Contacts of the strand formed by residues 160 - 166 (chain A) in PDB entry 3CMM
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 PHE 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A THR* 3.6 2.8 - - - -
157A ARG 3.0 37.8 + - - +
158A GLY 3.6 3.6 - - - +
159A LEU* 1.3 81.1 - - - +
161A GLY* 1.3 58.0 + - - +
292A LEU* 3.7 32.3 - - + -
296A PHE* 4.0 15.7 - - + -
347A LEU* 4.0 13.7 - - + -
350A GLU* 3.7 14.6 - - + -
351A LEU* 3.6 42.4 - - + -
354A GLN* 3.8 19.3 - - + -
362A VAL* 3.7 8.6 - - - +
391A PHE* 3.4 6.7 - - - +
392A ASP* 3.6 23.1 - - + -
394A LEU* 3.8 17.9 - - + -
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Residues in contact with GLY 161 (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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155A GLU 3.3 12.1 - - - -
156A THR* 4.3 0.7 - - - -
160A PHE* 1.3 76.3 - - - +
162A ASN* 1.3 62.2 + - - +
296A PHE* 4.0 9.2 - - - -
366A PHE* 3.3 22.1 - - - -
390A TYR* 3.5 3.6 - - - -
391A PHE 2.8 33.0 + - - +
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Residues in contact with ASN 162 (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 SER* 4.9 2.4 + - - +
154A SER* 2.9 21.0 + - - -
155A GLU* 3.0 28.4 + - - +
161A GLY* 1.3 73.0 - - - -
163A THR* 1.3 65.8 + - - +
164A PHE* 4.8 1.2 + - - +
296A PHE* 3.0 36.8 - - - +
366A PHE* 3.3 8.2 - - - -
388A PHE* 5.1 5.8 - - - -
389A MET 3.1 15.3 - - - +
390A TYR* 3.3 32.7 + - + -
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Residues in contact with THR 163 (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 ILE* 4.1 9.0 - - - +
153A SER 3.2 12.2 + - - -
162A ASN* 1.3 78.4 - - - +
164A PHE* 1.3 62.4 + - - +
165A VAL* 4.5 4.0 - - + +
366A PHE* 3.4 5.7 - - + -
369A LEU* 3.8 15.5 - - + -
370A VAL* 3.3 26.1 - - - +
373A GLU* 5.3 1.7 - - + +
385A LEU* 3.7 31.6 - - + -
387A GLN 3.6 0.9 - - - +
388A PHE* 3.6 4.9 - - - -
389A MET* 3.0 40.0 + - + +
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Residues in contact with PHE 164 (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 PHE* 4.0 18.2 - + - -
152A ILE* 3.3 5.7 - - - +
153A SER* 2.7 48.7 + - - +
162A ASN* 4.8 1.5 + - - +
163A THR* 1.3 74.3 + - - +
165A VAL* 1.3 63.0 - - - +
166A ASP* 3.6 20.4 - - + -
267A LYS 3.8 2.7 - - - -
269A LEU* 3.6 40.4 - - + -
272A GLN* 3.5 20.9 - - + -
387A GLN* 3.1 46.9 - - + -
388A PHE* 3.5 33.2 - + + -
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Residues in contact with VAL 165 (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 PHE 3.8 2.5 - - - -
152A ILE* 4.3 12.8 - - + -
163A THR* 4.5 5.6 - - - +
164A PHE* 1.3 81.8 - - - +
166A ASP* 1.3 61.4 + - - +
167A LEU* 3.6 34.1 - - + -
266A PHE* 3.8 5.6 - - + -
373A GLU* 4.0 22.0 - - + +
384A PRO* 4.8 3.8 - - + -
385A LEU* 3.4 41.1 - - + +
387A GLN* 2.9 37.7 + - - +
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Residues in contact with ASP 166 (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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141A ASN* 2.8 32.5 + - - +
145A HIS* 2.7 27.6 + - - +
149A ILE 4.7 0.9 - - - +
150A ARG* 3.7 0.3 - - - -
151A PHE* 2.7 41.7 + - - +
164A PHE* 3.6 13.5 - - + -
165A VAL* 1.3 73.4 - - - +
167A LEU* 1.3 63.1 + - - +
168A GLY 2.8 17.5 + - - -
266A PHE* 3.2 9.7 - - - +
267A LYS 3.3 15.9 - - - +
268A SER* 3.5 2.1 - - - -
387A GLN* 4.0 2.7 - - - +
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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