Contacts of the strand formed by residues 279 - 288 (chain H) in PDB entry 1S9C
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 ILE 279 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247H ALA* 3.1 21.1 - - + +
248H LYS* 3.2 20.0 + - - +
270H GLN* 3.3 29.4 - - + +
271H THR 3.6 5.2 - - - +
272H LYS* 3.9 21.5 - - + -
277H GLY 3.6 3.6 + - - +
278H ASP* 1.3 73.8 - - - +
280H VAL* 1.3 62.0 + - - +
281H ILE 3.5 25.1 - - - +
282H SER* 4.0 13.9 - - - -
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Residues in contact with VAL 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H THR* 3.8 16.6 - - + -
246H PHE* 3.7 3.6 - - - +
247H ALA 2.8 23.1 + - - -
248H LYS* 3.3 23.5 - - + +
249H PRO 3.6 5.8 - - - +
250H VAL* 3.3 26.9 - - + -
256H LEU* 4.7 0.2 - - + -
271H THR* 2.8 37.8 + - + +
272H LYS* 4.2 2.9 - - - +
273H VAL* 3.5 18.4 - - + -
278H ASP* 4.1 5.4 - - + +
279H ILE* 1.3 77.0 - - - +
281H ILE* 1.3 68.1 + - + +
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Residues in contact with ILE 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H THR* 3.6 27.1 - - + +
220H PHE* 3.7 27.1 - - + +
223H SER* 4.6 0.9 - - - +
244H ALA* 3.8 21.5 - - + -
245H ARG 3.2 10.3 - - - +
246H PHE* 4.2 16.6 - - + -
269H PHE* 4.0 19.3 - - + -
270H GLN* 3.5 4.3 - - - -
271H THR* 2.9 38.6 + - - +
279H ILE* 3.5 7.1 - - - +
280H VAL* 1.3 95.0 - - + +
282H SER* 1.3 63.2 + - - +
284H ALA* 4.1 4.5 - - + -
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Residues in contact with SER 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H ARG* 2.8 45.8 + - - +
247H ALA* 4.9 7.9 - - - +
270H GLN* 4.4 9.4 - - - +
279H ILE* 4.0 16.2 - - - -
281H ILE* 1.3 74.8 - - - +
283H ASN* 1.3 87.4 + - - +
284H ALA* 3.0 5.3 + - - +
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Residues in contact with ASN 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H ALA* 3.6 16.7 - - + +
165H VAL 2.8 44.9 + - - +
166H ALA* 3.2 23.0 - - - +
167H ILE* 4.2 17.1 + - - +
243H LYS* 4.2 2.6 - - - +
244H ALA* 4.8 0.7 - - - -
245H ARG* 3.8 20.7 - - + +
269H PHE 4.4 0.4 + - - -
270H GLN* 5.1 0.2 - - - +
282H SER* 1.3 96.8 + - - +
284H ALA* 1.3 57.5 + - - +
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Residues in contact with ALA 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H VAL 4.4 2.9 - - - +
167H ILE* 5.1 0.9 - - - +
243H LYS 2.9 19.1 - - - +
244H ALA* 3.5 13.0 - - + -
268H HIS* 3.6 6.2 + - - +
269H PHE* 3.0 59.1 + - + +
281H ILE* 4.1 3.4 - - + -
282H SER 3.1 4.0 - - - +
283H ASN* 1.3 80.9 - - - +
285H TYR* 1.3 63.8 + - - +
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Residues in contact with TYR 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H TYR* 3.9 15.5 - + - -
162H LYS* 5.6 1.6 - - - +
163H VAL 4.0 6.4 + - - -
165H VAL* 3.4 38.6 - - + -
241H ALA* 4.7 4.7 - - + +
242H VAL* 3.2 5.4 - - - +
243H LYS* 2.9 62.3 + - + +
266H ARG* 3.3 40.3 + - + -
267H ILE 3.2 14.6 - - - +
268H HIS* 4.1 6.3 - - - +
269H PHE* 3.7 5.4 - - - -
284H ALA* 1.3 78.9 - - - +
286H VAL* 1.3 70.8 + - - +
287H ASP* 3.2 26.4 + - - -
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Residues in contact with VAL 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224H ALA* 6.0 1.1 - - - -
227H VAL* 3.1 37.7 - - + -
239H PHE* 3.7 28.5 - - + -
241H ALA 3.0 14.1 - - - +
242H VAL* 4.1 7.6 - - + -
265H ASN 3.8 0.2 - - - +
266H ARG* 3.7 0.3 - - - -
267H ILE* 3.0 36.8 + - + +
269H PHE* 4.2 5.2 - - + -
285H TYR* 1.3 80.0 - - - +
287H ASP* 1.3 67.5 + - - +
288H LEU* 3.8 20.2 + - + -
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Residues in contact with ASP 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238H ARG 3.8 0.2 - - - +
240H LYS* 3.0 34.5 + - + +
241H ALA* 2.7 25.6 + - + +
265H ASN* 3.6 4.3 - - + +
266H ARG* 2.7 53.5 + - - +
285H TYR* 3.2 11.7 + - - -
286H VAL* 1.3 73.9 - - - +
288H LEU* 1.3 65.1 + - - +
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Residues in contact with LEU 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H VAL* 5.2 4.3 - - + -
228H LEU* 5.7 0.7 - - - -
231H PHE* 3.1 33.9 - - + +
232H ALA* 3.9 16.2 - - + -
238H ARG* 3.1 21.8 - - + +
239H PHE* 4.2 10.8 - - + -
240H LYS* 4.5 7.9 + - - +
265H ASN* 2.8 34.7 + - + +
267H ILE* 3.7 28.3 - - + -
286H VAL* 3.9 17.5 - - + +
287H ASP* 1.3 81.1 - - - +
289H ALA* 1.3 69.0 + - - +
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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
------------------------------------------------------------
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