Contacts of the helix formed by residues 162 - 178 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E GLY 3.7 3.2 - - - +
161E VAL* 1.3 80.8 - - - +
163E LYS* 1.3 59.6 + - - +
164E THR 3.5 1.8 - - - -
165E VAL* 3.5 16.2 + - - +
166E PHE* 2.9 27.8 + - - +
335E LEU* 4.8 0.6 - - - +
345E TYR* 4.7 15.1 + - - -
346E PRO* 5.9 1.7 - - - +
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Residues in contact with LYS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E LEU* 3.8 20.6 - - + -
157E GLY 3.8 19.8 + - - +
158E GLY* 3.8 21.9 + - - +
159E ALA* 5.5 3.2 - - - +
161E VAL* 3.5 2.0 - - - +
162E GLY* 1.3 72.4 - - - +
164E THR* 1.3 71.7 + - - +
165E VAL 3.0 2.0 - - - -
166E PHE* 3.0 6.0 + - - -
167E ILE* 3.0 47.7 + - + +
184E PHE* 6.5 0.7 - - - -
256E ASP* 3.1 33.0 + - - -
309E ALA* 4.9 8.4 - - + +
335E LEU* 4.0 13.0 - - + -
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Residues in contact with THR 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E ALA* 6.2 0.3 - - - +
162E GLY* 3.5 0.4 - - - -
163E LYS* 1.3 83.4 - - - +
165E VAL* 1.3 62.4 + - - +
167E ILE* 4.1 4.4 + - - +
168E GLN* 3.0 28.9 + - - +
197E LEU* 3.6 29.2 - - + +
200E GLU* 3.2 37.3 + - - +
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Residues in contact with VAL 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E GLY* 3.5 16.3 + - - +
163E LYS 3.0 0.8 - - - -
164E THR* 1.3 77.1 - - - +
166E PHE* 1.3 67.1 + - - +
167E ILE 3.2 0.2 - - - -
168E GLN* 3.0 10.0 + - - +
169E GLU* 2.9 21.1 + - - +
200E GLU* 4.4 11.2 - - - +
345E TYR* 6.3 5.2 - - + -
418E PHE* 4.2 15.0 - - + -
420E VAL* 3.9 20.1 - - + +
421E ALA* 4.0 21.5 - - + -
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Residues in contact with PHE 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E ILE* 4.5 9.5 - - + +
141E VAL* 4.2 15.5 - - + -
147E TYR* 3.7 13.2 - - - -
155E LEU* 4.2 12.3 - - + -
162E GLY 2.9 19.0 + - - +
163E LYS* 3.3 9.2 - - - +
165E VAL* 1.3 77.5 - - - +
167E ILE* 1.3 74.5 + - + +
169E GLU* 3.3 11.3 + - - +
170E LEU* 3.3 38.9 + - + +
307E VAL* 5.5 1.1 - - + -
333E THR* 3.6 24.0 - - + -
335E LEU* 4.2 11.7 - - + -
346E PRO* 4.0 21.3 - - + -
348E VAL* 3.9 22.4 - - + -
418E PHE* 4.6 13.0 - + + -
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Residues in contact with ILE 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E LEU* 3.7 18.6 - - + -
163E LYS* 3.0 53.5 + - + +
164E THR* 4.4 5.6 - - - +
166E PHE* 1.3 85.0 - - + +
168E GLN* 1.3 65.1 + - - +
170E LEU* 3.1 10.6 + - - +
171E ILE* 3.0 37.8 + - + +
184E PHE* 4.0 26.5 - - + -
197E LEU* 6.4 0.4 - - + -
201E MET* 5.1 4.0 - - + -
254E PHE* 4.0 28.3 - - + -
307E VAL* 5.6 0.2 - - + -
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Residues in contact with GLN 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E THR* 3.0 21.8 + - - +
165E VAL* 3.0 11.9 + - - +
167E ILE* 1.3 79.1 - - + +
169E GLU* 1.3 61.5 + - - +
171E ILE* 3.4 10.3 + - + +
172E ASN* 3.0 17.7 + - - +
197E LEU* 4.6 2.6 + - + +
200E GLU* 3.2 33.2 + - - +
201E MET* 3.2 30.7 - - + +
204E THR* 3.2 29.3 + - - +
206E VAL* 3.6 21.6 - - + +
420E VAL* 3.5 18.6 - - + +
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Residues in contact with GLU 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E ILE* 4.6 4.7 - - + -
165E VAL 2.9 12.4 + - - +
166E PHE 3.5 9.0 - - - +
167E ILE 3.2 0.2 - - - -
168E GLN* 1.3 74.3 - - - +
170E LEU* 1.3 57.3 + - + +
172E ASN* 3.1 2.5 + - - +
173E ASN* 2.8 75.3 + - - +
416E GLN* 4.5 4.0 + - - -
418E PHE* 3.2 60.0 - - + +
419E ALA* 3.3 15.0 + - - +
420E VAL* 3.2 18.2 + - + +
430E LYS 5.4 1.4 - - - +
431E LEU* 5.6 1.6 - - - +
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Residues in contact with LEU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E THR* 4.0 25.4 - - + +
138E ILE* 3.6 28.9 - - + -
147E TYR* 4.2 19.7 - - + +
166E PHE* 3.5 39.5 - - + +
167E ILE* 3.1 7.2 + - - +
169E GLU* 1.3 76.4 - - - +
171E ILE* 1.3 62.7 + - - +
173E ASN* 4.6 2.7 - - - +
174E ILE* 3.2 32.8 + - + +
252E LEU* 3.6 14.0 - - + +
254E PHE* 4.3 20.0 - - + -
307E VAL* 4.6 3.4 - - + -
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Residues in contact with ILE 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E ILE* 3.0 30.2 + - + +
168E GLN* 3.5 14.8 - - + +
169E GLU 3.2 0.2 - - - -
170E LEU* 1.3 77.8 - - - +
172E ASN* 1.3 64.0 + - - +
174E ILE* 4.4 0.3 - - - +
175E ALA* 3.5 19.6 + - - +
180E GLY 4.6 0.2 - - - +
182E SER* 3.7 18.1 + - - +
184E PHE* 5.4 0.9 - - + -
201E MET* 4.2 20.0 - - + -
206E VAL* 4.5 8.1 - - + -
214E LYS* 3.2 34.9 - - + +
215E VAL* 3.9 21.3 - - + -
252E LEU* 4.6 0.2 - - - -
254E PHE* 4.0 18.6 - - + -
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Residues in contact with ASN 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E GLN 3.0 13.7 + - - +
169E GLU* 3.4 6.9 + - - +
171E ILE* 1.3 76.1 - - - +
173E ASN* 1.3 77.2 + - - +
175E ALA* 3.2 13.3 + - - +
176E LYS* 3.3 25.4 + - - +
206E VAL* 4.7 5.1 - - + +
214E LYS* 3.3 27.8 + - - +
419E ALA* 3.9 24.9 - - - +
420E VAL* 3.8 17.2 - - + +
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Residues in contact with ASN 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLU 5.7 0.7 - - - -
136E THR* 2.9 31.9 + - - +
137E GLY* 3.8 13.9 + - - -
138E ILE* 4.2 1.4 - - - +
169E GLU* 2.8 57.7 + - - +
170E LEU* 4.4 2.7 - - - +
172E ASN* 1.3 80.4 + - - +
174E ILE* 1.3 53.4 + - + +
176E LYS* 3.0 4.9 + - - +
177E ALA* 2.7 38.8 + - + +
419E ALA* 5.4 0.5 - - - +
431E LEU* 3.7 26.0 - - + +
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Residues in contact with ILE 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LEU* 3.8 21.3 - - + -
135E GLU 3.2 27.6 - - - +
136E THR* 4.9 5.4 - - + -
170E LEU* 3.2 21.3 + - + +
171E ILE 4.4 1.3 - - - +
173E ASN* 1.3 72.7 - - + +
175E ALA* 1.3 58.0 + - - +
176E LYS 2.9 4.7 - - - -
177E ALA 4.5 0.2 - - - +
178E HIS* 2.9 43.9 + - + -
179E GLY 3.0 5.9 + - - -
180E GLY* 3.7 15.0 - - - +
182E SER* 5.1 1.1 - - - +
250E ASP* 3.6 23.8 - - + +
252E LEU* 3.6 22.9 - - + -
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Residues in contact with ALA 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E ILE 3.5 15.0 + - - +
172E ASN 3.2 5.6 + - - +
174E ILE* 1.3 77.0 - - - +
176E LYS* 1.3 63.5 + - + +
179E GLY* 3.6 13.4 - - - -
180E GLY 3.3 25.5 + - - +
181E PHE* 5.2 2.7 - - + -
214E LYS* 3.8 29.4 - - + -
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Residues in contact with LYS 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E ASN* 3.5 21.0 + - - +
173E ASN* 3.0 9.4 + - - +
174E ILE 2.9 0.6 - - - -
175E ALA* 1.3 84.8 + - - +
177E ALA* 1.3 62.2 + - - +
178E HIS 3.4 1.7 + - - -
179E GLY 4.3 2.0 + - - -
214E LYS* 4.0 27.7 - - - +
431E LEU* 4.8 7.9 - - + -
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Residues in contact with ALA 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLU* 4.5 16.7 - - + +
136E THR 6.4 0.2 - - - -
137E GLY 6.1 1.3 - - - +
173E ASN 2.7 18.3 + - - +
176E LYS* 1.3 73.4 - - - +
178E HIS* 1.3 82.4 + - + +
431E LEU* 4.4 21.5 - - + -
433E ARG* 4.9 10.0 + - - +
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Residues in contact with HIS 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ILE 5.5 1.6 - - - -
134E LEU* 3.9 13.4 - - + +
135E GLU* 3.2 46.4 + - + +
149E ARG* 6.4 0.4 - - - -
174E ILE* 2.9 40.1 + - + +
176E LYS 3.4 0.2 - - - -
177E ALA* 1.3 94.8 + - + +
179E GLY* 1.3 66.5 + - - +
180E GLY* 4.4 0.6 - - - +
249E GLN* 5.3 2.1 - - - +
250E ASP* 3.5 28.9 + - + +
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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
------------------------------------------------------------
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