Contacts of the strand formed by residues 255 - 263 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171H PRO* 4.8 7.4 - - + +
177I THR* 4.3 12.8 - - - -
178I ASP 3.4 18.8 - - - +
179I THR* 4.2 18.6 + - - +
253I GLY 4.4 1.2 + - - -
254I GLN* 1.3 74.2 + - - +
256I LEU* 1.3 69.7 + - - +
273I VAL* 3.3 5.9 - - - -
274I GLN* 2.9 49.5 + - + +
275I GLU* 2.7 26.1 + - - -
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Residues in contact with LEU 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I THR* 3.2 8.3 - - - -
178I ASP* 2.7 40.9 + - + +
180I THR* 3.9 15.5 - - - +
214I LEU* 5.4 1.6 - - + -
219I THR* 3.7 32.5 - - + +
222I PHE* 3.7 43.5 - - + -
223I SER* 5.5 0.2 - - - +
250I VAL* 4.0 27.8 - - + -
254I GLN 5.5 0.2 - - - +
255I THR* 1.3 77.0 - - - +
257I GLN* 1.3 61.9 + - - +
258I THR* 4.1 4.0 - - - +
271I THR* 4.4 8.5 - - + -
272I LYS 3.4 8.7 - - - +
273I VAL* 4.5 2.5 - - + -
280I VAL* 4.7 0.4 - - + -
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Residues in contact with GLN 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H PRO* 5.0 2.2 - - - +
172H PRO* 6.0 1.6 - - - +
175I VAL* 4.0 16.6 - - + -
176I LEU 3.8 2.7 - - - -
177I THR* 3.9 20.3 - - + +
256I LEU* 1.3 73.9 - - - +
258I THR* 1.3 62.2 + - - +
259I GLU* 3.6 9.1 + - + +
270I GLN 3.6 0.2 - - - +
271I THR* 3.3 4.8 - - - +
272I LYS* 2.8 60.7 + - + +
274I GLN* 3.0 43.9 - - - +
277I GLY* 5.7 1.4 - - - -
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Residues in contact with THR 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175I VAL* 3.2 4.8 - - - -
176I LEU 2.9 36.5 + - - -
178I ASP* 4.9 2.6 + - - -
222I PHE* 5.6 1.0 - - - +
223I SER* 2.8 51.1 + - - +
226I ARG* 4.7 7.8 - - + +
227I VAL* 4.8 0.2 - - + -
256I LEU* 5.0 3.8 - - - +
257I GLN* 1.3 72.4 + - - +
259I GLU* 1.3 61.0 + - - +
260I MET* 3.7 27.1 - - + +
269I PHE* 4.2 13.2 - - + -
270I GLN 3.6 3.4 - - - +
271I THR* 4.0 3.5 - - - +
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Residues in contact with GLU 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172I PRO* 4.1 15.4 - - + +
174I ALA 3.7 4.7 - - - -
175I VAL* 4.0 15.1 - - + +
257I GLN* 4.2 12.2 - - + +
258I THR* 1.3 73.9 - - - +
260I MET* 1.3 59.5 + - - +
261I TRP* 3.4 19.6 - - + -
269I PHE* 3.0 8.5 - - - +
270I GLN* 2.7 68.0 + - - +
272I LYS* 3.0 36.1 + - + +
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Residues in contact with MET 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I PRO* 3.6 2.1 - - - +
173I ASP* 2.7 32.8 + - - +
174I ALA 2.8 23.2 + - - +
176I LEU* 3.4 43.1 - - + +
226I ARG* 4.3 5.2 - - + -
227I VAL* 3.8 26.7 - - + -
230I GLN* 4.2 6.1 - - + -
231I PHE* 3.6 30.7 - - + -
258I THR* 3.7 26.0 - - + +
259I GLU* 1.3 80.3 - - - +
261I TRP* 1.3 57.9 + - - +
262I LYS 4.3 0.2 - - - -
267I ILE* 4.1 2.7 - - + -
268I HIS 3.3 6.5 - - - +
269I PHE* 4.2 6.7 - - + -
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Residues in contact with TRP 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167I ILE* 3.6 30.1 - - + -
168I PRO* 3.7 44.5 + - + -
170I ARG* 2.7 44.7 + - - +
172I PRO* 3.4 30.7 - - + +
173I ASP* 3.5 4.9 - - - -
259I GLU* 3.4 44.2 - - + -
260I MET* 1.3 76.7 - - - +
262I LYS* 1.3 62.5 + - - +
263I GLU 3.6 1.6 + - - -
267I ILE* 3.3 5.5 - - - -
268I HIS* 2.8 55.2 + - + +
269I PHE* 4.1 1.3 - - - -
270I GLN* 3.8 14.1 - - + -
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Residues in contact with LYS 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LYS* 5.1 13.9 + - - -
40H ASP* 6.0 1.0 - - - +
41H PRO* 5.4 7.5 - - - +
170I ARG* 3.4 14.4 + - - -
173I ASP* 2.8 17.8 + - - +
231I PHE* 3.7 31.5 - - + -
261I TRP* 1.3 71.7 - - - +
263I GLU* 1.3 62.5 + - - +
264I GLY* 3.0 28.2 + - - +
265I ASN* 5.8 0.7 - - - +
267I ILE* 3.5 19.7 - - + -
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Residues in contact with GLU 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I PRO* 3.8 15.5 - - + +
170I ARG* 2.8 36.9 + - - -
261I TRP 3.6 0.6 + - - +
262I LYS* 1.3 74.4 - - - +
264I GLY* 1.3 63.2 + - - +
265I ASN 3.3 0.7 + - - -
266I ARG* 3.0 28.0 + - - +
268I 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