Contacts of the helix formed by residues 162 - 177 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N GLY* 3.8 2.0 - - - +
161N VAL* 1.3 81.0 - - - +
163N LYS* 1.3 60.4 + - - +
164N THR 3.6 1.6 - - - -
165N VAL* 4.1 13.8 - - - +
166N PHE* 3.1 29.7 + - - +
335N LEU* 4.0 4.0 - - - +
345N TYR* 5.8 4.0 - - - -
346N PRO* 6.1 0.2 - - - +
418N PHE* 5.6 1.9 - - - -
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Residues in contact with LYS 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375J ARG* 5.2 1.8 - - - +
155N LEU* 3.7 32.1 - - + -
157N GLY 3.7 19.3 + - - +
158N GLY 3.9 20.4 + - - +
161N VAL* 3.7 2.3 - - + +
162N GLY* 1.3 74.4 - - - +
164N THR* 1.3 74.7 + - - +
165N VAL 3.1 1.6 - - - -
166N PHE* 3.0 1.8 + - - +
167N ILE* 2.9 37.9 + - + +
256N ASP* 3.4 25.7 + - - -
309N ALA* 4.9 7.1 - - + +
335N LEU* 3.8 15.3 - - + -
610N PO4 3.3 24.9 + - - -
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Residues in contact with THR 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162N GLY* 3.6 0.4 - - - -
163N LYS* 1.3 83.1 - - - +
165N VAL* 1.3 59.3 + - - +
167N ILE* 3.8 8.9 + - - +
168N GLN* 3.1 32.6 + - - +
197N LEU* 3.7 28.0 - - + +
200N GLU* 3.2 39.0 + - - +
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Residues in contact with VAL 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162N GLY* 3.9 14.5 + - - +
163N LYS 3.1 0.6 - - - -
164N THR* 1.3 76.1 - - - +
166N PHE* 1.3 66.9 + - - +
167N ILE 3.1 1.8 - - - -
168N GLN* 2.9 14.5 + - - +
169N GLU* 2.8 22.0 + - - +
200N GLU* 4.5 9.6 - - - +
418N PHE* 3.8 25.1 - - + -
420N VAL* 3.9 17.0 - - + -
421N ALA* 4.3 14.8 - - + +
424N PHE* 6.1 5.8 - - + -
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Residues in contact with PHE 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138N ILE* 3.5 24.5 - - + +
141N VAL* 3.8 16.4 - - + -
147N TYR* 3.6 13.0 - - - -
155N LEU* 4.9 11.7 - - + -
162N GLY 3.1 21.3 + - - +
163N LYS* 3.0 8.4 + - + +
165N VAL* 1.3 75.7 - - - +
167N ILE* 1.3 65.7 + - + +
169N GLU* 3.5 7.4 + - - +
170N LEU* 3.1 45.9 + - + +
307N VAL* 5.9 0.4 - - + -
333N THR* 4.0 11.7 - - + -
335N LEU* 4.3 10.5 - - + -
346N PRO* 4.0 21.3 - - + -
348N VAL* 3.6 24.9 - - + -
418N PHE* 4.3 10.3 - + + -
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Residues in contact with ILE 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155N LEU* 4.6 11.7 - - + -
163N LYS* 2.9 41.0 + - + +
164N THR* 3.9 7.9 - - - +
166N PHE* 1.3 77.2 - - + +
168N GLN* 1.3 66.6 + - - +
170N LEU* 3.1 9.4 + - - +
171N ILE* 2.9 35.3 + - + +
184N PHE* 3.6 31.6 - - + -
197N LEU* 6.1 2.5 - - + -
201N MET* 5.2 4.3 - - + -
254N PHE* 3.7 41.3 - - + -
256N ASP* 5.7 2.7 - - + +
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Residues in contact with GLN 168 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N THR* 3.1 24.2 + - + +
165N VAL* 2.9 20.0 + - - +
167N ILE* 1.3 79.4 - - + +
169N GLU* 1.3 56.8 + - - +
171N ILE* 3.4 12.0 + - - +
172N ASN* 3.0 25.8 + - - +
197N LEU* 5.7 0.2 - - + -
200N GLU* 3.7 28.5 - - - +
201N MET* 3.6 33.7 - - + +
204N THR* 3.4 31.7 + - + +
206N VAL* 3.6 13.7 - - + +
420N VAL* 3.7 12.3 - - + +
424N PHE* 6.1 1.2 - - - -
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Residues in contact with GLU 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137N GLY 5.8 0.2 - - - +
138N ILE* 5.0 5.8 - - + -
165N VAL 2.8 14.1 + - - +
166N PHE 3.7 5.8 - - - +
168N GLN* 1.3 75.5 - - - +
170N LEU* 1.3 60.7 + - - +
172N ASN* 2.9 7.2 + - - +
173N ASN* 2.8 63.4 + - - +
416N GLN* 5.3 2.3 + - - -
417N PRO 5.1 0.7 - - - +
418N PHE* 3.3 36.4 - - + +
419N ALA* 3.1 31.4 + - - +
420N VAL* 3.2 19.6 + - + +
430N LYS 5.4 2.6 - - - +
431N LEU* 5.7 1.2 - - - +
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Residues in contact with LEU 170 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N THR* 3.7 40.4 - - + +
138N ILE* 4.0 12.1 - - + -
147N TYR* 4.1 17.5 - - + +
166N PHE* 3.1 40.2 + - + +
167N ILE* 3.1 8.4 + - - +
169N GLU* 1.3 75.5 - - - +
171N ILE* 1.3 63.0 + - - +
173N ASN* 4.8 1.8 - - - -
174N ILE* 3.1 37.5 + - + +
252N LEU* 3.7 6.9 - - + +
254N PHE* 3.8 30.1 - - + -
307N VAL* 4.2 5.6 - - + -
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Residues in contact with ILE 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167N ILE* 2.9 29.7 + - + +
168N GLN* 3.4 15.0 - - + +
170N LEU* 1.3 75.4 - - - +
172N ASN* 1.3 62.1 + - - +
175N ALA* 3.3 23.0 + - - +
180N GLY 4.9 0.2 - - - +
182N SER* 3.7 18.6 + - - +
184N PHE* 5.5 0.7 - - + -
201N MET* 4.1 11.9 - - + -
206N VAL* 4.5 9.2 - - + -
214N LYS* 3.9 19.2 - - + +
215N VAL* 3.8 44.0 - - + -
254N PHE* 3.7 17.9 - - + -
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Residues in contact with ASN 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N GLN 3.0 13.2 + - - +
169N GLU* 2.9 9.9 + - - +
171N ILE* 1.3 79.3 - - - +
173N ASN* 1.3 78.5 + - - +
175N ALA* 3.6 2.6 + - - +
176N LYS* 3.2 35.5 + - - +
206N VAL* 4.8 0.7 - - + -
214N LYS* 2.8 31.9 + - - +
419N ALA* 3.6 27.8 - - - +
420N VAL* 3.8 16.8 - - + -
431N LEU* 5.8 0.2 - - - +
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Residues in contact with ASN 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N THR 2.8 30.4 + - - +
137N GLY* 3.5 22.2 + - - -
138N ILE* 4.7 0.8 - - - +
169N GLU* 2.8 50.2 + - - +
170N LEU 4.2 2.2 - - - +
172N ASN* 1.3 82.1 + - - +
174N ILE* 1.3 60.2 + - - +
175N ALA 3.2 0.4 - - - -
176N LYS* 4.6 0.4 - - - -
177N ALA* 2.7 40.1 + - + +
416N GLN* 5.1 0.2 - - - +
419N ALA* 5.3 0.2 - - - +
431N LEU* 3.4 25.8 - - + +
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Residues in contact with ILE 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134N LEU* 4.3 15.7 - - + -
135N GLU 3.6 20.9 - - - +
136N THR* 4.1 13.0 - - + +
170N LEU* 3.1 28.8 + - + +
171N ILE 4.6 0.7 - - - +
173N ASN* 1.3 77.7 - - - +
175N ALA* 1.3 57.9 + - - +
178N HIS* 3.2 21.5 + - + -
179N GLY 2.8 23.6 + - - -
180N GLY* 3.1 25.6 + - - +
181N PHE 4.6 0.7 - - - +
182N SER* 4.7 1.6 - - - +
250N ASP 3.7 15.3 - - - +
252N LEU* 3.4 29.6 - - + -
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Residues in contact with ALA 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171N ILE 3.3 20.1 + - - +
172N ASN 3.8 2.9 - - - +
173N ASN 3.2 0.2 - - - -
174N ILE* 1.3 79.5 - - - +
176N LYS* 1.3 63.0 + - + +
179N GLY* 3.1 18.2 - - - -
180N GLY 3.3 16.6 - - - +
181N PHE* 5.5 4.7 - - + -
214N LYS* 3.6 31.2 - - + +
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Residues in contact with LYS 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172N ASN* 3.2 27.6 + - - +
173N ASN* 3.9 4.0 - - - +
174N ILE 3.2 0.2 - - - -
175N ALA* 1.3 84.0 + - - +
177N ALA* 1.3 66.1 + - - +
178N HIS 3.4 1.0 + - - -
179N GLY* 4.1 2.4 + - - -
214N LYS* 4.0 26.7 - - - +
431N LEU* 5.1 7.6 - - + -
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Residues in contact with ALA 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N GLU* 4.9 6.5 - - + +
136N THR 6.2 1.1 - - - -
173N ASN* 2.7 22.8 + - + +
176N LYS* 1.3 76.1 - - - +
178N HIS* 1.3 76.6 + - + +
431N LEU* 4.8 14.3 - - + +
433N ARG* 4.4 22.5 + - - +
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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
------------------------------------------------------------
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