Contacts of the helix formed by residues 1119 - 1123 (chain A) in PDB entry 1Y1S
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 ALA1119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1071A GLY* 4.0 10.3 - - - +
1072A PRO 4.4 0.2 - - - -
1117A ASP* 3.7 1.0 + - - +
1118A GLY* 1.3 75.4 - - - +
1120A SER* 1.3 61.4 + - - +
1122A HIS* 2.8 26.7 + - - +
1123A PHE* 3.3 10.2 - - - -
1160A ASP* 5.9 0.2 - - - +
1201A THR* 3.3 31.2 - - + +
4160F ASP* 3.3 32.2 + - + +
4161F THR* 4.1 8.5 - - + -
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Residues in contact with SER1120 (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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1115A ARG* 3.0 31.5 + - - +
1117A ASP* 2.7 39.8 + - - -
1119A ALA* 1.3 75.9 - - - +
1121A LEU* 1.3 61.0 + - - +
1123A PHE* 2.9 23.4 + - - +
1124A ALA 2.9 12.5 + - - +
1200A ALA 4.0 4.0 - - - -
1201A THR* 4.1 4.7 + - - +
1204A THR* 3.5 24.6 - - - +
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Residues in contact with LEU1121 (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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1115A ARG* 4.0 4.0 - - - +
1117A ASP 4.3 9.4 - - - +
1118A GLY* 3.4 16.7 + - - +
1119A ALA 3.1 0.6 - - - -
1120A SER* 1.3 82.3 + - - +
1122A HIS* 1.3 59.9 + - - +
1123A PHE 3.1 2.1 + - - -
1124A ALA 3.2 16.6 + - - +
1125A PRO* 4.1 4.2 - - + +
1126A MET* 3.5 60.1 - - + +
4177F VAL* 4.0 10.4 - - - +
4179F ARG* 4.0 25.1 + - - +
4180F PHE* 4.2 3.5 - - - -
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Residues in contact with HIS1122 (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 GLY 3.2 18.9 + - - -
1119A ALA 2.8 11.2 + - - +
1121A LEU* 1.3 78.4 - - - +
1123A PHE* 1.3 61.2 + - + +
4116F LEU* 3.0 28.1 + - + -
4159F SER* 3.4 8.7 - - - -
4160F ASP* 3.3 19.9 - - + +
4161F THR* 2.7 38.6 + - + +
4164F PRO* 3.3 25.1 - - + +
4165F GLY* 3.6 3.2 - - - -
4177F VAL* 3.7 12.8 + - - +
4179F ARG* 3.8 8.2 + - - -
4180F PHE* 3.3 35.9 - + + -
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Residues in contact with PHE1123 (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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1075A SER* 4.2 11.0 - - - -
1079A GLU* 5.5 4.9 - - + -
1119A ALA 3.3 26.0 - - - -
1120A SER* 2.9 7.4 + - - +
1122A HIS* 1.3 82.0 - - - +
1124A ALA* 1.3 62.2 + - - +
1201A THR* 4.8 2.7 - - + -
1204A THR* 4.3 2.2 - - + -
1205A MET* 3.3 43.3 - - + -
1208A SER* 3.9 15.5 + - - +
1209A GLN* 3.4 35.7 - - + -
5190E MET* 3.6 2.4 - - - +
4161F THR* 3.9 14.1 - - + -
4164F PRO* 3.9 26.7 - - + -
4175F ARG* 3.4 24.8 + - - +
4177F VAL* 3.6 12.8 - - - +
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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