Contacts of the strand formed by residues 266 - 273 (chain L) 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 ARG 266 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165L VAL* 3.7 27.9 - - - +
261L TRP 3.7 0.2 - - - +
263L GLU* 3.0 34.5 + - + +
264L GLY 3.3 0.6 - - - -
265L ASN* 1.3 79.3 - - - +
267L ILE* 1.3 64.2 + - - +
268L HIS* 3.6 32.6 + - + +
285L TYR* 3.2 36.8 + - + -
286L VAL 3.7 2.9 - - - -
287L ASP* 2.7 39.6 + - - +
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Residues in contact with ILE 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227L VAL* 3.8 20.4 - - + -
231L PHE* 3.6 45.3 - - + -
260L MET* 4.1 5.8 - - + -
261L TRP 3.4 8.1 - - - +
262L LYS* 3.5 34.3 - - + -
264L GLY 4.8 3.1 - - - +
265L ASN 5.0 0.2 - - - -
266L ARG* 1.3 76.5 - - - +
268L HIS* 1.3 69.8 + - - +
269L PHE* 4.1 0.5 - - - -
285L TYR* 3.2 2.1 - - - -
286L VAL* 3.0 33.8 + - + +
288L LEU* 3.7 26.7 - - + -
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Residues in contact with HIS 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165L VAL* 3.7 27.4 - - + +
166L ALA 3.5 17.6 + - - -
167L ILE* 4.4 3.7 - - + -
168L PRO* 3.6 24.6 - - + +
260L MET* 3.3 1.9 - - - -
261L TRP* 2.8 38.2 + - + +
263L GLU* 3.6 34.2 - - + +
266L ARG* 3.6 32.2 - - + +
267L ILE* 1.3 76.7 - - - +
269L PHE* 1.3 62.5 + - - +
284L ALA 3.5 12.7 + - - +
285L TYR* 4.1 2.3 - - - +
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Residues in contact with PHE 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L ILE* 4.3 4.5 - - - +
220L PHE* 5.2 9.2 - + - -
223L SER* 3.6 28.3 - - - -
224L ALA* 4.9 9.2 - - + -
227L VAL* 4.2 14.4 - - + -
242L VAL* 5.3 3.4 - - + -
243L LYS 4.4 0.2 - - - -
244L ALA* 4.4 9.4 - - + -
258L THR* 4.2 4.3 - - + -
259L GLU 3.0 14.6 - - - +
260L MET* 4.2 10.8 - - + -
261L TRP* 4.1 4.2 - - - -
267L ILE 4.1 3.8 - - - -
268L HIS* 1.3 75.3 - - - +
270L GLN* 1.3 62.8 + - - +
271L THR* 3.8 15.3 - - - -
281L ILE* 4.0 9.6 - - + -
282L SER 4.6 0.2 - - - -
283L ASN 4.4 0.5 + - - -
284L ALA* 3.0 60.2 + - + +
285L TYR* 3.5 30.1 - - - -
286L VAL* 4.4 5.2 - - + -
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Residues in contact with GLN 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L ILE* 3.6 31.8 - - + +
257L GLN 3.6 0.2 - - - +
258L THR* 3.5 1.9 - - - +
259L GLU* 2.8 56.6 + - - +
261L TRP* 3.8 10.7 - - + -
269L PHE* 1.3 75.0 - - - +
271L THR* 1.3 66.7 + - - +
272L LYS* 3.8 10.3 - - - +
279L ILE* 3.2 32.9 - - + +
281L ILE 3.5 16.4 - - - +
282L SER* 4.4 9.5 - - - -
283L ASN 5.6 0.2 + - - -
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Residues in contact with THR 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L THR* 4.0 11.4 - - + -
223L SER* 2.6 34.2 + - - +
256L LEU* 4.4 6.3 - - + -
257L GLN 3.2 12.6 - - - +
258L THR* 4.0 4.7 - - - +
269L PHE* 3.8 3.1 - - - -
270L GLN* 1.3 77.3 + - - +
272L LYS* 1.3 64.2 + - - +
279L ILE* 3.5 4.0 - - - +
280L VAL* 2.8 43.3 + - + +
281L ILE* 2.9 31.9 + - - +
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Residues in contact with LYS 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256L LEU* 3.4 5.5 - - - +
257L GLN* 2.8 52.0 + - + +
259L GLU* 2.9 42.0 + - - +
270L GLN* 3.8 11.8 - - - +
271L THR* 1.3 81.9 - - - +
273L VAL* 1.3 64.6 + - - +
274L GLN 3.8 0.9 - - - -
277L GLY* 3.9 17.0 - - - +
278L ASP 3.0 14.1 - - - +
279L ILE* 3.9 19.3 - - + -
280L VAL* 4.3 1.3 - - - +
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Residues in contact with VAL 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249L PRO 4.5 2.2 - - - +
250L VAL* 3.8 15.7 - - + -
254L GLN* 3.8 34.1 - - + +
255L THR 3.3 6.3 - - - +
256L LEU* 4.5 4.7 - - + -
272L LYS* 1.3 77.7 - - - +
274L GLN* 1.3 50.0 + - - +
275L GLU* 2.7 31.1 + - + +
276L THR* 3.0 15.3 + - - +
277L GLY* 2.7 32.1 + - - -
278L ASP* 3.0 8.6 + - + +
280L VAL* 3.5 28.3 - - + -
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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