Contacts of the helix formed by residues 162 - 175 (chain W) 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 GLY 162 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160W GLY* 3.6 3.0 - - - +
161W VAL* 1.3 81.4 - - - +
163W LYS* 1.3 63.6 + - - +
164W THR* 3.4 2.5 - - - -
165W VAL* 3.6 16.6 + - - +
166W PHE* 3.2 21.8 + - - +
335W LEU* 4.6 1.6 - - - +
345W TYR* 5.0 13.2 - - - -
418W PHE* 5.8 1.4 - - - -
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Residues in contact with LYS 163 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155W LEU* 4.1 12.3 - - + -
157W GLY* 3.5 24.4 + - - +
158W GLY* 3.5 26.1 + - - +
159W ALA* 5.7 1.1 - - - -
160W GLY 5.8 0.4 - - - +
161W VAL* 3.4 3.2 - - + +
162W GLY* 1.3 76.4 - - - +
164W THR* 1.3 69.1 + - - +
166W PHE* 3.2 6.6 + - - +
167W ILE* 3.0 38.9 - - + +
256W ASP* 4.2 21.0 + - - -
335W LEU* 4.0 23.1 - - + -
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Residues in contact with THR 164 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162W GLY 3.4 0.4 - - - -
163W LYS* 1.3 81.5 + - - +
165W VAL* 1.3 62.7 + - - +
167W ILE* 4.2 4.5 - - - +
168W GLN* 2.9 32.1 + - - +
197W LEU* 3.6 32.2 - - + +
200W GLU* 3.1 38.0 + - + +
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Residues in contact with VAL 165 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162W GLY* 3.6 16.1 + - - +
163W LYS 3.2 0.6 - - - -
164W THR* 1.3 76.1 - - - +
166W PHE* 1.3 61.3 + - - +
168W GLN* 3.4 8.7 + - - +
169W GLU* 2.9 27.3 + - - +
200W GLU* 4.1 13.5 - - - +
418W PHE* 3.6 24.7 - - + -
420W VAL* 4.0 10.2 - - + +
421W ALA* 3.9 26.0 - - + -
424W PHE* 5.8 4.7 - - + -
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Residues in contact with PHE 166 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138W ILE* 4.2 17.7 - - + +
141W VAL* 3.9 17.9 - - + -
147W TYR* 3.6 18.2 - - - -
155W LEU* 4.5 15.0 - - + -
162W GLY 3.2 12.6 + - - +
163W LYS* 3.2 13.1 + - - +
165W VAL* 1.3 79.2 - - - +
167W ILE* 1.3 67.5 + - + +
169W GLU* 3.2 14.2 + - - +
170W LEU* 3.2 30.1 + - + +
307W VAL* 6.0 0.4 - - + -
333W THR* 3.8 21.8 - - + -
335W LEU* 4.5 10.8 - - + -
346W PRO* 4.0 22.0 - - + -
348W VAL* 3.5 23.3 - - + -
418W PHE* 4.4 8.5 - + + -
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Residues in contact with ILE 167 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155W LEU* 3.5 31.6 - - + -
163W LYS* 3.0 34.0 + - + +
164W THR* 4.2 6.1 - - - +
166W PHE* 1.3 84.0 - - + +
168W GLN* 1.3 66.4 + - + +
169W GLU 3.3 0.7 + - - -
170W LEU* 3.3 11.3 + - - +
171W ILE* 3.3 24.7 + - + +
184W PHE* 4.0 28.5 - - + -
197W LEU* 6.0 2.7 - - + -
201W MET* 5.7 0.9 - - + -
254W PHE* 3.8 39.2 - - + -
307W VAL* 5.3 0.9 - - + -
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Residues in contact with GLN 168 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164W THR* 2.9 27.6 + - + +
165W VAL* 3.8 7.1 - - - +
166W PHE 3.3 0.4 - - - -
167W ILE* 1.3 82.9 - - + +
169W GLU* 1.3 60.4 + - - +
171W ILE* 3.8 6.4 + - - +
172W ASN* 3.3 16.5 + - - +
197W LEU* 5.4 1.8 - - + -
200W GLU* 3.3 27.9 + - - +
201W MET* 3.3 57.5 - - + +
204W THR* 3.3 15.9 + - - +
206W VAL* 3.8 11.9 - - + +
420W VAL* 3.5 23.4 - - + +
424W PHE* 5.7 0.9 - - - -
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Residues in contact with GLU 169 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138W ILE* 4.5 7.4 - - + -
165W VAL 2.9 17.6 + - - +
166W PHE* 3.5 6.5 - - - +
167W ILE 3.1 0.4 - - - -
168W GLN* 1.3 76.9 - - - +
170W LEU* 1.3 60.7 + - - +
172W ASN* 3.4 2.9 + - - +
173W ASN* 3.0 59.9 + - - +
416W GLN* 4.9 3.5 + - - -
417W PRO 5.0 0.2 - - - +
418W PHE* 3.2 55.9 - - + +
419W ALA* 3.2 16.6 + - - +
420W VAL* 3.4 13.1 + - + +
430W LYS 5.3 2.1 - - - +
431W LEU* 5.8 1.0 - - - +
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Residues in contact with LEU 170 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136W THR* 3.9 27.1 - - + +
138W ILE* 3.8 25.1 - - + -
147W TYR* 4.1 20.0 - - + +
166W PHE* 3.2 34.0 + - + +
167W ILE* 3.3 6.3 + - + +
169W GLU* 1.3 78.1 - - - +
171W ILE* 1.3 56.4 + - - +
173W ASN* 4.6 2.9 - - - -
174W ILE* 2.9 40.8 + - + +
252W LEU* 3.7 15.3 - - + -
254W PHE* 4.1 19.1 - - + -
307W VAL* 4.1 9.9 - - + -
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Residues in contact with ILE 171 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167W ILE* 3.3 22.6 + - + +
168W GLN* 3.9 9.0 - - - +
169W GLU 3.3 0.4 - - - -
170W LEU* 1.3 77.1 - - - +
172W ASN* 1.3 63.5 + - - +
174W ILE* 3.9 0.7 - - - +
175W ALA* 3.0 28.0 + - + +
182W SER* 3.3 25.5 + - - +
184W PHE* 5.6 0.9 - - + -
201W MET* 4.1 17.5 - - + -
206W VAL* 4.9 5.8 - - + -
214W LYS* 3.1 38.8 - - + +
215W VAL* 3.9 24.9 - - + -
252W LEU* 4.0 0.4 - - - -
254W PHE* 3.6 17.5 - - + -
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Residues in contact with ASN 172 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168W GLN 3.3 16.2 + - - +
169W GLU* 3.8 4.9 + - - +
170W LEU 3.4 0.2 - - - -
171W ILE* 1.3 79.4 - - - +
173W ASN* 1.3 75.4 + - - +
175W ALA* 3.4 4.4 + - - +
176W LYS* 3.3 31.6 + - - +
206W VAL* 4.7 2.9 - - + +
214W LYS* 3.5 26.7 + - - +
419W ALA* 3.2 32.5 - - - +
420W VAL* 3.8 17.8 - - + +
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Residues in contact with ASN 173 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135W GLU 6.0 0.4 - - - -
136W THR 3.0 29.1 + - - +
137W GLY* 4.1 10.7 + - - -
138W ILE* 4.2 3.8 - - - +
169W GLU* 3.0 48.6 + - - +
170W LEU* 3.9 3.4 - - - +
172W ASN* 1.3 82.9 + - - +
174W ILE* 1.3 58.4 + - + +
175W ALA 3.1 4.5 - - - -
176W LYS* 3.1 3.4 + - - +
177W ALA* 2.8 35.3 + - + +
178W HIS* 5.5 0.2 - - - -
416W GLN* 5.1 0.8 - - - +
419W ALA* 5.1 1.0 - - - +
431W LEU* 3.5 30.2 - - + +
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Residues in contact with ILE 174 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134W LEU* 3.8 25.1 - - + -
135W GLU 4.7 6.1 - - - +
136W THR* 5.1 7.4 - - + -
147W TYR* 6.3 0.7 - - + -
170W LEU* 2.9 31.1 + - + +
171W ILE 4.3 1.1 - - - +
173W ASN* 1.3 73.7 - - + +
175W ALA* 1.3 56.3 + - - +
178W HIS* 3.7 25.8 - - + +
179W GLY 3.1 9.2 + - - -
180W GLY 2.9 20.8 + - - +
181W PHE 5.5 0.4 - - - +
182W SER* 5.4 1.3 - - - +
250W ASP* 3.5 26.2 - - + +
252W LEU* 3.5 38.8 - - + -
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Residues in contact with ALA 175 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171W ILE 3.0 19.1 + - - +
172W ASN 3.8 4.5 - - - +
173W ASN 3.1 0.2 - - - -
174W ILE* 1.3 76.9 - - - +
176W LYS* 1.3 64.1 + - - +
179W GLY* 3.6 15.0 - - - -
180W GLY 3.2 19.3 - - - +
181W PHE* 5.4 2.9 - - + -
214W LYS* 4.0 30.7 - - + +
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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