Contacts of the strand formed by residues 159 - 163 (chain B) in PDB entry 1Y7M
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 ARG 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.4 45.8 + - - +
159A ARG* 4.8 2.0 - - - +
51B PRO* 4.0 24.9 + - + +
52B TYR 5.7 0.6 - - - +
56B TYR 4.6 5.6 + - - +
57B HIS* 3.6 21.5 - - + -
58B ILE* 2.9 26.3 + - - +
94B GLU* 3.3 30.8 + - - +
95B PHE 3.6 8.5 - - - +
96B TYR* 3.3 26.0 + - + -
157B GLY 3.3 4.4 + - - -
158B THR* 1.3 79.0 - - - +
160B VAL* 1.3 61.8 + - - +
161B THR* 3.9 0.4 - - - +
205B SO4 2.7 32.9 + - - -
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.5 29.4 - - + -
60B VAL* 4.3 7.9 - - + -
93B GLY 3.8 1.4 - - - +
94B GLU* 3.9 0.5 - - - -
95B PHE* 2.9 37.4 + - + +
97B ILE* 3.8 37.0 - - + +
115B LEU* 3.8 23.8 - - + -
122B ILE* 4.4 7.0 - - + -
140B ILE* 5.1 0.2 - - + -
158B THR 3.8 1.6 - - - +
159B ARG* 1.3 77.4 - - - +
161B THR* 1.3 60.8 + - - +
162B ILE* 3.9 21.4 + - + -
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Residues in contact with THR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 3.4 6.7 + - - +
94A GLU* 6.5 1.1 - - + -
57B HIS* 2.8 29.2 + - + -
58B ILE 2.8 9.0 + - - -
59B ALA* 3.3 3.8 - - - -
60B VAL* 2.7 33.8 + - - +
93B GLY 3.6 6.3 - - - +
94B GLU* 2.6 35.9 + - - +
159B ARG* 3.9 0.5 - - - -
160B VAL* 1.3 71.3 - - - +
162B ILE* 1.3 58.6 + - - +
163B ASN* 4.2 22.2 + - - +
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Residues in contact with ILE 162 (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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60B VAL* 3.5 22.0 - - + -
62B ILE* 3.8 26.7 - - + -
90B THR* 4.1 9.2 - - + -
91B PRO* 3.3 28.9 - - + +
92B THR* 3.4 6.3 - - - -
93B GLY* 2.9 36.0 + - - +
95B PHE* 3.8 19.1 - - + -
115B LEU* 4.5 8.7 - - + -
140B ILE* 4.0 20.9 - - + -
160B VAL* 4.1 13.9 - - + -
161B THR* 1.3 75.3 - - - +
163B ASN* 1.3 66.0 + - - +
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Residues in contact with ASN 163 (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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5A GLN* 3.2 41.7 + - + +
7A LYS* 5.6 12.1 - - + -
94A GLU* 5.7 6.4 - - - +
59B ALA* 4.9 2.0 - - - +
60B VAL 2.9 10.2 + - - +
61B SER* 4.9 0.9 - - - -
62B ILE* 3.0 29.8 + - - +
92B THR* 4.2 6.5 - - - -
161B THR* 4.2 22.8 + - - +
162B ILE* 1.3 77.8 - - - +
164B ARG* 1.3 65.9 + - - +
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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