Contacts of the helix formed by residues 162 - 172 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B ARG* 4.1 9.2 - - - +
160F GLY 3.6 1.6 - - - -
161F VAL* 1.3 82.2 - - - +
163F LYS* 1.3 60.9 + - - +
164F THR 3.6 0.7 - - - -
165F VAL* 4.0 16.3 - - - +
166F PHE* 3.2 27.4 + - - +
335F LEU* 3.8 7.8 - - - +
345F TYR* 6.5 0.4 - - - -
346F PRO* 5.8 1.9 - - - +
605F PO4 3.1 6.7 + - - -
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Residues in contact with LYS 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B SER* 5.4 1.0 - - - -
155F LEU* 4.5 5.5 - - + +
156F PHE 4.9 1.3 - - - -
157F GLY* 3.2 23.6 - - - +
158F GLY 2.9 24.2 + - - +
159F ALA* 4.0 1.4 - - - +
161F VAL* 4.0 0.7 - - + -
162F GLY* 1.3 75.1 - - - +
164F THR* 1.3 62.6 + - - +
165F VAL 3.2 0.2 - - - -
166F PHE* 3.4 3.0 + - - +
167F ILE* 2.8 35.8 + - - +
189F GLU* 5.1 5.2 + - - -
256F ASP* 5.5 2.5 - - - +
257F ASN* 3.6 26.5 - - - +
260F ARG* 5.7 0.4 - - - +
309F ALA* 4.9 12.6 - - + -
310F VAL 4.2 10.1 - - - +
311F TYR* 3.8 13.7 - - - +
335F LEU* 3.7 20.9 - - + -
605F PO4 2.7 34.1 + - - +
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Residues in contact with THR 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ARG* 4.0 6.5 - - - -
163F LYS* 1.3 76.6 - - - +
165F VAL* 1.3 58.3 + - - +
167F ILE* 3.5 6.6 + - + +
168F GLN* 3.0 57.1 + - + +
189F GLU* 3.9 10.3 + - - +
190F ARG* 3.3 14.4 + - - -
193F GLU* 3.1 28.4 + - + +
256F ASP* 4.3 13.6 + - - +
605F PO4 3.0 16.1 + - - -
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Residues in contact with VAL 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ARG* 4.1 22.2 - - - +
162F GLY* 4.0 13.9 - - - +
163F LYS 3.2 0.2 - - - -
164F THR* 1.3 73.8 - - - +
166F PHE* 1.3 67.4 + - - +
168F GLN* 3.1 9.3 + - - +
169F GLU* 3.0 20.6 + - - +
418F PHE* 4.4 16.6 - - + -
420F VAL* 4.9 7.9 - - + +
421F ALA* 4.0 31.2 - - + +
424F PHE* 4.4 21.3 - - + -
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Residues in contact with PHE 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F ILE* 4.6 12.1 - - + -
141F VAL* 3.9 16.2 - - + -
147F TYR* 3.5 26.0 - - - -
155F LEU* 3.6 25.8 - - + -
162F GLY 3.2 18.5 + - - +
163F LYS 3.7 2.9 - - - +
165F VAL* 1.3 80.2 - - - +
167F ILE* 1.3 63.6 + - - +
169F GLU* 3.1 16.7 + - - +
170F LEU* 3.2 35.1 + - + +
333F THR* 4.6 4.3 - - - -
335F LEU* 4.8 3.4 - - + -
346F PRO* 3.9 36.3 - - + -
348F VAL* 4.1 12.3 - - + -
418F PHE* 4.1 15.0 - + + -
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Residues in contact with ILE 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F LEU* 3.8 24.9 - - + -
163F LYS 2.8 24.8 + - - +
164F THR* 3.6 7.9 - - + +
166F PHE* 1.3 77.4 - - - +
168F GLN* 1.3 68.6 + - + +
170F LEU* 3.0 18.5 + - + +
171F ILE* 3.2 25.7 + - + +
184F PHE* 4.4 14.4 - - + -
254F PHE* 4.8 6.7 - - + -
255F ILE 6.1 0.2 - - - -
256F ASP* 4.6 15.5 - - + +
307F VAL* 4.1 27.4 - - + +
309F ALA* 4.0 20.9 - - + +
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Residues in contact with GLN 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F THR* 3.0 40.2 + - + +
165F VAL* 3.1 4.7 + - - +
167F ILE* 1.3 79.1 - - + +
169F GLU* 1.3 60.6 + - - +
171F ILE* 3.6 13.4 + - + +
172F ASN* 3.3 19.1 + - - +
193F GLU* 4.1 21.0 - - - +
196F ASP* 5.7 5.9 + - - +
197F LEU* 4.3 29.2 + - + +
200F GLU* 5.5 7.1 - - - +
420F VAL* 3.5 37.9 - - + +
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Residues in contact with GLU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F ILE* 5.0 4.0 - - + -
165F VAL 3.0 11.3 + - - +
166F PHE* 3.3 13.9 - - + +
167F ILE 3.0 0.4 - - - -
168F GLN* 1.3 75.5 - - - +
170F LEU* 1.3 61.5 + - + +
171F ILE 3.0 4.7 - - - -
172F ASN* 3.2 3.8 + - - +
173F ASN* 3.2 51.7 + - - +
418F PHE* 3.3 36.6 - - + +
419F ALA* 3.2 28.8 + - - +
420F VAL* 3.2 31.1 + - - +
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Residues in contact with LEU 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F THR* 4.6 2.9 - - - -
138F ILE* 4.0 25.1 - - + -
147F TYR* 3.9 24.7 - - + +
155F LEU* 5.4 1.6 - - + -
166F PHE* 3.2 35.1 + - + +
167F ILE* 3.0 13.7 + - + +
169F GLU* 1.3 76.7 - - - +
171F ILE* 1.3 57.3 + - - +
173F ASN* 3.9 0.9 - - - -
174F ILE* 3.2 47.2 + - + +
175F ALA 3.6 5.2 + - - -
254F PHE* 3.9 14.4 - - + -
307F VAL* 3.5 28.9 - - + -
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Residues in contact with ILE 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F ILE* 3.2 18.8 + - + +
168F GLN* 3.6 13.2 - - + +
169F GLU 3.0 0.4 - - - -
170F LEU* 1.3 79.5 - - - +
172F ASN* 1.3 61.0 + - - +
173F ASN 3.2 2.9 + - - -
175F ALA* 3.0 35.6 + - + +
176F LYS* 3.5 8.7 + - - +
184F PHE* 3.9 30.1 - - + -
197F LEU* 3.8 26.5 - - + -
201F MET* 3.5 34.9 - - + +
254F PHE* 4.2 17.7 - - + -
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Residues in contact with ASN 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F GLN 3.3 14.3 + - - +
169F GLU* 3.2 8.9 + - - +
171F ILE* 1.3 79.8 - - - +
173F ASN* 1.3 66.4 + - - +
176F LYS* 3.6 46.5 + - - +
197F LEU* 6.0 0.7 - - - +
200F GLU* 3.7 27.5 + - - +
201F MET* 3.7 15.2 - - - +
204F THR* 5.0 0.2 - - - +
419F ALA* 5.6 7.3 - - + +
420F VAL* 4.1 16.3 - - + +
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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