Contacts of the helix formed by residues 162 - 174 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375T ARG* 3.0 18.8 - - - +
161X VAL* 1.3 81.7 - - - +
163X LYS* 1.3 60.8 + - - +
164X THR 3.7 0.9 - - - -
165X VAL* 4.1 12.5 - - - +
166X PHE* 3.4 18.1 + - - +
335X LEU* 3.3 15.2 - - - +
345X TYR* 6.3 1.1 - - - -
615X PO4 2.9 6.1 + - - -
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Residues in contact with LYS 163 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346T SER* 4.9 1.6 - - - -
155X LEU* 3.9 6.0 - - + +
156X PHE 4.1 17.0 - - - +
157X GLY 3.9 15.0 - - - +
158X GLY 3.2 17.8 + - - +
161X VAL* 4.2 0.7 - - + -
162X GLY* 1.3 71.2 - - - +
164X THR* 1.3 67.1 + - - +
166X PHE* 3.1 4.7 + - - +
167X ILE* 3.0 35.2 + - + +
189X GLU* 4.1 10.5 + - - -
256X ASP* 4.9 1.3 - - - +
257X ASN* 3.6 27.4 - - - +
309X ALA* 5.1 3.1 - - + -
310X VAL 4.3 7.0 - - - +
311X TYR* 3.4 20.2 - - - -
335X LEU* 4.0 9.4 - - + -
615X PO4 2.6 48.9 + - - +
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Residues in contact with THR 164 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375T ARG* 4.2 4.7 - - - +
163X LYS* 1.3 77.1 - - - +
165X VAL* 1.3 57.5 + - - +
167X ILE* 3.3 10.1 + - + +
168X GLN* 3.0 59.6 + - + +
189X GLU* 4.2 7.1 + - - -
190X ARG* 3.7 2.1 + - - -
193X GLU* 3.0 41.0 + - + +
256X ASP* 4.3 12.7 + - - +
615X PO4 3.3 14.4 + - - -
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Residues in contact with VAL 165 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375T ARG* 3.9 26.2 - - - +
162X GLY* 4.2 12.6 - - - +
163X LYS 3.2 0.4 - - - -
164X THR* 1.3 79.3 - - - +
166X PHE* 1.3 62.0 + - - +
167X ILE 3.4 0.5 + - - -
168X GLN* 3.7 5.3 + - - +
169X GLU* 3.4 20.3 + - - +
193X GLU* 5.9 0.4 - - - +
418X PHE* 4.8 14.4 - - + +
420X VAL* 4.9 8.7 - - + +
421X ALA* 3.9 32.5 - - + +
424X PHE* 4.1 24.0 - - + -
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Residues in contact with PHE 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138X ILE* 4.0 12.2 - - + +
140X VAL* 6.0 0.2 - - + -
141X VAL* 3.5 28.3 - - + -
147X TYR* 3.6 17.5 - + - -
155X LEU* 4.0 18.6 - - + -
162X GLY 3.4 16.9 + - - +
163X LYS 3.1 5.5 + - - +
165X VAL* 1.3 79.5 - - - +
167X ILE* 1.3 59.4 + - - +
169X GLU* 3.8 6.3 + - - +
170X LEU* 3.5 34.0 + - + +
333X THR* 4.4 7.9 - - - -
335X LEU* 4.8 7.0 - - + -
346X PRO* 4.0 22.7 - - + -
348X VAL* 3.7 25.8 - - + -
418X PHE* 4.2 19.3 - + + -
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Residues in contact with ILE 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155X LEU* 3.8 18.4 - - + -
163X LYS* 3.0 23.5 + - + +
164X THR* 3.6 7.2 - - + +
165X VAL 3.2 0.2 - - - -
166X PHE* 1.3 74.6 - - - +
168X GLN* 1.3 60.8 + - + +
169X GLU 3.0 4.3 - - - -
170X LEU* 2.9 29.4 + - + +
171X ILE* 3.2 18.5 + - + +
184X PHE* 4.7 11.2 - - + -
254X PHE* 4.1 24.0 - - + -
256X ASP* 3.4 26.5 - - + +
307X VAL* 5.4 1.8 - - + +
309X ALA* 3.4 29.4 - - + -
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Residues in contact with GLN 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X THR* 3.0 42.2 + - + +
165X VAL* 4.3 1.5 - - - +
167X ILE* 1.3 75.9 - - + +
169X GLU* 1.3 60.3 + - - +
171X ILE* 3.5 14.0 + - + +
172X ASN* 3.0 31.0 + - - +
193X GLU* 4.6 12.9 - - - +
196X ASP* 5.4 3.4 + - - +
197X LEU* 4.2 34.8 - - + +
200X GLU* 5.7 5.9 - - - +
420X VAL* 3.7 33.9 - - + +
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Residues in contact with GLU 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138X ILE* 4.4 5.4 - - + -
165X VAL 3.4 14.3 + - - +
166X PHE* 3.8 7.2 - - - +
167X ILE 3.0 0.6 - - - -
168X GLN* 1.3 76.3 - - - +
170X LEU* 1.3 60.4 + - - +
171X ILE 3.1 1.3 - - - -
172X ASN* 3.0 4.3 + - - +
173X ASN* 2.9 64.7 + - - +
418X PHE* 3.3 37.4 - - + +
419X ALA* 3.3 32.4 + - - +
420X VAL* 3.4 17.6 + - - +
431X LEU* 6.0 1.2 - - - +
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Residues in contact with LEU 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X THR* 4.7 5.2 - - + -
138X ILE* 4.9 8.0 - - + +
147X TYR* 3.9 29.6 - - + +
153X ILE* 5.7 0.4 - - + -
155X LEU* 5.0 3.6 - - + -
166X PHE* 3.5 37.2 + - + +
167X ILE* 2.9 14.7 + - - +
169X GLU* 1.3 78.4 - - - +
171X ILE* 1.3 55.9 + - - +
173X ASN* 4.6 0.4 - - - -
174X ILE* 3.0 52.8 + - + +
175X ALA 3.5 1.0 + - - -
254X PHE* 3.9 14.2 - - + -
307X VAL* 3.7 32.3 - - + -
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Residues in contact with ILE 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X ILE* 3.3 19.1 - - + +
168X GLN* 3.7 16.8 - - + +
169X GLU 3.1 0.8 - - - -
170X LEU* 1.3 80.3 - - - +
172X ASN* 1.3 58.9 + - - +
173X ASN 3.3 0.4 - - - -
175X ALA* 3.2 30.1 - - + +
176X LYS* 3.3 15.9 + - - +
184X PHE* 4.2 28.0 - - + -
197X LEU* 4.1 19.7 - - + -
201X MET* 4.1 30.1 - - + -
254X PHE* 4.0 18.6 - - + -
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Residues in contact with ASN 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X GLN* 3.0 18.6 + - - +
169X GLU* 3.0 12.0 + - - +
171X ILE* 1.3 82.4 - - - +
173X ASN* 1.3 67.7 + - - +
176X LYS* 3.6 47.5 + - - +
197X LEU* 5.8 2.1 - - - +
200X GLU* 3.8 24.0 + - - +
201X MET* 4.3 9.0 - - - +
419X ALA* 5.7 6.5 - - + +
420X VAL* 4.5 12.3 - - + +
431X LEU* 5.7 0.3 - - - +
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Residues in contact with ASN 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X GLU 5.2 1.4 - - - +
136X THR 3.3 26.6 + - - +
137X GLY* 4.3 7.3 + - - -
138X ILE* 4.6 4.6 - - - +
169X GLU* 2.9 44.4 + - - +
170X LEU* 4.6 0.2 - - - -
172X ASN* 1.3 89.2 - - - +
174X ILE* 1.3 68.5 + - + +
176X LYS* 5.0 2.0 - - - -
177X ALA* 5.4 5.1 + - - +
419X ALA* 5.9 0.2 - - - +
431X LEU* 3.7 32.6 - - + +
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Residues in contact with ILE 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X LEU* 4.6 26.2 - - + -
135X GLU 3.9 15.9 - - - +
136X THR* 3.7 21.1 - - + +
149X ARG* 6.2 0.2 - - - +
170X LEU* 3.0 38.2 + - + +
173X ASN* 1.3 97.6 - - + +
175X ALA* 1.3 65.8 + - - +
176X LYS 3.1 3.1 + - - -
177X ALA 3.5 6.7 + - - +
178X HIS* 3.5 23.0 + - - +
252X LEU* 3.7 20.6 - - + -
254X PHE* 5.5 2.0 - - + -
305X THR* 6.2 0.4 - - + -
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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
------------------------------------------------------------
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