Contacts of the strand formed by residues 255 - 263 (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 THR 255 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177L THR* 4.4 9.9 - - + -
178L ASP 3.3 20.4 - - - +
179L THR* 4.0 19.9 + - - +
253L GLY 4.4 1.2 + - - -
254L GLN* 1.3 74.4 + - - +
256L LEU* 1.3 70.7 + - - +
273L VAL* 3.3 5.9 - - - -
274L GLN* 2.9 50.8 + - + +
275L GLU* 2.7 23.9 + - - -
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Residues in contact with LEU 256 (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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176L LEU 4.8 0.2 - - - -
177L THR* 3.3 5.7 - - - +
178L ASP* 2.8 39.3 + - + +
180L THR* 3.9 14.6 - - - +
214L LEU* 5.4 1.6 - - + -
219L THR* 3.7 32.3 - - + +
222L PHE* 3.6 44.9 - - + -
223L SER* 5.5 0.2 - - - +
250L VAL* 4.0 28.9 - - + -
255L THR* 1.3 79.5 - - - +
257L GLN* 1.3 61.3 + - - +
258L THR* 4.1 3.8 - - - +
271L THR* 4.4 7.6 - - + -
272L LYS 3.4 8.5 - - - +
273L VAL* 4.5 2.7 - - + -
280L VAL* 4.7 0.2 - - + -
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Residues in contact with GLN 257 (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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175L VAL* 4.1 15.9 - - + -
176L LEU 3.9 2.2 - - - -
177L THR* 4.0 21.0 - - + +
256L LEU* 1.3 73.3 - - - +
258L THR* 1.3 61.5 + - - +
259L GLU* 3.6 9.1 + - + +
270L GLN 3.6 0.9 - - - +
271L THR* 3.2 4.6 - - - -
272L LYS* 2.8 62.1 + - + +
274L GLN* 2.9 43.8 - - + +
277L GLY* 5.7 1.6 - - - -
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Residues in contact with THR 258 (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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175L VAL* 3.2 4.8 - - - -
176L LEU 3.0 36.6 + - - +
178L ASP* 5.1 2.3 + - - -
222L PHE* 5.6 0.9 - - - +
223L SER* 2.7 52.1 + - - +
226L ARG* 4.6 8.6 - - + +
256L LEU* 4.1 3.8 - - - +
257L GLN* 1.3 72.8 + - - +
259L GLU* 1.3 61.0 + - - +
260L MET* 3.8 26.6 - - + +
269L PHE* 4.2 9.0 - - + -
270L GLN 3.5 7.2 - - - +
271L THR* 4.0 2.5 - - - +
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Residues in contact with GLU 259 (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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172L PRO* 4.2 15.6 - - + +
174L ALA 3.8 4.0 - - - -
175L VAL* 4.0 15.0 - - + +
257L GLN* 4.3 13.8 - - + +
258L THR* 1.3 74.1 - - - +
260L MET* 1.3 59.5 + - - +
261L TRP* 3.4 21.0 - - + -
269L PHE* 3.0 8.8 - - - +
270L GLN* 2.8 67.1 + - - +
272L LYS* 2.9 35.9 + - - +
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Residues in contact with MET 260 (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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172L PRO* 3.5 2.8 - - - +
173L ASP* 2.7 33.1 + - - -
174L ALA 2.8 23.0 + - - +
176L LEU* 3.5 42.0 - - + +
226L ARG* 4.3 4.5 - - + -
227L VAL* 3.7 29.2 - - + -
230L GLN* 4.2 6.7 - - + -
231L PHE* 3.6 30.7 - - + -
258L THR* 3.8 25.6 - - + +
259L GLU* 1.3 80.7 - - - +
261L TRP* 1.3 58.1 + - - +
267L ILE* 4.1 2.0 - - + -
268L HIS 3.3 5.6 - - - +
269L PHE* 4.2 7.0 - - + -
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Residues in contact with TRP 261 (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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167L ILE* 3.4 35.9 - - + -
168L PRO* 3.7 43.7 + - + -
170L ARG* 2.7 40.8 + - - +
171L PRO 3.9 4.0 - - - -
172L PRO* 3.4 29.8 - - + +
173L ASP* 3.5 4.9 - - - -
231L PHE* 5.2 0.2 - - - -
259L GLU* 3.4 43.7 - - + -
260L MET* 1.3 78.1 - - - +
262L LYS* 1.3 62.2 + - - +
263L GLU 3.6 1.6 + - - -
267L ILE* 3.4 5.4 - - - -
268L HIS* 2.8 52.1 + - + +
269L PHE* 4.1 0.7 - - - -
270L GLN* 3.8 14.4 - - + -
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Residues in contact with LYS 262 (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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170L ARG* 3.3 14.9 + - - -
173L ASP* 2.6 18.2 + - - +
231L PHE* 3.8 30.4 - - + -
261L TRP* 1.3 71.7 - - - +
263L GLU* 1.3 62.6 + - - +
264L GLY* 3.0 27.6 + - - +
265L ASN* 5.9 0.7 - - - +
267L ILE* 3.5 20.6 - - + -
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Residues in contact with GLU 263 (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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168L PRO* 3.7 17.0 - - + +
170L ARG* 2.8 37.4 + - - +
261L TRP 4.6 0.2 - - - +
262L LYS* 1.3 73.1 - - - +
264L GLY* 1.3 63.1 + - - +
265L ASN 3.3 0.5 + - - -
266L ARG* 3.0 28.4 + - + +
268L HIS* 3.6 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