Contacts of the helix formed by residues 1232 - 1236 (chain N) in PDB entry 4G7Z
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 PRO1232 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228N SER 3.2 21.8 - - - +
1229N ILE 3.3 15.7 - - - +
1231N GLU* 1.3 100.6 - - + +
1233N GLY* 1.3 52.8 + - - +
1234N THR 3.4 0.4 - - - -
1235N GLN* 2.5 46.5 + - + +
1236N LEU* 3.5 4.1 + - + +
1356N TYR* 3.7 16.4 - - + -
1361N VAL* 3.5 36.3 - - + -
1363N LEU* 5.3 1.3 - - + -
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Residues in contact with GLY1233 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087N ARG* 5.9 0.3 - - - +
1091N SER* 3.5 13.5 - - - -
1094N LEU* 6.6 0.2 - - - -
1229N ILE 4.1 3.3 + - - -
1230N GLY 2.8 22.3 + - - -
1232N PRO* 1.3 66.7 - - - +
1234N THR* 1.3 51.3 + - - +
1235N GLN 2.3 18.9 + - - -
1236N LEU* 2.3 34.9 + - - +
1256N LEU* 5.0 10.3 - - - +
1356N TYR* 5.0 3.3 - - - -
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Residues in contact with THR1234 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708N LEU* 4.6 15.0 - - + +
1084N THR* 5.7 6.5 - - - +
1087N ARG* 5.0 9.9 - - - +
1088N THR* 4.0 40.2 - - + +
1091N SER* 3.5 16.6 + - - +
1231N GLU 3.6 14.2 + - - -
1233N GLY* 1.3 68.4 - - - +
1235N GLN* 1.3 61.9 + - - +
1236N LEU 3.3 2.4 + - - -
1237N THR* 4.0 10.6 + - - +
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Residues in contact with GLN1235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737N ASN* 6.0 1.6 - - - +
1231N GLU* 4.3 17.4 + - - -
1232N PRO* 2.5 26.9 + - + +
1233N GLY 2.3 12.3 + - - -
1234N THR* 1.3 73.4 + - - +
1236N LEU* 1.3 55.7 + - - -
1237N THR* 3.2 10.6 + - - -
1359N GLN* 2.9 32.4 + - + +
1361N VAL* 4.1 19.2 - - + +
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Residues in contact with LEU1236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087N ARG* 4.2 6.0 - - - -
1232N PRO 4.4 5.2 - - - +
1233N GLY* 2.3 38.4 + - - +
1234N THR 3.3 0.6 - - - -
1235N GLN* 1.3 64.9 - - - +
1237N THR* 1.3 64.7 + - - +
1238N MET* 3.6 3.8 - - - -
1255N GLY* 3.8 1.2 - - - -
1256N LEU* 3.4 47.2 + - + +
1259N VAL* 3.6 16.4 - - + -
1355N VAL* 2.9 37.5 - - + +
1356N TYR* 4.6 21.8 - - + +
1359N GLN* 3.7 30.3 - - + +
1361N VAL* 4.9 2.5 - - + -
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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