Contacts of the strand formed by residues 255 - 263 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D THR* 4.3 5.6 - - - -
178D ASP 3.3 20.9 - - - +
179D THR* 4.1 18.7 + - - +
253D GLY 4.4 1.0 + - - -
254D GLN* 1.3 76.9 + - - +
256D LEU* 1.3 68.9 + - - +
273D VAL* 3.3 6.4 - - - -
274D GLN* 3.0 40.2 + - + +
275D GLU* 2.6 25.5 + - - -
171G PRO* 4.3 21.7 - - + +
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Residues in contact with LEU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D THR* 3.2 8.3 - - - -
178D ASP* 2.8 38.2 + - + +
180D THR* 4.0 15.7 - - - +
214D LEU* 5.4 1.8 - - + -
219D THR* 3.6 32.8 - - + -
222D PHE* 3.6 44.2 - - + -
223D SER* 5.4 0.4 - - - +
250D VAL* 4.0 28.3 - - + -
254D GLN 5.5 0.2 - - - +
255D THR* 1.3 79.5 - - - +
257D GLN* 1.3 60.0 + - - +
258D THR* 4.1 4.5 - - - +
271D THR* 4.4 8.3 - - + -
272D LYS 3.4 9.6 - - - +
273D VAL* 4.5 2.2 - - + -
280D VAL* 4.7 0.2 - - + -
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Residues in contact with GLN 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D VAL* 4.0 16.4 - - + -
176D LEU 3.9 2.9 - - - -
177D THR* 4.0 20.6 - - + +
256D LEU* 1.3 73.5 - - - +
258D THR* 1.3 62.0 + - - +
259D GLU* 3.6 8.7 + - + +
270D GLN 3.6 1.4 - - - +
271D THR* 3.3 3.3 - - - +
272D LYS* 2.8 62.3 + - + +
274D GLN* 2.9 43.9 - - + +
277D GLY* 5.7 1.6 - - - -
171G PRO* 4.9 1.8 - - - +
172G PRO* 5.7 2.4 - - - +
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Residues in contact with THR 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D VAL* 3.1 4.8 - - - -
176D LEU 2.9 36.9 + - - -
178D ASP* 5.1 2.1 + - - -
222D PHE* 5.0 0.7 - - - +
223D SER* 2.6 52.5 + - - +
226D ARG* 4.8 8.3 - - + +
227D VAL* 4.8 0.2 - - + -
256D LEU* 5.0 4.3 - - - +
257D GLN* 1.3 73.1 + - - +
259D GLU* 1.3 61.0 + - - +
260D MET* 3.8 25.5 - - + +
269D PHE* 4.2 13.9 - - + -
270D GLN 3.5 3.1 - - - +
271D THR* 3.9 2.9 - - - +
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Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D PRO* 4.1 16.3 - - + +
174D ALA 3.7 3.8 - - - -
175D VAL* 4.0 17.0 - - + +
257D GLN* 4.3 11.7 - - + +
258D THR* 1.3 73.3 - - - +
260D MET* 1.3 61.1 + - - +
261D TRP* 3.4 20.0 - - + -
269D PHE* 3.0 8.8 - - - +
270D GLN* 2.7 68.2 + - + +
272D LYS* 3.0 36.0 + - + +
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Residues in contact with MET 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D PRO* 3.5 2.1 - - - +
173D ASP* 2.7 33.7 + - - -
174D ALA 2.7 22.9 + - - +
176D LEU* 3.5 42.8 - - + +
226D ARG* 4.5 4.5 - - + -
227D VAL* 3.8 28.3 - - + -
230D GLN* 4.2 6.5 - - + -
231D PHE* 3.6 31.2 - - + -
258D THR* 3.8 25.8 - - + +
259D GLU* 1.3 80.0 - - - +
261D TRP* 1.3 58.5 + - - +
267D ILE* 4.1 2.7 - - + -
268D HIS 3.3 6.7 - - - +
269D PHE* 4.2 6.3 - - + -
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Residues in contact with TRP 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ILE* 3.5 31.9 - - + -
168D PRO* 3.7 42.9 + - + -
170D ARG* 2.6 41.9 + - - +
171D PRO 3.7 4.5 - - - -
172D PRO* 3.2 32.2 - - + +
173D ASP* 3.3 4.5 - - - -
259D GLU* 3.4 42.6 - - + -
260D MET* 1.3 76.9 - - - +
262D LYS* 1.3 60.7 + - - +
263D GLU 3.6 1.0 + - - -
266D ARG 3.7 0.2 - - - +
267D ILE* 3.4 5.7 - - - -
268D HIS* 2.8 54.1 + - + +
269D PHE* 4.1 1.3 - - - -
270D GLN* 3.8 14.4 - - + -
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Residues in contact with LYS 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ARG* 3.4 14.4 + - - -
173D ASP* 2.6 17.8 + - - +
231D PHE* 3.8 26.0 - - + -
261D TRP* 1.3 71.5 - - - +
263D GLU* 1.3 63.7 + - - +
264D GLY* 3.0 26.8 + - - +
265D ASN* 5.9 0.9 - - - +
267D ILE* 3.5 25.1 - - + -
39G LYS* 5.7 3.1 + - - -
41G PRO* 6.2 2.0 - - - +
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Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D PRO* 3.9 14.4 - - + +
170D ARG* 2.7 36.8 + - - +
261D TRP 4.6 0.4 - - - +
262D LYS* 1.3 73.8 - - - +
264D GLY* 1.3 63.0 + - - +
265D ASN 3.3 0.5 + - - -
266D ARG* 3.0 28.8 + - - +
268D HIS* 3.6 28.7 - - + +
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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