Contacts of the strand formed by residues 146 - 151 (chain A) in PDB entry 4II9
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 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PRO* 3.5 2.3 - - - +
145A ARG* 1.3 84.3 - - + +
147A ASN* 1.3 64.0 + - - +
291A GLY* 3.3 5.5 - - - -
292A ILE* 3.0 48.5 + - + +
293A GLU 3.6 27.1 - - - +
294A SER* 4.2 8.7 - - - -
295A GLU* 4.7 5.4 - - + +
313A PRO* 4.7 8.1 - - + +
314A ARG 3.3 3.6 - - - +
315A GLU* 3.6 37.2 - - + -
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Residues in contact with ASN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 4.9 7.6 - - - +
110A GLU* 5.2 0.7 - - - -
144A PRO* 2.9 27.0 + - - +
145A ARG 3.3 3.6 - - - +
146A LEU* 1.3 75.9 + - - +
148A MET* 1.3 65.0 + - - +
149A VAL* 3.6 2.3 + - + -
288A ASP* 4.2 11.8 + - - +
290A GLY* 3.4 10.5 - - - +
291A GLY* 3.3 26.1 - - - +
292A ILE 4.7 0.2 - - - +
313A PRO* 3.4 3.0 - - - +
314A ARG* 2.8 35.6 + - - +
316A TYR* 3.2 37.2 - - + +
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Residues in contact with MET 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASN* 1.3 71.7 - - - +
149A VAL* 1.3 57.5 + - - +
288A ASP* 3.7 0.3 - - - +
289A LEU* 2.8 35.3 + - + +
290A GLY 2.9 13.6 + - - +
292A ILE* 3.6 26.2 - - + -
302A TYR* 3.5 25.8 - - + -
305A LYS* 3.6 21.3 - - + +
306A HIS* 3.4 36.3 - - - +
309A VAL* 3.8 25.8 - - + +
311A ASP 5.0 1.1 - - - +
313A PRO* 3.8 34.3 - - - -
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASN* 3.6 11.2 + - + +
148A MET* 1.3 78.4 - - - +
150A LEU* 1.3 61.4 + - - +
151A ASP* 3.8 2.8 + - - +
286A LEU* 4.0 33.0 - - + -
287A TYR 3.5 10.3 - - - +
288A ASP* 3.6 20.9 - - + +
309A VAL* 3.7 16.2 - - - +
311A ASP* 5.0 7.4 - - - +
312A ALA 5.3 1.9 + - - +
313A PRO* 5.4 0.4 - - - +
314A ARG* 3.7 43.5 + - + +
316A TYR* 3.8 15.0 - - - +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL* 1.3 70.6 - - - +
151A ASP* 1.3 66.7 + - - +
152A LEU* 3.3 30.5 + - + -
155A PHE* 4.9 13.5 - - + -
164A LEU* 4.0 11.7 - - + +
165A TYR* 3.5 25.1 - - + +
276A ILE* 4.4 4.9 - - + -
286A LEU* 3.4 3.8 - - - +
287A TYR* 2.7 61.5 + - + +
308A PHE 3.9 12.6 - - - +
309A VAL* 4.0 16.0 - - + +
310A LYS 5.8 0.7 - - - +
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Residues in contact with ASP 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 3.8 3.8 + - - +
150A LEU* 1.3 73.7 - - - +
152A LEU* 1.3 62.3 + - - +
153A THR* 2.7 36.3 + - - +
154A LYS* 3.3 46.3 + - + +
155A PHE* 4.1 8.5 - - - -
250A ARG* 5.6 1.2 + - - -
285A ASP 3.7 2.3 - - - +
286A LEU* 3.8 18.8 - - + +
311A ASP* 5.1 5.0 + - - +
314A ARG* 4.3 14.5 + - - +
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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