Contacts of the strand formed by residues 165 - 169 (chain A) in PDB entry 2A3K
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 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A TYR* 3.7 3.3 - - - -
155A ILE* 2.8 38.9 + - + +
156A ARG 4.1 9.6 - - - -
157A GLY* 4.0 13.6 - - - -
163A LYS* 4.2 4.0 - - - -
164A VAL* 1.3 97.9 - - + +
166A ILE* 1.3 63.3 + - - +
167A ALA 4.1 0.2 - - - -
286A PRO* 4.2 2.9 - - - -
287A ILE* 3.2 42.2 - - + +
289A VAL* 4.4 3.4 - - + -
301A PHE* 5.0 4.7 - + - -
302A ILE* 3.5 49.8 - - + -
305A ARG* 3.0 42.9 + - + +
306A ILE* 4.1 8.2 - - + +
309A GLN* 4.1 3.3 + - - -
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Residues in contact with ILE 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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136A VAL* 4.1 9.6 - - + -
152A ALA* 4.1 8.3 - - + -
153A ASN 3.5 3.8 - - - +
154A TYR* 4.0 18.8 - - + -
165A TYR* 1.3 77.7 - - - +
167A ALA* 1.3 70.9 + - - +
168A THR* 4.1 1.5 + - - -
182A MET* 3.8 34.5 - - + -
186A GLU* 3.9 31.2 - - + -
188A VAL* 4.4 8.3 - - + -
286A PRO* 3.8 23.1 - - + +
287A ILE 2.9 7.3 + - - +
288A VAL* 3.3 10.0 - - + +
289A VAL* 2.8 27.2 + - - +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ALA* 3.3 2.4 - - - +
153A ASN 2.9 32.3 + - - -
155A ILE* 3.8 21.3 - - + +
166A ILE* 1.3 72.7 - - - +
168A THR* 1.3 62.2 + - - +
289A VAL 3.4 4.7 - - - -
294A GLY 4.2 1.3 - - - +
298A THR* 3.5 25.1 - - + -
302A ILE* 4.5 2.0 - - + -
330A ARG* 4.1 20.4 - - - -
333A MET* 4.2 5.8 - - + -
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Residues in contact with THR 168 (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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150A ILE* 4.5 6.1 - - - +
151A ASN 2.9 21.6 + - - -
152A ALA* 3.4 13.0 - - - +
166A ILE* 4.4 1.1 - - - +
167A ALA* 1.3 77.7 - - - +
169A GLN* 1.3 73.8 + - - +
179A PHE* 4.1 12.7 - - + -
182A MET* 4.2 11.2 - - + +
288A VAL* 4.1 18.4 - - + -
289A VAL 3.3 4.7 + - - +
290A HIS* 3.1 35.7 - - + +
294A GLY* 3.4 14.8 + - - -
330A ARG* 4.3 3.6 - - - +
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Residues in contact with GLN 169 (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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122A LYS 2.8 25.2 + - - -
123A ASP* 3.5 1.4 - - - -
124A ARG* 3.2 24.7 + - + -
150A ILE* 6.3 1.2 - - + +
151A ASN* 3.5 32.5 + - - +
168A THR* 1.3 94.6 + - - +
170A GLY* 1.3 77.2 + - - +
171A PRO* 3.5 4.2 - - + +
172A MET* 3.8 13.1 - - - +
175A THR* 4.0 14.6 + - - +
179A PHE* 5.1 0.9 - - - -
290A HIS* 3.6 1.4 - - - +
291A CYS 3.6 6.5 - - - -
292A SER 3.5 13.2 - - - +
293A ALA* 3.9 12.8 - - - +
330A ARG* 4.1 4.8 - - - +
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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