Contacts of the helix formed by residues 1201 - 1205 (chain A) in PDB entry 1PHW
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 THR1201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A ASP* 3.3 8.5 + - - -
1200A VAL* 1.3 84.6 - - + +
1202A HIS* 1.3 65.0 + - - +
1204A LEU* 3.5 6.3 + - - -
1221A VAL* 4.7 7.0 - - + -
1238A ILE* 3.1 34.2 - - + -
1239A GLU* 3.4 37.8 + - - +
1252A PRO* 3.8 0.6 - - - +
1253A SER* 3.2 55.3 + - - +
1255A LEU 4.4 1.6 - - - +
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Residues in contact with HIS1202 (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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70A N 2.7 41.3 + - - +
1026A ASN* 4.0 2.5 + - - -
1055A LYS* 4.7 4.5 - - - -
1138A LYS* 3.8 4.6 + - - -
1168A ARG* 2.7 27.0 + - + -
1177A LEU* 3.8 4.7 - - - +
1199A ASP* 2.4 40.2 + - + +
1201A THR* 1.3 74.8 - - - +
1203A ALA* 1.3 52.1 + - - +
1204A LEU 3.1 7.5 + - - -
1205A GLN* 3.9 6.2 + - - -
1237A PHE* 3.7 12.1 - + - -
1239A GLU* 3.1 37.8 + - - -
1251A GLY 5.0 0.2 - - - +
1252A PRO* 2.9 42.6 - - + +
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Residues in contact with ALA1203 (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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1168A ARG* 3.4 22.7 - - - +
1169A GLY* 4.5 0.2 - - - -
1177A LEU* 4.0 22.9 - - - +
1179A VAL* 3.6 29.0 - - + +
1198A PHE* 3.8 7.2 - - + -
1199A ASP 3.1 17.2 + - - +
1200A VAL 3.1 6.6 + - - +
1202A HIS* 1.3 75.3 - - - +
1204A LEU* 1.3 65.6 + - - +
1205A GLN* 3.6 2.1 + - - +
1224A LEU* 4.6 2.7 - - + +
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Residues in contact with LEU1204 (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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1200A VAL* 3.4 13.7 + - + +
1201A THR 3.5 6.5 + - - +
1202A HIS 3.1 0.6 - - - -
1203A ALA* 1.3 86.7 - - - +
1205A GLN* 1.3 70.3 + - - +
1218A ARG* 3.4 22.8 + - + +
1220A GLN* 3.9 28.9 - - + +
1221A VAL* 3.7 45.8 - - + +
1224A LEU* 4.3 17.7 - - + -
1253A SER* 3.1 19.6 + - - +
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Residues in contact with GLN1205 (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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1175A ASP* 3.4 29.2 + - - +
1176A ASN* 3.4 29.0 + - - +
1177A LEU* 3.8 23.7 + - + +
1202A HIS 3.9 6.5 + - - -
1203A ALA 3.6 1.4 - - - +
1204A LEU* 1.3 84.6 - - - +
1218A ARG* 4.4 18.3 + - - +
1250A ASP* 4.5 7.1 - - - +
1251A GLY 2.6 36.3 + - - +
1252A PRO* 3.1 20.4 - - - +
1253A SER* 4.4 1.8 - - - -
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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