Contacts of the strand formed by residues 146 - 153 (chain A) in PDB entry 1CPJ
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 TYR 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A TRP* 3.6 9.9 - - - -
84A THR 4.5 4.3 - - - -
85A ARG 3.5 12.4 + - - -
86A LYS* 3.0 34.9 + - - +
87A GLY* 3.5 12.3 - - - -
144A LYS* 3.9 26.9 - - + +
145A HIS* 1.3 74.6 - - - +
147A GLY* 1.3 59.9 + - - +
251A PRO* 3.8 4.5 - - - +
252A ARG* 2.9 70.6 + - + +
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Residues in contact with GLY 147 (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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83A TRP* 3.1 40.7 + - - -
84A THR* 3.3 26.8 - - - +
146A TYR* 1.3 73.8 - - - +
148A TYR* 1.3 65.0 + - - +
149A THR 3.7 0.7 - - - -
250A ILE 3.6 7.9 - - - -
252A ARG* 4.0 10.1 + - - -
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Residues in contact with TYR 148 (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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84A THR* 4.1 5.2 - - - +
147A GLY* 1.3 75.7 - - - +
149A THR* 1.3 85.4 + - + +
250A ILE* 2.7 26.1 + - + +
251A PRO 3.8 3.8 - - - +
252A ARG* 3.4 39.6 + - + +
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Residues in contact with THR 149 (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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83A TRP* 4.4 1.6 - - - -
84A THR* 3.5 9.2 - - - +
148A TYR* 1.3 107.1 - - + +
150A SER* 1.3 62.2 + - - +
151A TYR* 3.5 23.0 - - - -
249A GLY* 3.1 2.3 - - - -
250A ILE* 2.9 37.4 + - - +
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Residues in contact with SER 150 (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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77A SER 5.0 0.2 + - - -
80A TRP* 3.5 33.9 + - - +
81A ASN* 3.3 25.6 + - - -
84A THR* 3.6 6.4 + - - +
149A THR* 1.3 77.0 - - - +
151A TYR* 1.3 71.8 + - - +
247A VAL* 5.5 0.2 - - - -
248A ALA 3.2 13.5 - - - -
249A GLY* 4.4 0.7 - - - -
154B SER* 4.6 4.7 + - - -
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Residues in contact with TYR 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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41A ARG* 4.0 3.1 + - - -
149A THR* 3.5 24.2 - - - -
150A SER* 1.3 81.5 + - - +
152A SER* 1.3 66.1 + - - +
153A VAL* 4.2 13.2 - - + -
163A GLU* 3.0 34.6 + - - -
167A ASN* 3.7 4.3 + - - -
247A VAL* 3.3 9.2 - - - +
248A ALA* 2.8 42.4 + - + -
249A GLY* 3.9 9.0 - - - -
250A ILE* 3.4 28.2 - - + +
154B SER* 3.5 16.4 - - - +
155B ASP 5.9 0.2 - - - -
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Residues in contact with SER 152 (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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77A SER* 5.0 4.7 - - - -
151A TYR* 1.3 83.6 - - - +
153A VAL* 1.3 60.7 + - - +
154A SER 4.3 0.7 + - - -
246A ILE 3.5 10.1 - - - -
247A VAL* 4.4 9.6 - - - +
152B SER* 4.1 24.8 - - - +
153B VAL 3.9 4.5 + - - -
154B SER* 3.1 30.2 + - - -
155B ASP 4.1 4.5 + - - -
244B SER 4.8 7.8 + - - -
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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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151A TYR* 4.2 16.4 - - + -
152A SER* 1.3 75.6 - - - +
154A SER* 1.3 74.9 + - - +
155A ASP 3.7 0.3 + - - -
159A GLU* 3.6 31.6 - - + +
160A ILE* 3.9 17.5 - - + -
163A GLU* 4.1 22.7 - - + -
243A GLU 5.0 1.2 - - - +
244A SER 5.2 2.1 - - - +
246A ILE* 2.9 45.5 + - + +
248A ALA* 4.7 4.3 - - + -
152B SER* 4.0 8.2 + - - -
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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