Contacts of the strand formed by residues 255 - 263 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D PRO* 4.5 9.2 - - + +
177G THR* 4.3 11.7 - - - -
178G ASP 3.4 15.5 - - - +
179G THR* 4.0 19.2 + - - +
253G GLY 4.4 0.9 + - - -
254G GLN* 1.3 73.5 + - - +
256G LEU* 1.3 71.7 + - - +
273G VAL* 3.3 6.1 - - - -
274G GLN* 2.9 50.1 + - + +
275G GLU* 2.7 23.9 + - - -
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Residues in contact with LEU 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G LEU 4.7 0.2 - - - -
177G THR* 3.1 9.4 - - - -
178G ASP* 2.7 40.6 + - + +
180G THR* 3.9 17.9 - - - +
214G LEU* 5.3 2.0 - - + -
219G THR* 3.7 32.3 - - + +
222G PHE* 3.6 42.6 - - + -
223G SER* 5.6 0.2 - - - +
250G VAL* 4.0 27.6 - - + -
254G GLN 5.4 0.2 - - - +
255G THR* 1.3 77.5 - - - +
257G GLN* 1.3 58.8 + - - +
258G THR* 4.1 4.3 - - - +
271G THR* 4.4 8.1 - - + -
272G LYS 3.4 9.6 - - - +
273G VAL* 4.5 2.5 - - + -
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Residues in contact with GLN 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D PRO* 5.0 1.6 - - - +
172D PRO* 5.8 2.6 - - - +
175G VAL* 4.0 16.4 - - + +
176G LEU 3.8 2.7 - - - -
177G THR* 3.9 20.8 - - + +
256G LEU* 1.3 73.9 - - - +
258G THR* 1.3 61.6 + - - +
259G GLU* 3.6 9.3 + - + +
270G GLN 3.6 1.2 - - - +
271G THR* 3.2 4.1 - - - -
272G LYS* 2.8 62.8 + - + +
274G GLN* 3.0 43.2 - - + +
277G GLY* 5.8 1.2 - - - -
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Residues in contact with THR 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175G VAL* 3.1 22.3 - - - -
176G LEU 2.9 20.3 + - - -
178G ASP* 5.0 2.3 + - - -
222G PHE* 5.6 1.0 - - - +
223G SER* 2.7 52.2 + - - +
226G ARG* 4.7 8.5 - - + +
227G VAL* 4.8 0.2 - - + -
256G LEU* 4.1 4.5 - - - +
257G GLN* 1.3 72.5 + - - +
259G GLU* 1.3 60.9 + - - +
260G MET* 3.8 26.5 - - + +
269G PHE* 4.1 13.2 - - + -
270G GLN 3.5 3.1 - - - +
271G THR* 4.0 2.3 - - - +
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Residues in contact with GLU 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G PRO* 4.1 15.6 - - + +
174G ALA 3.7 4.0 - - - -
175G VAL* 4.0 15.9 - - + +
257G GLN* 4.3 12.5 - - + +
258G THR* 1.3 73.8 - - - +
260G MET* 1.3 60.6 + - - +
261G TRP* 3.4 19.2 - - + -
269G PHE* 3.0 8.3 - - - +
270G GLN* 2.7 68.4 + - - +
272G LYS* 3.1 35.4 + - + +
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Residues in contact with MET 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G PRO* 3.6 1.4 - - - +
173G ASP* 2.7 34.0 + - - +
174G ALA 2.7 22.9 + - - +
176G LEU* 3.4 42.8 - - + +
226G ARG* 4.4 8.1 - - + -
227G VAL* 3.7 29.2 - - + -
230G GLN* 4.1 8.5 - - + -
231G PHE* 3.6 29.8 - - + -
258G THR* 3.8 20.9 - - + +
259G GLU* 1.3 79.4 - - - +
261G TRP* 1.3 58.6 + - - +
267G ILE* 4.0 3.1 - - + -
268G HIS 3.3 6.5 - - - +
269G PHE* 4.2 7.2 - - + -
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Residues in contact with TRP 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G ILE* 3.5 36.1 - - + -
168G PRO* 3.7 42.6 + - + -
170G ARG* 2.7 40.2 + - - +
171G PRO 3.8 4.5 - - - -
172G PRO* 3.3 31.8 - - + +
173G ASP* 3.5 4.3 - - - -
231G PHE* 5.2 0.2 - - - -
259G GLU* 3.4 42.4 - - + -
260G MET* 1.3 76.7 - - - +
262G LYS* 1.3 62.1 + - - +
263G GLU 3.6 1.0 + - - -
267G ILE* 3.4 5.3 - - - -
268G HIS* 2.8 53.0 + - + +
269G PHE* 4.1 0.7 - - - -
270G GLN* 3.8 14.8 - - + -
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Residues in contact with LYS 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LYS* 5.6 9.8 + - - +
41D PRO* 6.3 1.0 - - - +
170G ARG* 3.3 15.1 + - - -
173G ASP* 2.7 16.9 + - - +
231G PHE* 3.7 26.8 - - + -
260G MET 4.3 0.2 - - - -
261G TRP* 1.3 72.3 - - - +
263G GLU* 1.3 63.0 + - - +
264G GLY* 2.9 27.9 + - - +
265G ASN* 5.8 0.7 - - - +
267G ILE* 3.4 24.0 - - + -
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Residues in contact with GLU 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G PRO* 3.8 15.7 - - + +
170G ARG* 2.8 37.4 + - - -
261G TRP 3.6 0.4 + - - +
262G LYS* 1.3 73.6 - - - +
264G GLY* 1.3 63.0 + - - +
265G ASN 3.3 0.7 + - - -
266G ARG* 3.0 28.7 + - - +
268G HIS* 3.6 29.8 - - + +
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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