Contacts of the strand formed by residues 263 - 271 (chain B) in PDB entry 40ER
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 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B GLU* 3.9 29.6 + - + -
233B PRO* 3.6 35.1 + - + -
235B HIS* 5.6 1.6 - - - +
238B LEU* 3.6 22.4 - - + -
256B THR* 4.6 2.5 - - + -
257B HIS 3.8 4.5 - - - +
258B ARG* 2.8 59.2 + - + -
261B LYS 4.3 13.7 - - - -
262B LYS* 1.3 74.3 - - - +
264B VAL* 1.3 71.0 + - - +
43G PRO 4.4 1.2 - - - +
44G THR* 2.5 28.6 + - + +
45G SER* 3.3 5.8 - - - +
46G SER* 3.2 20.0 + - - -
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Residues in contact with VAL 264 (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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255B ALA 3.6 0.9 - - - +
256B THR* 4.2 1.6 - - - -
257B HIS* 2.8 52.9 + - + +
258B ARG* 5.6 2.0 - - - -
259B TYR* 5.7 2.0 - - + +
262B LYS* 5.4 2.5 - - + -
263B TYR* 1.3 83.3 - - - +
265B THR* 1.3 62.8 + - - +
266B THR* 3.7 13.9 + - - +
42G ILE* 5.1 7.9 - - + -
46G SER* 3.6 16.2 - - - +
48G LEU* 5.8 3.8 - - + -
163G THR 4.9 2.7 - - - +
164G LEU* 3.1 52.5 - - + +
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Residues in contact with THR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ILE* 3.8 19.3 - - + +
217B LEU* 3.9 16.4 - - + -
230B LEU* 3.6 24.6 - - - +
254B SER* 4.2 9.4 - - - +
255B ALA* 3.5 9.9 - - - +
256B THR* 3.3 31.7 + - - +
264B VAL* 1.3 71.4 - - - +
266B THR* 1.3 59.4 + - - +
267B LEU* 3.5 5.7 - - + +
45G SER* 5.3 2.4 + - - -
46G SER 3.0 9.4 + - - -
47G LYS* 3.7 0.4 - - - +
48G LEU* 3.0 25.5 + - - +
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A THR* 3.9 30.3 + - + +
535A ILE* 5.1 4.0 - - + -
538A PHE* 3.2 15.1 - - + -
254B SER* 3.2 20.2 - - - -
255B ALA 3.1 9.7 + - - -
257B HIS* 4.5 0.9 - - - -
264B VAL* 4.1 18.4 + - - +
265B THR* 1.3 71.5 - - - +
267B LEU* 1.3 66.1 + - - +
48G LEU* 3.4 28.4 - - + +
50G VAL* 4.4 13.5 - - + -
82G PHE* 6.6 0.2 - - + -
163G THR* 4.7 6.0 + - - +
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Residues in contact with LEU 267 (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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398A TRP* 4.3 11.9 - - + +
217B LEU* 3.8 28.7 - - + -
253B LEU 5.4 0.2 - - - -
254B SER* 3.7 16.4 - - - -
265B THR 3.5 13.0 - - - +
266B THR* 1.3 75.5 - - - +
268B LEU* 1.3 60.2 + - - +
269B TYR* 4.9 10.8 - - + +
47G LYS* 3.9 17.3 - - + -
48G LEU 2.7 21.6 + - - +
49G VAL* 3.9 15.0 - - + -
50G VAL* 2.9 32.4 + - - +
67G ASN* 3.5 27.4 - - - +
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Residues in contact with LEU 268 (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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535A ILE* 3.9 27.1 - - + +
538A PHE* 3.6 34.8 - - + -
539A GLU 4.9 0.7 - - - +
251B MET 3.5 1.9 - - - +
252B VAL* 3.4 5.7 - - - -
253B LEU* 3.1 41.2 + - + +
267B LEU* 1.3 76.4 - - - +
269B TYR* 1.3 83.6 + - - +
270B LYS* 3.8 23.3 + - + +
50G VAL* 3.5 24.7 - - + +
51G PHE 4.8 0.4 - - - -
52G ASP* 4.5 9.9 - - + +
75G TRP* 5.5 5.8 - - + -
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Residues in contact with TYR 269 (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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244B LEU* 5.2 7.4 - - + +
250B VAL* 4.5 14.4 - - + -
251B MET 3.4 4.7 - - - +
252B VAL* 3.3 27.6 - - + -
267B LEU* 4.9 16.2 - - + +
268B LEU* 1.3 77.8 - - - +
270B LYS* 1.3 59.5 + - - +
271B PRO* 4.0 3.1 - - - +
49G VAL* 4.9 2.2 - - + -
50G VAL 3.2 8.2 + - - -
51G PHE* 3.7 20.0 - + + -
52G ASP* 3.3 25.3 + - - +
55G LEU* 3.7 24.0 - - + +
59G LYS* 5.4 2.7 - - + -
63G ALA* 3.5 26.6 - - + +
66G THR* 4.1 6.6 + - - -
67G ASN* 3.2 28.9 + - - -
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Residues in contact with LYS 270 (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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538A PHE 5.4 0.2 - - - -
539A GLU* 3.9 36.6 - - + +
542A ALA* 3.8 24.8 - - - +
543A ASN* 4.0 16.0 + - - -
250B VAL* 4.4 0.9 - - - -
251B MET* 2.7 49.0 + - + +
253B LEU* 5.4 4.0 - - + -
268B LEU* 3.8 19.2 + - + +
269B TYR* 1.3 73.6 - - - +
271B PRO* 1.3 71.6 + - + +
272B ILE 6.1 0.8 - - - -
52G ASP* 3.4 27.3 + - + +
75G TRP* 5.9 1.1 - - + -
77G SER* 5.1 5.6 + - - +
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Residues in contact with PRO 271 (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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249B SER 4.0 1.6 - - - +
250B VAL* 3.9 20.8 - - + -
251B MET* 5.7 1.2 - - - +
269B TYR 4.0 6.1 - - - +
270B LYS* 1.3 103.9 + - + +
272B ILE* 1.3 70.8 + - + +
52G ASP* 4.0 4.9 - - + -
54G SER* 3.4 33.0 - - - +
55G LEU* 3.6 24.9 - - + +
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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