Contacts of the helix formed by residues 1148 - 1152 (chain A) in PDB entry 3AVS
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 GLU1148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1146A HIS* 3.2 3.3 + - - -
1147A GLN* 1.3 81.9 - - - +
1149A ASN* 1.3 66.2 + - - +
1150A ASN 3.2 1.4 + - - -
1151A ASN* 3.0 14.4 + - - +
1152A PHE 3.0 34.1 - - - +
1154A SER* 3.7 15.0 + - - +
1220A ILE* 4.9 3.8 - - + -
1221A ASN 6.0 0.2 - - - +
1223A GLY* 5.7 1.9 - - - +
1224A THR 4.9 1.0 + - - +
1226A HIS* 2.8 12.9 + - + -
1240A ASN* 3.0 26.4 + - - +
1255A ARG* 5.0 3.3 + - - -
1501A OGA 3.2 0.3 - - - +
1503A NI 2.1 45.0 - - - +
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Residues in contact with ASN1149 (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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1127A LEU 5.9 0.2 + - - -
1129A MET* 3.6 38.1 - - + +
1147A GLN 3.7 0.5 + - - +
1148A GLU* 1.3 72.1 + - - +
1150A ASN* 1.3 72.1 + - - +
1151A ASN 2.9 1.4 + - - -
1152A PHE* 3.2 17.5 + - - -
1240A ASN* 5.5 0.4 + - - -
1265A LYS 5.5 1.0 - - - +
1267A ILE* 3.8 33.1 + - + +
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Residues in contact with ASN1150 (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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1148A GLU 3.2 1.8 + - - -
1149A ASN* 1.3 73.6 - - - +
1151A ASN* 1.3 68.0 + - - +
1152A PHE* 3.1 21.9 + - + -
1252A ALA* 3.2 35.7 - - + +
1255A ARG* 3.7 17.8 - - - +
1256A TYR* 3.6 11.6 + - - +
1259A ASN* 4.4 4.6 - - - +
1266A SER* 3.3 23.7 + - - +
1267A ILE 3.4 12.9 - - - +
1268A VAL* 3.2 35.6 - - + +
1270A MET* 4.0 2.8 - - - +
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Residues in contact with ASN1151 (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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1147A GLN* 3.6 23.1 + - - +
1148A GLU* 3.0 10.0 + - - +
1149A ASN 2.9 3.0 + - - -
1150A ASN* 1.3 77.4 - - - +
1152A PHE* 1.3 64.2 + - - +
1171A GLU* 5.1 2.0 + - - -
1174A TRP* 6.0 0.4 - - - +
1222A ALA* 3.4 2.6 - - - -
1223A GLY* 3.3 38.0 + - - +
1248A GLN* 3.0 14.5 + - - -
1251A LEU* 3.2 43.6 + - + +
1254A GLU* 5.6 0.8 - - - +
1255A ARG* 3.6 26.8 + - - +
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Residues in contact with PHE1152 (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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1118A LEU* 4.1 18.8 - - + -
1119A LEU* 3.7 24.9 - - + -
1129A MET* 4.0 11.0 - - + -
1148A GLU* 3.0 24.0 - - - +
1149A ASN 3.2 17.9 + - - +
1150A ASN* 3.1 28.3 + - + -
1151A ASN* 1.3 79.2 - - - +
1153A CYS* 1.3 67.7 + - - +
1221A ASN 5.0 0.7 - - - +
1222A ALA* 4.7 0.7 - - - -
1223A GLY 4.9 2.1 + - - -
1240A ASN* 4.3 4.3 - - + +
1241A VAL 3.9 3.6 - - - +
1242A GLY* 3.6 31.0 - - - -
1248A GLN* 3.5 7.9 - - - +
1252A ALA* 3.8 15.7 - - + -
1268A VAL* 3.7 33.0 - - + -
1270A MET* 4.1 5.8 - - - -
1273A LEU* 4.4 6.3 - - + -
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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