Contacts of the strand formed by residues 255 - 263 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B THR* 4.3 11.0 - - + -
178B ASP 3.2 20.6 - - - +
179B THR* 3.8 21.1 + - - +
253B GLY 4.4 0.7 + - - -
254B GLN* 1.3 77.2 + - - +
256B LEU* 1.3 68.2 + - - +
273B VAL* 3.3 6.4 - - - -
274B GLN* 2.9 50.2 + - + +
275B GLU* 2.7 23.2 + - - -
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Residues in contact with LEU 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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177B THR* 3.2 8.0 - - - -
178B ASP* 2.7 45.3 + - + +
180B THR* 3.9 15.5 - - - +
214B LEU* 5.3 2.0 - - + -
219B THR* 3.7 31.4 - - + +
222B PHE* 3.6 44.6 - - + -
223B SER* 5.5 0.2 - - - +
250B VAL* 4.0 27.4 - - + -
254B GLN 5.5 0.2 - - - +
255B THR* 1.3 75.9 - - - +
257B GLN* 1.3 60.5 + - - +
258B THR* 4.1 4.7 - - - +
271B THR* 4.4 8.3 - - + -
272B LYS 3.4 9.2 - - - +
273B VAL* 4.5 2.7 - - + -
280B VAL* 4.7 0.2 - - + -
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Residues in contact with GLN 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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175B VAL* 3.9 18.3 - - + +
176B LEU 3.7 2.5 - - - -
177B THR* 3.9 21.2 - - + +
256B LEU* 1.3 72.6 - - - +
258B THR* 1.3 62.9 + - - +
259B GLU* 3.6 9.4 + - + +
270B GLN 3.6 0.2 - - - +
271B THR* 3.3 4.0 - - - -
272B LYS* 2.8 58.4 + - + +
274B GLN* 3.0 42.1 - - - +
277B GLY* 5.7 1.6 - - - -
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 3.2 3.1 - - - -
176B LEU 2.9 36.5 + - - -
178B ASP* 5.0 2.8 + - - -
222B PHE* 5.0 0.7 - - - +
223B SER* 2.8 49.8 + - - +
226B ARG* 4.6 9.7 - - + +
227B VAL* 4.8 0.2 - - + -
256B LEU* 4.1 4.0 - - - +
257B GLN* 1.3 73.9 + - - +
259B GLU* 1.3 60.6 + - - +
260B MET* 3.8 27.8 - - + +
269B PHE* 4.2 8.7 - - + -
270B GLN 3.5 7.0 - - - +
271B THR* 4.0 3.0 - - - +
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Residues in contact with GLU 259 (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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172B PRO* 4.2 17.0 - - + +
174B ALA 3.7 4.7 - - - -
175B VAL* 4.0 15.5 - - + +
257B GLN* 4.2 12.7 - - + +
258B THR* 1.3 73.2 - - - +
260B MET* 1.3 60.1 + - - +
261B TRP* 3.3 19.2 - - + -
269B PHE* 3.0 8.1 - - - +
270B GLN* 2.7 68.0 + - + +
272B LYS* 3.1 35.5 + - + +
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Residues in contact with MET 260 (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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172B PRO* 3.7 1.3 - - - +
173B ASP* 2.8 31.7 + - - +
174B ALA 2.7 23.6 + - - +
176B LEU* 3.4 43.1 - - + +
226B ARG* 4.3 9.4 - - + -
227B VAL* 3.7 28.7 - - + -
230B GLN* 4.2 7.0 - - + -
231B PHE* 3.5 31.0 - - + -
258B THR* 3.8 20.6 - - + +
259B GLU* 1.3 79.5 - - - +
261B TRP* 1.3 59.1 + - - +
262B LYS 4.3 0.2 - - - -
267B ILE* 4.0 2.7 - - + -
268B HIS 3.2 5.6 - - - +
269B PHE* 4.2 7.0 - - + -
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Residues in contact with TRP 261 (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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167B ILE* 3.6 30.5 - - + -
168B PRO* 3.8 36.4 + - + -
170B ARG* 2.8 50.1 + - - +
171B PRO 3.8 0.2 - - - -
172B PRO* 3.2 34.8 - - + +
173B ASP* 3.5 4.3 - - - -
231B PHE* 5.3 0.2 - - - -
259B GLU* 3.3 43.3 - - + -
260B MET* 1.3 75.9 - - - +
262B LYS* 1.3 62.3 + - - +
263B GLU 3.6 1.4 + - - -
266B ARG 3.6 0.2 - - - +
267B ILE* 3.4 5.7 - - - -
268B HIS* 2.8 54.3 + - + +
269B PHE* 4.1 1.6 - - - -
270B GLN* 3.8 14.1 - - + -
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Residues in contact with LYS 262 (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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170B ARG* 3.5 14.6 + - - -
173B ASP* 2.8 16.2 + - - +
231B PHE* 3.8 26.6 - - + -
261B TRP* 1.3 71.7 - - - +
263B GLU* 1.3 62.6 + - - +
264B GLY* 3.0 27.6 + - - +
265B ASN* 5.8 0.9 - - - +
267B ILE* 3.5 25.1 - - + -
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Residues in contact with GLU 263 (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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168B PRO* 3.9 14.5 - - + +
170B ARG* 2.7 37.3 + - - +
261B TRP 4.5 0.4 - - - +
262B LYS* 1.3 73.3 - - - +
264B GLY* 1.3 62.8 + - - +
265B ASN 3.3 2.9 + - - -
266B ARG* 3.0 25.2 + - + +
268B HIS* 3.5 30.1 - - + +
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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