Contacts of the helix formed by residues 155 - 167 (chain A) in PDB entry 1Q0R
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 GLN 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A PRO* 4.8 7.1 - - - +
153A GLY 3.7 9.4 - - - +
154A PRO* 1.3 78.7 - - - +
156A GLN* 1.3 68.0 + - - +
157A PRO* 3.3 11.2 - - + +
158A PHE* 3.0 17.9 + - - +
159A LEU* 3.4 8.2 + - - +
247A HIS 5.5 1.0 - - - +
248A ASP 4.1 2.4 - - - +
249A PRO* 2.8 28.6 + - + +
252A PRO* 3.6 23.5 - - + +
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Residues in contact with GLN 156 (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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155A GLN* 1.3 73.6 - - - +
157A PRO* 1.3 65.3 - - + +
159A LEU* 3.0 28.9 + - - +
160A ASP* 2.8 55.0 + - - +
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Residues in contact with PRO 157 (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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155A GLN* 3.4 14.1 - - + +
156A GLN* 1.3 94.5 - - + +
158A PHE* 1.3 55.5 + - - +
160A ASP* 4.1 6.7 - - + +
161A ALA* 3.0 25.3 + - - +
185A ILE* 3.2 38.0 - - + +
186A LEU* 4.0 2.2 - - - +
249A PRO* 3.7 20.9 - - + -
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Residues in contact with PHE 158 (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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134A PHE* 4.4 2.0 - + - -
138A ILE* 3.9 35.0 - - + -
154A PRO* 3.4 20.4 - - + -
155A GLN 3.0 10.8 + - - +
157A PRO* 1.3 78.9 - - - +
159A LEU* 1.3 73.0 + - + +
161A ALA* 3.2 5.5 + - + +
162A LEU* 3.1 46.7 + - + +
186A LEU* 4.1 9.0 - - + -
249A PRO* 4.0 16.5 - - - +
250A ILE* 3.6 25.4 - - + -
600A AKT 3.2 49.4 - - + -
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Residues in contact with LEU 159 (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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138A ILE* 5.1 2.0 - - + -
141A VAL* 4.7 16.8 - - + +
142A MET* 4.1 35.7 - - + -
154A PRO 5.4 1.8 - - - +
155A GLN 3.9 10.5 - - - +
156A GLN* 3.0 35.0 + - - +
158A PHE* 1.3 93.1 - - + +
160A ASP* 1.3 61.5 + - - +
162A LEU* 3.3 13.1 + - + +
163A ALA* 3.0 22.2 + - - +
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Residues in contact with ASP 160 (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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156A GLN* 2.8 48.6 + - - +
157A PRO* 3.6 9.3 - - - +
159A LEU* 1.3 76.8 - - - +
161A ALA* 1.3 57.4 + - - +
163A ALA* 3.2 9.0 + - - +
164A LEU* 3.0 31.2 + - - +
185A ILE* 4.1 17.7 - - + +
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Residues in contact with ALA 161 (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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157A PRO 3.0 17.3 + - - +
158A PHE* 3.5 6.5 - - + +
160A ASP* 1.3 73.6 - - - +
162A LEU* 1.3 60.6 + - + +
164A LEU* 3.4 7.1 + - - +
165A MET* 3.0 38.1 + - - +
182A LYS* 4.2 15.2 - - + +
185A ILE* 4.1 10.0 - - + +
186A LEU* 3.8 28.3 - - + -
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Residues in contact with LEU 162 (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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138A ILE* 4.9 8.5 - - + -
142A MET* 5.9 3.6 - - - -
158A PHE* 3.1 42.8 + - + +
159A LEU* 3.3 18.1 + - + +
161A ALA* 1.3 76.5 - - + +
163A ALA* 1.3 53.6 + - - +
165A MET* 3.3 20.2 + - + +
166A ASN* 2.4 37.9 + - - +
220A TYR* 5.7 1.8 - - + +
600A AKT 4.0 37.9 - - + -
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Residues in contact with ALA 163 (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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159A LEU 3.0 13.0 + - - +
160A ASP* 3.2 12.5 + - - +
162A LEU* 1.3 74.3 - - - +
164A LEU* 1.3 65.8 + - + +
166A ASN* 3.2 25.0 + - - +
167A GLN* 3.5 16.2 + - - +
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Residues in contact with LEU 164 (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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160A ASP 3.0 10.3 + - - +
161A ALA* 3.7 9.4 - - - +
163A ALA* 1.3 73.4 - - + +
165A MET* 1.3 66.0 + - - +
166A ASN 3.1 0.4 - - - -
167A GLN* 3.1 45.5 + - - +
178A LYS* 3.2 18.7 - - + +
181A SER* 3.0 35.2 - - - +
182A LYS* 4.2 5.6 - - + +
185A ILE* 3.3 33.0 - - + -
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Residues in contact with MET 165 (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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161A ALA* 3.0 29.4 + - - +
162A LEU* 3.5 27.6 - - + +
163A ALA 3.3 0.2 - - - -
164A LEU* 1.3 76.0 - - - +
166A ASN* 1.3 58.8 + - - +
167A GLN 3.4 0.2 - - - -
178A LYS* 3.0 25.2 + - - +
182A LYS* 3.7 29.4 - - + -
186A LEU* 6.3 0.2 - - - -
215A GLU* 4.2 12.8 - - - +
220A TYR* 3.1 28.3 - - + +
600A AKT 4.5 4.5 - - + -
3482A SO4 3.6 22.4 - - - +
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Residues in contact with ASN 166 (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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162A LEU* 2.4 27.8 + - - +
163A ALA* 3.2 19.3 - - - +
164A LEU 3.1 1.0 - - - -
165A MET* 1.3 78.3 - - - +
167A GLN* 1.3 61.5 + - + +
168A PRO* 3.7 4.5 - - - +
178A LYS* 4.6 0.2 - - - -
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Residues in contact with GLN 167 (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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163A ALA* 3.5 15.4 + - - +
164A LEU* 3.1 36.9 + - - +
166A ASN* 1.3 76.6 - - + +
168A PRO* 1.4 71.7 - - + +
178A LYS* 2.6 35.4 + - + +
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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