Contacts of the helix formed by residues 165 - 178 (chain D) in PDB entry 3FKS
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 VAL 165 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C ARG* 4.1 18.6 - - + +
162D GLY* 4.4 12.1 - - - +
163D LYS 3.1 0.6 - - - -
164D THR* 1.3 75.8 - - - +
166D PHE* 1.3 63.5 + - - +
168D GLN* 3.7 25.1 - - - +
169D GLU* 3.8 7.3 + - - +
193D GLU* 4.8 8.5 - - - +
420D VAL* 4.7 6.3 - - + +
421D ALA* 4.3 18.4 - - + -
424D PHE* 4.1 35.9 - - + -
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Residues in contact with PHE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ILE* 5.0 13.5 - - + -
141D VAL* 4.4 11.4 - - + -
147D TYR* 3.7 21.5 - - - -
155D LEU* 3.4 23.6 - - + -
162D GLY 3.4 15.5 + - - +
163D LYS* 2.9 13.7 + - - +
165D VAL* 1.3 76.5 - - - +
167D ILE* 1.3 61.1 + - - +
168D GLN 3.0 3.8 - - - -
169D GLU* 3.0 21.2 + - + +
170D LEU* 3.5 23.1 + - + +
333D THR* 4.0 25.1 - - + -
335D LEU* 4.7 7.0 - - + -
346D PRO* 3.7 37.5 - - + -
348D VAL* 4.6 1.8 - - + -
418D PHE* 5.2 5.2 - + - -
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Residues in contact with ILE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 3.9 28.3 - - + -
163D LYS 3.7 8.7 - - - +
164D THR* 3.5 17.9 - - + +
166D PHE* 1.3 74.5 - - - +
168D GLN* 1.3 63.9 + - + +
169D GLU 3.3 0.2 - - - -
170D LEU* 3.5 19.7 + - + +
171D ILE* 3.1 32.0 + - + +
184D PHE* 4.1 19.3 - - + -
197D LEU* 6.2 0.7 - - + -
254D PHE* 4.7 10.5 - - + -
255D ILE 5.6 0.7 - - - +
256D ASP* 3.2 41.3 - - + +
307D VAL* 4.5 8.3 - - + +
309D ALA* 4.5 6.5 - - + -
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Residues in contact with GLN 168 (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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164D THR* 3.2 27.7 + - + +
165D VAL* 3.7 17.0 - - - +
166D PHE 3.0 0.8 - - - -
167D ILE* 1.3 80.1 - - + +
169D GLU* 1.3 61.9 + - - +
171D ILE* 3.7 8.6 + - - +
172D ASN* 3.6 15.4 + - - +
193D GLU* 4.6 7.3 + - - +
196D ASP* 4.4 10.3 + - - +
197D LEU* 3.9 40.2 - - + +
200D GLU* 4.9 9.1 - - - +
420D VAL* 3.7 31.8 - - + +
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Residues in contact with GLU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ILE* 4.8 7.9 - - + -
165D VAL 3.8 7.0 + - - +
166D PHE* 3.0 13.4 + - + +
168D GLN* 1.3 77.6 - - - +
170D LEU* 1.3 64.5 + - + +
172D ASN* 3.4 4.0 + - - +
173D ASN* 3.1 60.1 + - - +
416D GLN* 5.5 0.9 + - - -
417D PRO 5.2 0.2 - - - +
418D PHE* 3.2 55.9 - - + +
419D ALA* 4.5 2.9 + - - +
420D VAL* 3.1 29.8 + - + +
430D LYS 5.7 0.5 - - - +
431D LEU* 5.0 2.4 - - - +
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Residues in contact with LEU 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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136D THR* 4.4 4.3 - - + -
138D ILE* 4.4 23.1 - - + -
147D TYR* 4.1 27.1 - - + +
155D LEU* 5.4 0.7 - - + -
166D PHE* 3.5 20.8 + - + +
167D ILE* 3.6 21.3 - - + +
169D GLU* 1.3 78.4 - - + +
171D ILE* 1.3 56.4 + - - +
173D ASN* 4.9 1.8 - - - +
174D ILE* 2.8 61.3 + - + +
254D PHE* 4.4 10.7 - - + -
307D VAL* 3.7 29.8 - - + -
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Residues in contact with ILE 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 3.1 21.7 + - + +
168D GLN* 4.0 6.1 - - - +
169D GLU 3.3 0.4 - - - -
170D LEU* 1.3 77.9 - - - +
172D ASN* 1.3 63.2 + - - +
175D ALA* 2.8 42.2 + - + +
176D LYS* 3.7 3.8 + - - +
184D PHE* 4.3 22.9 - - + -
197D LEU* 3.8 29.8 - - + -
201D MET* 4.7 20.6 - - + -
206D VAL* 5.9 7.6 - - + -
254D PHE* 4.1 21.5 - - + -
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Residues in contact with ASN 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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168D GLN 3.6 9.6 + - - +
169D GLU* 3.4 7.5 + - - +
170D LEU 3.3 0.4 - - - -
171D ILE* 1.3 80.9 - - - +
173D ASN* 1.3 77.4 + - - +
176D LYS* 3.0 57.2 + - - +
204D THR* 4.3 10.1 - - + +
419D ALA* 5.3 9.7 - - - +
420D VAL* 4.5 16.2 - - + +
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Residues in contact with ASN 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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136D THR 4.4 13.3 + - - +
137D GLY* 5.0 1.0 - - - -
138D ILE* 4.9 9.7 - - - +
169D GLU* 3.1 47.8 + - - +
170D LEU* 4.1 1.5 - - - +
172D ASN* 1.3 95.1 + - - +
174D ILE* 1.3 68.4 + - + +
176D LYS* 4.9 0.2 - - - +
177D ALA* 3.5 19.9 + - - +
416D GLN* 5.4 2.2 - - - +
431D LEU* 3.3 34.5 - - + +
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Residues in contact with ILE 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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134D LEU* 4.0 35.2 - - + -
135D GLU 4.8 4.7 - - - +
136D THR* 3.8 28.9 - - + +
147D TYR* 5.0 2.2 - - + -
170D LEU* 2.8 47.2 + - + +
173D ASN* 1.3 77.7 - - + +
175D ALA* 1.3 54.7 + - - +
176D LYS 3.2 2.5 - - - -
177D ALA* 3.0 6.7 + - + +
178D HIS* 2.6 41.2 + - + +
252D LEU* 4.5 15.7 - - + -
254D PHE* 5.8 2.9 - - + -
307D VAL* 5.7 4.5 - - + -
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Residues in contact with ALA 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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170D LEU 3.6 1.2 + - - -
171D ILE* 2.8 39.6 + - + +
174D ILE* 1.3 79.5 - - - +
176D LYS* 1.3 57.7 + - + +
178D HIS* 3.5 12.0 + - - +
182D SER* 4.9 12.6 + - - +
206D VAL* 5.9 6.5 - - + -
214D LYS* 2.8 28.9 + - + -
252D LEU* 4.3 12.3 - - + +
254D PHE* 4.9 6.7 - - + -
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Residues in contact with LYS 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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171D ILE 3.7 5.1 + - - +
172D ASN* 3.0 44.4 + - - +
173D ASN 4.9 0.2 - - - +
174D ILE 3.2 0.4 - - - -
175D ALA* 1.3 78.5 - - + +
177D ALA* 1.3 61.4 + - - +
178D HIS 3.9 0.2 - - - +
204D THR* 4.0 27.3 + - + +
205D GLY 6.2 0.2 - - - -
206D VAL* 4.1 20.2 - - + -
214D LYS* 3.2 18.3 + - + +
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Residues in contact with ALA 177 (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 ASN 3.5 17.8 + - - +
174D ILE* 3.0 7.6 + - + +
176D LYS* 1.3 76.3 - - - +
178D HIS* 1.3 64.4 + - - +
179D GLY* 3.5 2.6 + - - -
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Residues in contact with HIS 178 (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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134D LEU* 5.3 5.2 - - + -
149D ARG* 5.0 19.0 + - + +
174D ILE* 2.6 27.0 + - + +
175D ALA 3.6 7.9 - - - +
176D LYS 3.3 0.8 - - - +
177D ALA* 1.3 72.7 - - - +
179D GLY* 1.3 62.5 + - - +
180D GLY* 3.3 14.3 + - - -
181D PHE 4.5 2.6 + - - -
182D SER* 6.2 0.2 - - - -
214D LYS* 2.7 30.8 + - - -
250D ASP* 3.6 43.6 - - + +
251D VAL 4.0 15.2 + - - -
252D LEU* 3.8 27.6 - - + +
305D THR* 4.5 9.5 + - - -
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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