Contacts of the strand formed by residues 149 - 153 (chain A) in PDB entry 2R5N
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 THR 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.3 13.6 - - + +
61A VAL* 5.2 0.7 - - + -
123A ALA* 3.4 42.2 - - + +
126A MET* 3.8 15.5 + - + +
127A ALA* 3.6 24.2 + - - +
130A GLU* 5.2 0.9 - - - +
147A HIS* 5.0 5.2 + - - -
148A TYR* 1.3 75.1 + - - +
150A TYR* 1.3 64.2 + - - +
177A LYS* 2.9 10.2 + - - +
178A LEU* 3.4 10.3 - - + +
179A ILE 2.9 26.2 + - - +
424A HIS* 6.0 0.2 - - - -
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Residues in contact with TYR 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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40A LEU* 3.6 42.4 - - + -
44A PHE* 4.0 9.4 + - + +
45A LEU* 3.6 23.1 - - + -
58A ASP* 3.5 23.5 + - + -
59A ARG 2.8 11.5 + - - +
60A PHE* 3.3 8.4 - - + -
61A VAL* 2.8 26.7 + - - +
148A TYR* 3.6 17.2 - - + -
149A THR* 1.3 74.7 - - - +
151A ALA* 1.3 59.1 + - - +
179A ILE* 3.3 35.0 - - + +
181A PHE* 3.9 12.6 - + + -
228A VAL* 4.7 7.2 - - + -
232A ARG* 2.9 31.7 + - - -
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Residues in contact with ALA 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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61A VAL* 3.3 11.7 - - + +
63A SER* 5.5 0.4 - - - -
120A ILE* 3.9 30.5 - - + -
123A ALA* 3.9 16.8 - - + -
149A THR 4.2 0.4 - - - -
150A TYR* 1.3 75.6 - - - +
152A PHE* 1.3 64.0 + - - +
153A MET* 5.7 0.7 - - - -
178A LEU* 5.0 2.0 - - + +
179A ILE 3.0 7.2 + - - +
180A ALA* 3.3 5.1 - - + +
181A PHE* 2.7 35.9 + - - -
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Residues in contact with PHE 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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33A MET* 3.5 26.5 - - + -
36A ILE* 3.7 19.3 - - + -
37A ALA* 4.0 24.7 - - + -
40A LEU* 3.8 17.3 - - + -
60A PHE* 3.7 25.8 - + - -
61A VAL 2.9 8.2 + - - +
62A LEU* 4.0 7.0 - - + -
63A SER* 2.8 31.5 + - - -
64A ASN* 3.3 13.6 - - - +
70A LEU* 3.8 22.7 - - + -
151A ALA* 1.3 80.7 - - - +
153A MET* 1.3 61.2 + - - +
181A PHE* 3.5 34.3 - + + -
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Residues in contact with MET 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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33A MET* 5.1 0.2 - - - +
63A SER* 4.0 9.6 - - - -
64A ASN* 3.8 11.6 + - - +
120A ILE* 4.0 45.1 - - + -
151A ALA* 5.5 0.4 - - - -
152A PHE* 1.3 76.1 - - - +
154A GLY* 1.3 53.2 + - - +
157A CYS* 3.9 21.1 - - + -
158A MET* 3.8 43.3 - - + +
163A SER* 4.6 6.1 - - - -
167A CYS* 5.0 0.2 - - - -
180A ALA* 4.2 14.8 - - + -
181A PHE 3.0 13.9 + - - +
182A TYR* 3.4 2.7 - - - -
183A ASP* 2.8 32.1 + - - +
205A PHE* 4.7 6.5 - - + -
210A TRP* 6.1 0.2 - - - -
240A LEU* 4.4 2.5 - - - -
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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