Contacts of the strand formed by residues 151 - 153 (chain C) in PDB entry 5IYB
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 VAL 151 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C SER* 3.6 23.8 - - - +
58C VAL* 5.1 1.6 - - + +
59C LEU* 3.6 29.4 - - + -
64C ILE* 5.0 4.3 - - + -
115C VAL* 3.2 43.1 + - + +
149C LEU* 3.3 11.0 - - - +
150C ILE* 1.3 81.9 - - + +
152C LYS* 1.3 72.5 + - - +
153C LEU* 4.4 9.4 - - + -
159C LEU* 4.1 22.7 - - + -
2J ILE* 5.1 1.6 - - - -
56J ILE* 4.8 8.1 - - + -
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Residues in contact with LYS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER* 4.2 3.6 - - - -
58C VAL* 4.5 5.4 + - - +
112C THR* 4.2 5.1 - - + +
113C ARG 3.7 10.5 - - - +
114C HIS* 3.5 30.8 + - + -
149C LEU* 3.4 33.0 - - + -
151C VAL* 1.3 87.3 - - - +
153C LEU* 1.3 73.2 + - - +
157C GLN* 4.3 1.0 - - - +
18J TRP* 6.1 0.4 - - - +
19J GLU* 3.7 9.1 + - - -
54J ASP* 4.5 3.4 + - - -
56J ILE* 4.0 17.1 - - + +
57J GLU* 2.8 26.9 + - - +
60J LEU* 3.6 37.9 - - + +
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER* 3.5 31.4 - - - +
105C VAL* 3.9 35.9 - - + +
106C ARG* 4.8 3.4 - - - -
107C CYS* 3.9 13.3 - - + +
112C THR* 3.6 4.2 - - - +
113C ARG* 3.3 34.5 + - + +
115C VAL* 4.0 15.7 - - + -
151C VAL* 4.4 4.3 - - + -
152C LYS* 1.3 84.7 - - - +
154C ARG* 1.3 67.7 + - - +
157C GLN* 3.2 25.8 - - + +
158C GLU 4.6 3.8 - - - +
159C LEU* 4.5 9.0 - - + +
60J LEU* 4.4 0.9 - - - -
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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
------------------------------------------------------------
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