Contacts of the helix formed by residues 6030 - 6036 (chain B) 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 ARG6030 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6025B PRO* 4.4 6.1 - - + -
6027B ASP* 3.1 33.2 + - + +
6028B PRO 3.1 1.0 - - - -
6029B GLU* 1.3 106.3 + - - +
6031B VAL* 1.3 68.2 + - - +
6032B GLU 3.1 2.9 - - - -
6033B LYS* 2.9 42.0 + - - +
6034B ILE* 2.9 41.6 + - + +
6233B THR* 5.3 3.7 + - - -
6234B MET* 4.0 30.0 - - - +
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Residues in contact with VAL6031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6025B PRO* 4.0 8.0 - - + +
6027B ASP 4.0 0.6 + - - -
6028B PRO* 3.5 16.5 + - + +
6030B ARG* 1.3 78.0 - - - +
6032B GLU* 1.3 56.3 + - - +
6035B ALA* 2.9 28.9 + - - +
6051B THR* 2.8 34.1 - - + +
6053B TRP* 3.5 26.0 - - + -
6064B VAL* 3.3 32.7 - - + +
6065B CYS 4.2 1.1 - - - -
6066B SER* 3.5 24.5 - - - +
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Residues in contact with GLU6032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6028B PRO 4.7 1.6 + - - +
6029B GLU 5.1 6.1 - - - +
6030B ARG 3.1 0.8 - - - +
6031B VAL* 1.3 79.7 - - - +
6033B LYS* 1.3 70.0 + - + +
6035B ALA* 3.3 1.9 + - - +
6036B ALA* 2.9 28.3 + - + +
6051B THR* 5.5 0.2 - - - +
6053B TRP* 3.7 47.9 + - + +
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Residues in contact with LYS6033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6029B GLU* 2.9 51.6 + - - +
6030B ARG* 2.9 46.3 + - - +
6032B GLU* 1.3 84.6 - - + +
6034B ILE* 1.3 63.8 + - + +
6036B ALA* 3.3 18.8 + - - +
6037B LEU* 3.6 14.3 - - - +
6242B VAL* 5.9 0.2 - - - -
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Residues in contact with ILE6034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6023B ILE* 4.3 16.6 - - + -
6025B PRO* 3.8 33.4 - - + -
6030B ARG* 2.9 27.8 + - + +
6031B VAL 4.0 2.0 - - - +
6033B LYS* 1.3 75.4 - - + +
6035B ALA* 1.3 64.8 + - - +
6036B ALA 3.0 1.8 - - - -
6037B LEU* 3.0 23.0 + - - +
6038B MET* 3.6 20.4 - - + +
6064B VAL* 4.1 10.5 - - + -
6092B ILE* 4.2 16.2 - - + -
6242B VAL* 4.0 32.1 - - + -
6245B VAL* 4.9 0.2 - - + -
6246B VAL* 4.4 4.7 - - + +
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Residues in contact with ALA6035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6031B VAL 2.9 18.3 + - - +
6032B GLU 3.8 3.1 - - - +
6034B ILE* 1.3 76.4 - - - +
6036B ALA* 1.3 57.1 + - - +
6037B LEU 3.1 0.2 - - - -
6038B MET* 3.0 36.6 + - - +
6041B PRO* 3.5 17.2 - - + +
6053B TRP* 3.9 36.1 - - + -
6055B ALA* 4.1 6.5 - - + +
6064B VAL* 4.0 8.9 - - + +
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Residues in contact with ALA6036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6032B GLU* 2.9 22.5 + - + +
6033B LYS* 3.3 13.7 - - - +
6034B ILE 3.0 0.2 - - - -
6035B ALA* 1.3 77.7 - - - +
6037B LEU* 1.3 61.9 + - + +
6038B MET 3.2 7.1 + - - +
6041B PRO* 4.4 12.5 - - - +
6053B TRP* 6.3 0.2 - - - -
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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