIS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA 2.8 17.6 + - - +
154B LYS* 3.8 3.4 - - - +
156B ALA* 1.3 77.9 - - - +
158B GLN* 1.3 84.5 + - + +
160B LYS* 3.1 15.9 + - - +
161B THR 4.6 3.8 - - - -
163B VAL* 4.3 3.1 - - + +
179B ALA 5.0 6.3 - - - -
180B LEU* 3.5 42.8 + - + +
182B ASP* 5.6 3.0 + - - -
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Residues in contact with GLN 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 6.2 1.1 - - - +
154B LYS* 3.1 19.0 + - + +
155B ILE* 3.9 4.7 - - - +
157B HIS* 1.3 99.4 + - + +
159B ASN* 1.3 68.6 + - - +
160B LYS* 3.4 6.0 + - - +
134D ASN* 5.1 6.1 - - - +
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Residues in contact with ASN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 5.0 6.9 - - - +
133B ALA* 3.2 47.0 - - - +
155B ILE* 3.1 28.5 + - - +
156B ALA 2.9 5.3 + - - +
158B GLN* 1.3 86.1 - - - +
160B LYS* 1.3 79.0 + - - +
161B THR* 3.0 3.2 + - - +
159D ASN 4.7 1.0 - - - +
160D LYS* 3.0 16.5 + - - +
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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