Contacts of the strand formed by residues 150 - 156 (chain A) in PDB entry 2CAS
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 LEU 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 3.8 23.6 - - + -
149A VAL* 1.3 77.3 - - - +
151A LYS* 1.3 65.8 + - - +
167A ASN* 3.7 5.2 + - - +
168A ASP* 2.9 28.9 + - - +
171A ALA* 3.6 43.1 - - + +
172A SER* 3.8 19.5 - - - +
173A LEU* 3.9 2.9 - - + +
255A LEU 4.4 0.4 - - - +
256A ARG* 5.1 1.8 - - - -
257A THR* 5.2 4.4 + - - +
502A VAL* 3.8 26.5 - - + -
523A THR* 3.8 11.9 - - + -
524A TYR 3.3 3.4 - - - -
525A SER* 3.7 18.2 - - - -
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Residues in contact with LYS 151 (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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149A VAL* 4.0 19.3 - - + +
150A LEU* 1.3 80.4 - - - +
152A THR* 1.3 65.3 + - - +
165A TYR* 4.5 16.6 + - + +
166A ASN 3.0 14.6 - - - +
167A ASN* 3.1 35.6 - - - +
168A ASP 4.3 0.4 - - - +
523A THR* 3.2 4.3 - - - +
524A TYR* 2.8 69.8 + - + +
526A ASP* 5.5 2.2 - - - +
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS* 1.3 78.0 - - - +
153A VAL* 1.3 63.5 + - - +
154A SER* 3.5 5.4 + - - -
164A VAL 3.5 2.6 - - - +
165A TYR* 4.7 1.3 - - - -
166A ASN* 2.8 40.1 + - - +
167A ASN 5.1 0.2 - - - -
168A ASP* 3.9 17.7 + - + +
505A ASN* 3.4 12.3 - - - +
521A ILE* 3.5 17.2 - - + +
522A VAL 3.0 6.7 - - - +
523A THR* 3.0 31.6 - - + +
524A TYR* 5.0 0.2 - - - -
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Residues in contact with VAL 153 (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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152A THR* 1.3 70.4 - - - +
154A SER* 1.3 60.8 + - - +
155A GLU* 4.1 2.9 + - + +
163A LYS* 3.6 30.3 - - + +
164A VAL 3.7 3.4 - - - -
165A TYR* 3.6 27.1 - - + -
521A ILE* 5.7 1.4 - - - +
522A VAL* 2.9 41.6 + - + +
524A TYR* 3.6 28.7 - - + -
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Residues in contact with SER 154 (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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152A THR* 3.7 3.5 + - - -
153A VAL* 1.3 72.5 - - - +
155A GLU* 1.3 57.9 - - - +
163A LYS* 3.1 2.9 - - - -
164A VAL* 2.6 53.1 + - - +
166A ASN* 2.8 26.7 + - - -
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Residues in contact with GLU 155 (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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153A VAL* 4.1 3.1 + - + +
154A SER* 1.3 71.5 - - - +
156A SER* 1.3 56.7 + - - +
157A ALA* 2.9 23.4 + - + +
161A PRO* 4.9 7.8 - - + +
162A THR 2.9 21.8 - - - +
163A LYS* 3.4 29.6 + - + +
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Residues in contact with SER 156 (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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154A SER 3.8 3.6 + - - -
155A GLU* 1.3 64.0 - - - +
157A ALA* 1.3 52.4 - - - +
158A THR* 2.2 35.3 + - - -
162A THR* 2.2 57.2 + - - +
163A LYS* 4.0 0.6 - - - +
164A VAL* 5.9 4.9 - - - -
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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