Contacts of the strand formed by residues 253 - 260 (chain B) in PDB entry 2P82
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 SER 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.6 12.3 - - - +
33B GLY 4.3 2.5 - - - -
247B CYS* 3.0 29.8 + - - +
248B PHE* 3.6 16.4 - - - -
250B MET 2.9 14.7 + - - -
251B PRO 3.2 1.0 - - - -
252B GLN* 1.3 75.8 - - - +
254B LEU* 1.3 53.4 + - - +
255B GLY* 3.0 19.1 + - - -
321B GLY 4.3 1.2 + - - -
322B PHE* 3.8 12.4 - - - -
360B EDO 2.8 28.1 + - - -
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Residues in contact with LEU 254 (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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32B LEU* 3.4 10.3 - - - -
85B MET* 3.7 17.0 - - + +
88B GLN* 3.8 6.3 - - + -
89B ALA* 3.6 39.0 - - + +
224B LEU* 3.4 32.3 - - + -
253B SER* 1.3 71.8 - - - +
255B GLY* 1.3 59.3 + - - +
266B TYR* 2.6 32.0 + - - +
321B GLY 2.8 14.1 + - - +
322B PHE 3.5 18.4 - - - +
323B PHE* 3.7 13.9 - - + +
360B EDO 3.3 24.0 - - - -
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Residues in contact with GLY 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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32B LEU* 3.5 6.8 - - - +
85B MET* 3.9 0.9 - - - -
247B CYS* 6.0 0.5 - - - +
248B PHE* 3.6 16.6 - - - -
253B SER* 3.0 13.7 + - - -
254B LEU* 1.3 78.7 - - - +
256B ALA* 1.3 63.4 + - - +
267B PHE 3.2 13.2 - - - -
320B LEU* 3.7 5.4 - - - +
321B GLY 2.9 23.0 + - - +
322B PHE* 5.9 0.3 - - - -
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Residues in contact with ALA 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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85B MET* 3.8 7.8 - - - +
244B PHE* 4.2 20.6 - - + -
248B PHE* 4.1 16.6 - - + -
254B LEU 3.8 2.2 + - - -
255B GLY* 1.3 75.9 - - - +
257B LEU* 1.3 65.8 + - - +
266B TYR* 3.6 5.1 - - - -
267B PHE* 2.9 38.6 + - + -
318B VAL* 5.0 2.0 - - + -
319B ALA 3.1 15.5 - - - +
320B LEU* 4.3 2.9 - - + -
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Residues in contact with LEU 257 (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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78B MET* 4.0 10.1 - - - -
81B CYS* 3.4 42.4 - - + +
82B GLY* 3.8 6.7 - - - +
85B MET* 3.9 28.3 - - + -
148B PRO* 4.3 9.4 - - + +
151B VAL* 3.6 31.0 - - + -
152B ALA* 5.3 1.1 - - - +
155B LEU* 5.2 4.9 - - + -
226B ILE* 5.5 3.8 - - + -
256B ALA* 1.3 76.6 - - - +
258B GLY* 1.3 59.3 + - - +
265B TYR 4.0 2.2 - - - -
266B TYR* 4.4 3.4 - - + -
267B PHE* 4.5 1.8 - - - -
318B VAL* 3.2 9.9 - - - +
319B ALA* 2.8 44.2 + - + +
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Residues in contact with GLY 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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78B MET* 3.8 9.3 - - - +
257B LEU* 1.3 76.4 - - - +
259B GLY* 1.3 61.0 + - - -
264B ALA* 3.2 9.4 - - - +
265B TYR 2.9 29.5 + - - +
267B PHE* 3.8 16.0 - - - -
317B SER 4.0 13.2 - - - -
318B VAL* 4.5 5.2 - - - -
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Residues in contact with GLY 259 (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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78B MET* 5.1 0.9 - - - +
145B TRP* 4.3 4.2 - - - -
148B PRO* 6.0 0.2 - - - +
258B GLY* 1.3 75.4 - - - -
260B LYS* 1.3 66.3 + - - +
263B ASN 3.3 13.2 - - - -
264B ALA* 4.8 0.4 - - - -
265B TYR* 4.6 5.6 - - - -
314B LEU* 3.9 16.7 - - - +
315B ASP* 3.7 19.1 - - - +
317B SER 4.5 2.5 + - - +
361B EDO 3.9 14.4 + - - -
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Residues in contact with LYS 260 (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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145B TRP* 3.6 4.8 - - - -
259B GLY* 1.3 76.1 - - - -
261B PRO* 1.4 81.2 - - + +
262B ASN 3.3 0.3 + - - -
263B ASN* 2.9 34.6 + - + +
313B ASN 6.2 0.2 - - - +
315B ASP* 3.8 22.5 - - + +
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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