Contacts of the strand formed by residues 255 - 263 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177F THR* 4.3 12.3 - - + -
178F ASP 3.4 19.3 - - - +
179F THR* 4.0 18.9 + - - +
253F GLY 4.5 0.9 + - - -
254F GLN* 1.3 74.7 + - - +
256F LEU* 1.3 70.3 + - - +
273F VAL* 3.3 6.4 - - - -
274F GLN* 3.0 47.5 + - + +
275F GLU* 2.7 26.2 + - - -
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Residues in contact with LEU 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F THR* 3.3 8.2 - - - -
178F ASP* 2.8 39.9 + - + +
180F THR* 4.0 14.6 - - - +
214F LEU* 5.3 1.3 - - + -
219F THR* 3.8 31.6 - - + +
222F PHE* 3.7 44.9 - - + -
223F SER* 5.5 0.2 - - - +
250F VAL* 4.0 28.7 - - + -
254F GLN 5.5 0.2 - - - +
255F THR* 1.3 78.1 - - - +
257F GLN* 1.3 60.7 + - - +
258F THR* 4.1 4.0 - - - +
271F THR* 4.4 7.6 - - + -
272F LYS 3.4 9.9 - - - +
273F VAL* 4.5 2.2 - - + -
280F VAL* 4.7 0.2 - - + -
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Residues in contact with GLN 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F VAL* 4.0 16.4 - - + -
176F LEU 3.8 3.1 - - - -
177F THR* 4.0 21.0 - - + +
256F LEU* 1.3 74.5 - - - +
258F THR* 1.3 61.5 + - - +
259F GLU* 3.6 9.0 + - + +
270F GLN 3.7 0.2 - - - +
271F THR* 3.3 4.0 - - - +
272F LYS* 2.8 61.8 + - + +
274F GLN* 2.9 43.9 - - - +
277F GLY* 5.8 1.2 - - - -
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Residues in contact with THR 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175F VAL* 3.2 4.9 - - - -
176F LEU 3.0 36.8 + - - -
178F ASP* 5.2 1.9 + - - -
222F PHE* 5.6 0.7 - - - +
223F SER* 2.6 52.1 + - - +
226F ARG* 4.7 9.3 - - + +
227F VAL* 4.8 0.2 - - + -
256F LEU* 4.1 4.4 - - - +
257F GLN* 1.3 72.1 + - - +
259F GLU* 1.3 60.8 + - - +
260F MET* 3.8 26.2 - - + +
269F PHE* 4.2 13.2 - - + -
270F GLN 3.6 2.9 - - - +
271F THR* 4.0 2.7 - - - +
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Residues in contact with GLU 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F PRO* 4.1 15.7 - - + +
174F ALA 3.8 4.3 - - - -
175F VAL* 4.0 14.8 - - + +
257F GLN* 4.2 12.5 - - + +
258F THR* 1.3 73.9 - - - +
260F MET* 1.3 59.4 + - - +
261F TRP* 3.4 21.4 - - + -
269F PHE* 3.0 8.3 - - - +
270F GLN* 2.8 66.4 + - - +
272F LYS* 3.0 36.0 + - + +
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Residues in contact with MET 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F PRO* 3.5 1.9 - - - +
173F ASP* 2.7 32.8 + - - -
174F ALA 2.8 21.7 + - - +
176F LEU* 3.4 42.4 - - + +
226F ARG* 4.4 4.9 - - + -
227F VAL* 3.8 27.6 - - + -
230F GLN* 4.2 7.0 - - + -
231F PHE* 3.6 31.4 - - + -
258F THR* 3.8 26.0 - - + +
259F GLU* 1.3 79.8 - - - +
261F TRP* 1.3 59.3 + - - +
262F LYS 4.3 0.2 - - - -
267F ILE* 4.0 3.1 - - + -
268F HIS 3.2 6.5 - - - +
269F PHE* 4.2 6.3 - - + -
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Residues in contact with TRP 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ILE* 3.6 33.4 - - + -
168F PRO* 3.7 45.5 + - + -
170F ARG* 2.6 40.1 + - + +
171F PRO 3.8 4.7 - - - -
172F PRO* 3.3 32.6 - - + -
173F ASP* 3.4 4.7 - - - -
259F GLU* 3.4 44.2 - - + -
260F MET* 1.3 77.5 - - - +
262F LYS* 1.3 61.1 + - - +
263F GLU 3.6 1.0 + - - -
267F ILE* 3.4 4.8 - - - -
268F HIS* 2.8 51.4 + - + +
269F PHE* 4.1 0.4 - - - -
270F GLN* 3.9 13.7 - - + -
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Residues in contact with LYS 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ARG* 3.3 14.6 + - - -
173F ASP* 2.6 17.5 + - - +
231F PHE* 3.8 26.2 - - + -
261F TRP* 1.3 71.9 - - - +
263F GLU* 1.3 61.9 + - - +
264F GLY* 3.0 27.4 + - - +
265F ASN* 5.9 0.9 - - - +
267F ILE* 3.5 24.5 - - + -
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Residues in contact with GLU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F PRO* 3.8 15.5 - - + +
170F ARG* 2.8 35.9 + - - +
261F TRP 4.6 0.2 - - - +
262F LYS* 1.3 74.3 - - - +
264F GLY* 1.3 63.8 + - - +
265F ASN 3.3 0.3 + - - -
266F ARG* 3.0 28.3 + - + +
268F HIS* 3.5 29.2 - - + +
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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