Contacts of the strand formed by residues 266 - 273 (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 ARG 266 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I VAL* 3.8 26.5 - - - +
263I GLU* 3.0 35.1 + - + +
264I GLY 3.4 0.2 - - - -
265I ASN* 1.3 79.7 - - - +
267I ILE* 1.3 63.1 + - - +
268I HIS* 3.6 30.7 + - + +
285I TYR* 3.3 37.1 + - + -
286I VAL 3.7 3.8 - - - -
287I ASP* 2.8 39.8 + - - +
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Residues in contact with ILE 267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I VAL* 3.9 22.0 - - + -
231I PHE* 3.6 44.9 - - + -
260I MET* 4.1 5.6 - - + -
261I TRP 3.3 7.2 - - - +
262I LYS* 3.5 33.7 - - + -
264I GLY 4.8 3.4 - - - +
265I ASN 5.0 0.7 - - - -
266I ARG* 1.3 75.3 - - - +
268I HIS* 1.3 67.2 + - - +
269I PHE* 3.8 0.5 + - - -
285I TYR* 3.2 2.9 - - - -
286I VAL* 3.0 34.4 + - + +
288I LEU* 3.8 27.4 - - + -
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Residues in contact with HIS 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I VAL* 3.8 23.6 - - + +
166I ALA 3.6 17.1 + - - -
167I ILE* 4.5 3.6 - - + -
168I PRO* 3.7 23.6 - - + -
260I MET* 3.3 2.4 - - - +
261I TRP* 2.8 38.7 + - + +
263I GLU* 3.5 38.6 - - + +
266I ARG* 3.6 32.1 - - + +
267I ILE* 1.3 73.9 - - - +
269I PHE* 1.3 62.9 + - - +
284I ALA 3.5 12.3 + - - +
285I TYR* 4.1 1.7 - - - +
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Residues in contact with PHE 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I ILE* 4.4 4.5 - - - +
220I PHE* 5.4 8.1 - + - -
223I SER* 3.5 28.0 - - - -
224I ALA* 4.9 9.6 - - + -
227I VAL* 4.3 14.4 - - + -
242I VAL* 5.3 3.4 - - + -
243I LYS 4.4 0.2 - - - -
244I ALA* 4.5 9.0 - - + -
258I THR* 4.2 3.1 - - + -
259I GLU 3.0 16.2 - - - +
260I MET* 4.2 9.4 - - + -
261I TRP* 4.1 3.8 - - - -
267I ILE 4.1 3.6 - - - -
268I HIS* 1.3 75.3 - - - +
270I GLN* 1.3 63.6 - - - +
271I THR* 3.8 15.0 - - - -
281I ILE* 4.0 9.9 - - + -
283I ASN 4.4 0.5 + - - -
284I ALA* 3.0 58.1 + - + +
285I TYR* 3.5 30.1 - - - -
286I VAL* 4.3 6.1 - - + -
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Residues in contact with GLN 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I ILE* 3.5 33.8 - - + +
257I GLN 3.6 0.5 - - - +
258I THR* 3.6 2.4 - - - +
259I GLU* 2.7 58.0 + - - +
261I TRP* 3.8 10.3 - - + -
269I PHE* 1.3 74.7 - - - +
271I THR* 1.3 62.9 + - - +
272I LYS* 3.9 10.0 - - - +
279I ILE* 3.3 32.9 - - + +
281I ILE 3.5 15.7 - - - +
282I SER* 4.4 8.9 - - - -
283I ASN 5.6 0.2 + - - -
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Residues in contact with THR 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219I THR* 4.0 11.4 - - + -
223I SER* 2.6 33.9 + - - +
256I LEU* 4.4 6.3 - - + -
257I GLN 3.3 12.6 - - - +
258I THR* 4.0 4.5 - - - +
269I PHE* 3.8 3.5 - - - -
270I GLN* 1.3 75.7 + - - +
272I LYS* 1.3 70.7 + - - +
279I ILE* 3.5 4.5 - - - +
280I VAL* 2.8 37.9 + - + -
281I ILE* 2.9 31.8 + - - +
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Residues in contact with LYS 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I LEU* 3.4 6.9 - - - +
257I GLN* 2.8 50.5 + - + +
259I GLU* 3.0 39.7 + - - +
270I GLN* 3.9 12.0 - - - +
271I THR* 1.3 82.0 - - - +
273I VAL* 1.3 65.7 + - - +
274I GLN 3.8 0.9 - - - -
277I GLY* 3.9 17.0 + - - +
278I ASP 3.1 15.3 - - - +
279I ILE* 3.9 18.6 - - + -
280I VAL* 4.3 1.8 - - - +
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Residues in contact with VAL 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249I PRO 4.6 2.5 - - - +
250I VAL* 3.8 16.2 - - + -
254I GLN* 3.8 33.9 - - + +
255I THR 3.3 6.1 - - - +
256I LEU* 4.5 4.7 - - + -
272I LYS* 1.3 78.2 - - - +
274I GLN* 1.3 49.3 + - - +
275I GLU* 2.8 30.4 + - + +
276I THR* 3.0 15.2 + - - +
277I GLY* 2.7 32.0 + - - -
278I ASP* 3.0 9.0 + - + +
280I VAL* 3.5 27.1 - - + -
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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
------------------------------------------------------------
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