Contacts of the strand formed by residues 248 - 257 (chain B) in PDB entry 3HCD
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 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B LEU* 4.6 3.3 - - - +
198B LEU* 4.3 5.6 - - + +
201B ILE* 5.2 0.3 - - - +
202B THR* 2.8 45.4 + - + +
205B LEU* 3.7 21.9 - - + +
211B LEU* 3.6 37.7 - - + +
243B LEU* 3.2 33.6 + - + +
244B VAL* 3.9 20.1 + - - +
246B SER* 3.8 13.0 - - - -
247B GLY* 1.3 81.8 - - - +
249B LYS* 1.3 61.5 + - - +
250B VAL 3.9 1.4 + - - -
277B ALA* 3.7 24.2 - - + -
278B GLN 3.4 5.6 - - - -
279B LYS* 3.6 22.0 - - + -
280B VAL* 4.3 4.7 - - - +
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Residues in contact with LYS 249 (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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248B TYR* 1.3 74.1 - - - +
250B VAL* 1.3 71.5 + - - +
251B ARG* 3.2 29.0 + - - +
277B ALA* 3.3 0.7 - - - -
278B GLN* 2.8 46.6 + - + +
280B VAL* 4.1 13.5 - - + +
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ARG* 4.0 34.3 - - + +
243B LEU* 4.0 34.1 - - + -
244B VAL* 4.3 10.5 - - + +
248B TYR 3.9 0.8 + - - +
249B LYS* 1.3 80.1 - - - +
251B ARG* 1.3 60.0 + - - +
252B ASP 3.8 21.8 - - - +
253B LEU* 4.0 18.8 - - + -
276B TRP 4.1 3.4 - - - +
277B ALA* 4.5 1.8 - - + +
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Residues in contact with ARG 251 (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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69B GLU* 2.4 37.0 + - - -
210B HIS* 3.8 11.9 - - - -
249B LYS* 3.8 37.6 - - - +
250B VAL* 1.3 73.3 - - - +
252B ASP* 1.3 64.9 + - - +
276B TRP* 2.9 47.4 + - + +
278B GLN* 2.7 45.6 + - + +
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Residues in contact with ASP 252 (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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64B THR* 5.2 1.6 + - - -
250B VAL* 3.5 6.7 - - - +
251B ARG* 1.3 83.2 - - - +
253B LEU* 1.3 68.2 + - - +
254B ARG* 2.8 47.9 + - - +
274B PHE* 4.0 10.8 - - - -
275B ALA* 3.3 2.9 - - - -
276B TRP* 2.7 53.5 + - + +
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Residues in contact with LEU 253 (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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236B GLU* 3.8 36.8 - - + +
239B VAL* 4.5 4.7 - - + -
240B ARG* 3.7 52.6 + - + +
243B LEU* 5.1 1.1 - - + -
250B VAL* 4.0 12.3 - - + -
252B ASP* 1.3 80.6 + - - +
254B ARG* 1.3 62.1 + - - +
273B PHE* 4.3 19.3 - - + -
274B PHE 3.3 17.9 - - - +
275B ALA* 3.5 19.7 - - + -
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Residues in contact with ARG 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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56B TRP* 3.9 16.7 - - + +
60B CYS* 3.9 18.6 - - - +
63B GLN* 4.2 16.1 + - - -
236B GLU* 4.0 2.5 - - - -
252B ASP* 2.8 39.2 + - - +
253B LEU* 1.3 75.8 - - - +
255B THR* 1.3 66.9 + - - +
273B PHE* 3.3 5.9 - - - +
274B PHE* 2.9 40.0 + - + +
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Residues in contact with THR 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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56B TRP* 3.7 9.5 + - - -
217B LEU* 3.6 29.5 - - + +
236B GLU* 2.9 30.7 + - - +
254B ARG* 1.3 78.0 + - - +
256B TYR* 1.3 72.1 + - - +
257B ILE* 4.2 13.0 + - + +
271B GLY* 5.4 0.9 - - - -
272B VAL 3.4 3.1 - - - -
273B PHE* 4.6 0.7 - - - +
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Residues in contact with TYR 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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51B ASN* 2.5 30.9 + - - -
52B GLY* 3.2 16.2 - - - -
53B VAL* 3.3 33.9 + - + -
56B TRP* 3.5 45.3 - + + +
59B ARG* 6.1 0.4 - - - -
255B THR* 1.3 80.0 - - - +
257B ILE* 1.3 65.7 + - - +
258B MET* 4.1 7.6 - - - -
259B PRO* 3.3 36.1 - - + +
262B LEU* 3.9 0.9 - - - +
271B GLY* 3.0 4.5 - - - -
272B VAL* 2.8 39.8 + - + +
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Residues in contact with ILE 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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255B THR* 4.2 13.2 + - + +
256B TYR* 1.3 82.6 - - - +
258B MET* 1.3 73.7 + - - +
259B PRO* 3.1 11.5 - - + +
270B LYS 3.9 9.4 - - - +
271B GLY* 4.2 0.7 - - - -
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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