Contacts of the strand formed by residues 249 - 256 (chain X) in PDB entry 4HSC
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 ARG 249 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205X ASP* 4.8 5.1 + - - -
248X ALA* 1.3 72.6 - - - +
250X THR* 1.3 63.6 + - - +
251X GLN* 6.3 0.4 - - - +
298X LYS 3.6 1.2 - - - +
300X ILE* 2.8 81.0 + - + +
303X THR* 3.8 16.0 - - - +
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Residues in contact with THR 250 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248X ALA* 3.8 6.4 + - - +
249X ARG* 1.3 72.7 - - - +
251X GLN* 1.3 70.9 + - - +
252X TYR* 3.9 10.4 + - + +
297X TYR* 4.1 20.6 - - + -
298X LYS 3.6 4.7 - - - +
299X GLN* 2.5 30.8 + - - +
300X ILE* 5.6 0.2 - - - -
420X ALA* 5.5 1.2 - - - +
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Residues in contact with GLN 251 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162X ASP* 2.9 37.8 + - - +
249X ARG* 3.7 0.8 + - - +
250X THR* 1.3 71.6 - - - +
252X TYR* 1.3 59.3 + - - +
253X THR* 4.3 4.4 + - + +
268X ASN* 5.0 5.5 - - - +
296X ALA 3.5 2.9 - - - +
297X TYR 3.8 0.2 - - - -
298X LYS* 2.8 73.3 + - + +
300X ILE* 4.4 18.6 - - + +
432X SER* 4.7 4.7 + - - -
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Residues in contact with TYR 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250X THR* 3.8 14.5 + - + +
251X GLN* 1.3 73.3 - - - +
253X THR* 1.3 70.4 + - - +
254X GLU* 2.7 44.2 + - + +
295X ALA* 3.6 8.9 - - + +
296X ALA 3.4 10.8 - - - -
297X TYR* 3.3 45.8 - + + -
369X LEU* 3.4 23.1 - - + +
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Residues in contact with THR 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251X GLN* 5.5 4.3 - - + -
252X TYR* 1.3 85.7 - - - +
254X GLU* 1.3 64.2 + - - +
266X ALA 4.0 10.1 - - - +
267X LEU* 3.1 42.5 + - - +
268X ASN* 5.5 2.2 - - + -
295X ALA* 3.3 3.1 - - - +
296X ALA* 2.8 40.8 + - - +
298X LYS* 5.8 0.5 - - - -
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Residues in contact with GLU 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252X TYR* 2.7 40.8 + - + +
253X THR* 1.3 78.2 - - - +
255X SER* 1.3 69.7 + - - +
266X ALA 5.3 1.7 - - - +
267X LEU* 3.7 2.5 - - - +
293X MET* 3.8 19.3 - - + +
294X ILE 3.5 6.7 - - - -
295X ALA* 4.2 4.3 - - + -
366X SER* 2.7 33.6 + - - +
369X LEU* 3.6 10.6 - - + +
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Residues in contact with SER 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254X GLU* 1.3 83.5 - - - +
256X MET* 1.3 79.0 + - - +
262X GLN* 3.3 13.3 + - - -
263X ILE* 4.0 11.4 - - - +
266X ALA* 3.7 23.1 - - - +
267X LEU* 4.0 1.8 - - - -
293X MET* 3.9 6.5 - - - -
294X ILE* 3.0 31.1 + - - +
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Residues in contact with MET 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255X SER* 1.3 88.2 + - - +
257X VAL* 1.3 60.6 + - - +
258X TYR* 3.3 32.8 - - + +
262X GLN* 3.1 12.5 + - - -
263X ILE* 4.0 0.3 - - - +
291X LYS* 4.2 15.5 - - + -
292X VAL 3.3 30.3 - - - +
293X MET* 3.5 28.0 - - + +
361X VAL* 5.1 1.3 - - + -
362X GLU* 3.4 51.9 + - + +
365X PHE* 4.5 4.7 - - + -
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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