Contacts of the helix formed by residues 300 - 312 (chain A) in PDB entry 5AJQ
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 ASN 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A VAL* 3.9 10.5 - - + -
140A GLN* 3.8 15.3 - - - +
168A GLU* 3.0 21.6 + - - +
169A GLY 3.4 13.9 + - - +
170A ASP* 2.8 24.0 + - - -
299A SER* 1.3 70.9 + - - +
301A LYS* 1.3 63.2 + - - +
302A ALA 3.3 2.2 - - - -
303A LEU* 3.0 6.4 + - - +
304A ARG* 2.6 49.6 + - - +
1314A EDO 3.9 4.1 + - - +
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Residues in contact with LYS 301 (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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299A SER* 3.0 19.6 + - - +
300A ASN* 1.3 78.7 + - - +
302A ALA* 1.3 54.2 + - - +
304A ARG* 2.9 23.3 + - - +
305A GLU* 2.8 56.9 + - + +
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Residues in contact with ALA 302 (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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132A PRO* 3.9 40.2 - - + +
133A GLN* 3.5 21.2 + - + +
136A VAL* 4.3 6.0 - - + +
299A SER 5.0 0.4 + - - -
300A ASN 3.3 0.6 - - - -
301A LYS* 1.3 80.1 - - - +
303A LEU* 1.3 57.9 + - - +
305A GLU* 3.6 14.8 + - - +
306A LEU 3.1 19.8 + - - -
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Residues in contact with LEU 303 (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 LEU* 4.6 0.9 - - + -
133A GLN* 4.1 9.2 - - + +
136A VAL* 3.5 28.1 - - + +
137A VAL* 3.7 19.5 - - + -
140A GLN* 4.6 0.4 - - - +
165A MET* 3.4 28.5 - - + -
169A GLY* 3.2 30.1 - - - +
170A ASP 4.5 1.8 - - - -
171A ILE* 3.8 27.8 - - + -
300A ASN 3.0 6.6 + - - +
302A ALA* 1.3 77.4 - - - +
304A ARG* 1.3 65.8 + - - +
306A LEU* 3.2 16.8 + - + +
307A VAL* 3.1 27.2 + - - +
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Residues in contact with ARG 304 (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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167A LEU 4.0 11.4 - - - +
168A GLU* 3.2 32.7 + - - +
169A GLY* 3.8 10.9 - - - +
299A SER* 5.5 1.0 + - - -
300A ASN* 2.6 30.8 + - - +
301A LYS* 2.9 24.2 + - - +
303A LEU* 1.3 73.2 - - - +
305A GLU* 1.3 66.6 + - + +
307A VAL* 3.3 4.5 + - - +
308A ALA* 2.9 25.8 + - + +
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Residues in contact with GLU 305 (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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133A GLN* 5.4 2.6 + - - +
301A LYS* 2.8 43.6 + - + +
302A ALA* 3.7 12.6 - - - +
304A ARG* 1.3 73.1 - - + +
306A LEU* 1.3 61.0 + - - +
308A ALA* 3.6 7.5 + - - +
309A GLU* 3.3 24.4 + - - +
168B GLU* 4.8 17.7 - - - +
170B ASP* 5.6 2.3 - - - +
300B ASN* 5.0 9.5 + - - -
304B ARG* 5.8 7.0 + - - +
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Residues in contact with LEU 306 (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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118A VAL* 5.9 0.2 - - + -
121A ILE* 4.4 11.4 - - + -
125A LEU* 3.9 24.1 - - + +
127A ARG* 4.1 10.8 - - - +
129A LEU* 3.4 40.8 - - + -
133A GLN* 3.8 26.9 - - - +
165A MET* 4.0 20.0 - - + -
302A ALA 3.1 14.1 + - - +
303A LEU* 3.4 12.6 - - + +
304A ARG 3.2 0.6 - - - -
305A GLU* 1.3 77.0 - - - +
307A VAL* 1.3 62.1 + - - +
309A GLU* 3.4 9.1 + - - +
310A ALA* 3.3 18.5 + - - +
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Residues in contact with VAL 307 (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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115A GLY* 4.4 9.6 - - - -
121A ILE* 4.6 6.1 - - + -
165A MET* 3.5 38.1 - - + -
166A THR 3.9 18.6 - - - +
167A LEU* 3.7 36.1 - - + +
169A GLY* 5.0 3.1 - - - -
303A LEU 3.1 11.8 + - - +
304A ARG* 4.0 4.9 - - - +
306A LEU* 1.3 72.0 - - - +
308A ALA* 1.3 66.0 + - - +
310A ALA* 3.3 7.1 + - + +
311A LYS* 3.1 21.9 + - + +
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Residues in contact with ALA 308 (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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304A ARG* 2.9 20.0 + - + +
305A GLU* 3.6 9.6 - - - +
307A VAL* 1.3 77.2 - - - +
309A GLU* 1.3 61.0 + - - +
311A LYS* 3.4 7.2 + - - +
312A ALA* 3.2 22.4 + - - +
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Residues in contact with GLU 309 (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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125A LEU* 4.6 11.5 - - + +
127A ARG* 3.0 41.4 + - - +
305A GLU 3.3 11.3 + - - +
306A LEU* 3.6 10.1 - - - +
307A VAL 3.3 0.4 - - - -
308A ALA* 1.3 80.4 - - - +
310A ALA* 1.3 58.8 + - - +
312A ALA* 3.6 22.2 - - - +
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Residues in contact with ALA 310 (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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121A ILE* 4.3 28.3 - - + -
124A GLU* 3.5 16.7 - - - +
125A LEU* 4.3 14.5 - - + +
306A LEU 3.3 8.5 + - - +
307A VAL* 3.3 9.8 + - + +
309A GLU* 1.3 76.1 - - - +
311A LYS* 1.3 63.9 + - - +
312A ALA 4.5 2.4 - - - -
800A DB8 3.4 25.2 - - - -
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Residues in contact with LYS 311 (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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167A LEU* 5.5 10.5 - - + -
307A VAL* 3.1 13.2 + - + +
308A ALA* 3.6 10.1 - - - +
310A ALA* 1.3 78.3 - - - +
312A ALA* 1.3 62.8 + - - +
800A DB8 5.0 9.1 - - - -
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Residues in contact with ALA 312 (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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308A ALA 3.2 14.0 + - - +
309A GLU* 3.6 17.9 - - - +
310A ALA 3.5 2.9 - - - -
311A LYS* 1.3 84.3 - - - +
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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