Contacts of the strand formed by residues 253 - 258 (chain B) in PDB entry 2B4M
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 MET 253 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 3.8 15.0 - - + -
30B LEU* 3.8 23.8 - - + -
71B GLY 3.5 12.3 - - - +
72B TRP* 4.2 3.4 - - + -
85B TYR* 3.8 8.0 - - - -
88B ASP* 6.0 0.3 - - - +
93B TYR* 3.4 41.9 - - + +
97B GLU* 3.5 41.3 - - + +
225B TRP* 4.4 16.8 - - - -
228B ASN* 3.8 9.0 - - + -
229B THR* 3.6 13.7 - - - +
252B LYS* 1.3 77.1 - - - +
254B GLY* 1.3 59.1 + - - +
310B PBE 5.1 7.4 - - - +
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Residues in contact with GLY 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.3 1.4 - - - +
70B THR* 3.5 5.0 - - - -
71B GLY* 2.8 36.0 + - - +
85B TYR* 3.6 7.6 - - - -
86B LEU 6.0 0.4 - - - -
93B TYR* 3.5 29.6 - - - -
253B MET* 1.3 77.0 - - - +
255B LEU* 1.3 61.1 + - - -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 4.1 28.0 - - + -
31B THR* 4.3 9.2 - - + -
34B ALA* 5.7 3.4 - - + -
40B LEU* 5.3 2.0 - - + -
68B ILE* 4.2 6.1 - - + -
69B ILE 3.5 11.4 - - - +
70B THR* 4.5 2.7 - - + -
85B TYR* 3.6 5.9 - - - -
86B LEU* 2.9 47.7 + - + +
93B TYR* 3.2 25.4 + - - +
254B GLY* 1.3 72.0 - - - -
256B VAL* 1.3 59.3 + - - +
267B ILE* 3.8 29.1 - - + +
270B LEU* 3.8 29.4 - - + -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ILE 4.0 0.3 - - - +
68B ILE* 3.5 2.9 - - - -
69B ILE* 2.8 60.3 + - + +
71B GLY* 3.6 23.1 - - - +
78B PHE* 3.7 14.1 - - + -
83B LEU* 3.7 31.4 - - + -
84B LYS 3.3 10.5 - - - +
85B TYR* 3.6 28.9 - - + -
255B LEU* 1.3 72.9 - - - +
257B VAL* 1.3 64.9 + - - +
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE 3.4 15.0 - - - +
68B ILE* 3.5 21.5 - - + -
69B ILE* 5.6 0.2 - - - -
83B LEU* 3.5 5.9 - - - +
84B LYS* 2.9 57.6 + - + -
86B LEU* 3.4 28.3 - - + -
256B VAL* 1.3 74.1 - - - +
258B PRO* 1.3 74.3 - - + +
261B MET* 3.8 15.7 - - + -
264B VAL* 4.0 12.3 - - + +
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Residues in contact with PRO 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 4.9 0.9 - - + -
61B TYR* 3.8 17.5 - - + -
67B ILE* 3.3 31.4 - - + +
82B LYS 3.6 5.8 - - - +
83B LEU* 3.7 9.4 - - + -
84B LYS* 3.9 0.9 - - - -
257B VAL* 1.3 93.4 - - + +
259B GLN* 1.3 65.2 + - - +
260B TYR* 3.2 46.3 + - + +
261B MET* 3.2 22.9 + - - +
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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