Contacts of the helix formed by residues 153 - 158 (chain V) in PDB entry 2AXT
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 GLY 153 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81V ARG* 5.0 2.6 + - - -
149V PRO* 2.8 30.7 + - - +
150V LYS 4.5 0.9 - - - -
151V ILE 3.5 1.6 - - - -
152V LEU* 1.3 70.1 - - - +
154V ASP* 1.3 67.0 - - - +
156V TRP* 3.1 18.4 + - - +
157V GLY 4.1 1.2 + - - -
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Residues in contact with ASP 154 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81V ARG* 3.7 17.4 + - - +
152V LEU 3.4 1.6 + - - -
153V GLY* 1.3 71.5 - - - -
155V LYS* 1.3 65.8 + - - +
157V GLY 3.0 11.8 + - - -
158V GLY 3.5 8.5 + - - -
162V TYR* 4.2 34.4 + - + -
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Residues in contact with LYS 155 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A HIS* 4.3 18.8 - - - +
313A VAL* 4.4 23.4 + - + +
315A ASN* 5.4 4.9 - - - +
69V GLY* 3.9 3.1 - - - +
152V LEU* 3.5 42.0 + - + +
153V GLY 3.1 0.2 - - - -
154V ASP* 1.3 76.3 - - - +
156V TRP* 1.3 64.1 + - - +
158V GLY 2.9 20.4 - - - +
162V TYR* 4.1 34.7 - - + +
163V TYR* 4.5 5.3 - - - -
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Residues in contact with TRP 156 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59V PHE* 3.9 24.7 - + - -
69V GLY* 2.4 41.3 - - - +
70V GLY* 3.2 36.8 - - - +
80V LEU* 3.0 41.6 + - + -
81V ARG* 4.1 9.4 - - + -
144V HIS* 4.7 3.8 - + - -
145V ILE* 4.0 15.9 + - - -
148V GLU* 3.6 31.0 - - + -
149V PRO* 3.5 40.5 - - + +
152V LEU* 4.0 18.8 - - + +
153V GLY 3.1 13.6 + - - +
155V LYS* 1.3 78.5 - - - +
157V GLY* 1.3 64.1 + - - +
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Residues in contact with GLY 157 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134U LYS* 3.7 6.5 + - - -
70V GLY 3.5 5.0 - - - +
71V ILE* 3.1 18.2 - - - +
79V ASP* 4.4 1.1 - - - +
81V ARG* 3.1 43.5 - - - +
153V GLY 4.1 0.2 + - - -
154V ASP 3.0 8.1 + - - -
156V TRP* 1.3 83.8 - - - +
158V GLY* 1.3 61.0 + - - +
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Residues in contact with GLY 158 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134U LYS* 3.9 17.9 - - - -
69V GLY* 4.3 2.3 - - - +
71V ILE* 3.9 9.2 - - - +
81V ARG* 3.1 16.5 - - - +
154V ASP 3.5 3.8 + - - -
155V LYS 2.9 18.7 - - - +
156V TRP 4.1 0.5 - - - +
157V GLY* 1.3 75.7 - - - +
159V GLY* 1.3 59.1 + - - -
162V TYR* 4.0 14.8 - - - +
163V TYR* 5.2 1.6 - - - -
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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