Contacts of the strand formed by residues 168 - 176 (chain D) in PDB entry 6CET
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 SER 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D PHE* 4.6 0.9 - - - -
105D LYS* 3.3 7.3 + - - +
106D ASP* 2.4 34.1 + - - -
107D GLN 4.5 3.1 - - - -
166D SER* 2.7 18.8 + - - -
167D THR* 1.3 71.5 + - - +
169D ALA* 1.3 58.5 + - - +
213D SER* 3.0 23.5 + - - -
327D ASP 3.8 6.1 - - - -
328D ARG* 3.2 36.6 - - - -
329D THR 3.4 2.4 + - - -
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Residues in contact with ALA 169 (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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166D SER* 4.3 5.8 - - - +
168D SER* 1.3 78.5 - - - +
170D MET* 1.3 67.5 + - - +
213D SER 3.0 5.9 + - - -
214D HIS* 2.9 47.1 + - + +
215D GLU 2.9 3.8 + - - -
328D ARG* 3.9 2.8 - - - -
330D GLY* 3.3 29.8 - - - +
331D GLN 5.7 0.2 - - - -
332D MET* 5.8 0.7 - - + -
750D PRO* 4.1 14.8 - - + -
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Residues in contact with MET 170 (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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169D ALA* 1.3 78.6 - - - +
171D VAL* 1.3 60.2 + - - +
172D TYR* 3.7 28.3 - - + +
215D GLU* 3.5 36.1 - - + +
261D ASN* 5.7 2.5 - - - +
317D PHE* 4.2 17.3 - - + -
320D HIS* 6.0 4.3 - - + -
324D ARG* 4.6 14.6 - - - -
325D ASN* 4.3 13.2 - - - +
328D ARG* 4.2 12.6 - - + +
329D THR 5.4 0.9 - - - +
330D GLY 2.8 17.2 + - - +
331D GLN* 3.6 10.6 - - - +
332D MET* 2.9 26.7 + - - +
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Residues in contact with VAL 171 (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 MET* 1.3 73.4 - - - +
172D TYR* 1.3 66.8 + - - +
173D ILE* 3.7 21.3 - - + -
207D TRP* 3.6 31.6 - - + -
214D HIS* 3.8 19.5 - - + +
215D GLU 2.9 22.2 + - - +
216D VAL* 3.1 17.2 - - + +
217D THR 3.0 15.2 + - - -
332D MET* 3.3 33.4 - - + +
334D VAL* 4.6 5.2 - - + -
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Residues in contact with TYR 172 (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 MET* 3.7 26.6 - - + +
171D VAL* 1.3 82.4 - - - +
173D ILE* 1.3 62.1 + - - +
174D PHE* 4.5 15.8 - + + -
215D GLU 4.5 7.4 - - - -
217D THR* 3.3 34.8 - - + +
261D ASN* 5.3 7.4 + - - -
313D SER* 4.7 11.9 - - - -
316D VAL* 3.5 36.7 - - + +
317D PHE* 3.5 40.4 - + - -
332D MET 2.9 10.2 + - - +
333D SER* 3.5 7.1 - - - +
334D VAL 2.9 24.3 + - - +
1435D LEU* 6.4 1.3 - - + -
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Residues in contact with ILE 173 (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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171D VAL* 3.7 19.1 - - + -
172D TYR* 1.3 76.2 - - - +
174D PHE* 1.3 65.1 + - - +
175D ILE* 4.3 17.0 - - + -
200D LEU* 4.8 18.4 - - + -
203D LEU* 6.5 0.9 - - + -
204D PHE* 6.2 3.4 - - + -
207D TRP* 6.1 2.0 - - + -
216D VAL* 4.4 5.6 - - + -
217D THR 2.9 18.8 + - - +
218D VAL* 3.3 32.5 - - + -
219D VAL 3.1 22.2 + - - -
274D ILE* 6.0 0.2 - - + -
334D VAL* 3.1 30.3 - - + +
336D ILE* 5.1 4.0 - - + -
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Residues in contact with PHE 174 (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 TYR* 4.5 12.6 - + + -
173D ILE* 1.3 83.6 - - - +
175D ILE* 1.3 63.6 + - - +
176D GLN 4.1 0.4 - - - -
217D THR* 4.5 9.9 - - - -
219D VAL* 3.5 34.5 - - + -
221D PHE* 3.6 16.4 - + + -
309D ALA* 3.2 44.0 - - + -
310D ILE* 5.0 0.7 - - - -
312D LEU* 3.9 20.6 - - + -
313D SER* 4.2 15.5 - - - -
333D SER* 6.4 1.1 - - - -
334D VAL 2.9 9.5 + - - +
335D VAL* 4.2 21.3 - - + -
336D ILE* 2.9 30.9 + - - +
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Residues in contact with ILE 175 (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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173D ILE* 4.3 20.9 - - + -
174D PHE* 1.3 78.3 - - - +
176D GLN* 1.3 72.6 + - - +
177D MET* 4.4 9.5 - - + +
181D MET* 4.9 9.4 - - + -
192D PHE* 6.3 1.3 - - + -
195D ALA* 6.4 1.3 - - + -
196D VAL* 4.8 12.1 - - + -
200D LEU* 4.6 12.3 - - + -
218D VAL* 4.4 2.7 - - + -
219D VAL 2.9 9.4 + - - +
220D LEU* 3.7 30.4 - - + -
221D PHE* 3.1 29.2 + - - -
274D ILE* 4.3 18.4 - - + -
336D ILE* 3.8 20.6 - - + +
338D PRO* 5.9 0.2 - - + -
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Residues in contact with GLN 176 (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 ILE* 1.3 79.1 - - - +
177D MET* 1.3 91.0 + - - +
178D SER* 3.3 14.0 + - - -
181D MET* 4.3 1.9 - - - +
221D PHE* 3.5 33.8 - - + +
222D SER* 5.2 2.1 - - - -
298D ASN* 4.7 5.9 - - - +
299D SER 5.5 0.3 - - - +
300D THR* 3.4 29.2 - - + +
305D ASN* 4.6 7.1 - - - +
306D TYR* 6.0 5.4 - - + -
335D VAL* 5.6 1.6 - - + -
336D ILE 3.1 17.8 + - - +
337D THR* 3.6 8.7 + - - +
338D PRO* 3.3 38.8 - - + +
343D PHE* 5.8 5.4 - - + -
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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