Contacts of the strand formed by residues 350 - 354 (chain L) 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 350 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166L ARG 3.9 0.5 - - - +
167L GLU* 3.3 6.5 - - - -
168L LEU 3.3 12.1 + - - -
345L ILE 5.1 0.4 + - - -
348L THR* 2.8 22.3 + - - -
349L ASP* 1.3 76.4 - - - +
351L GLN* 1.3 77.9 + - - +
373L VAL* 3.2 18.4 - - - -
375L ARG* 3.9 6.3 - - - +
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Residues in contact with GLN 351 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159L VAL* 4.6 0.3 - - - +
167L GLU* 3.1 12.3 + - - +
168L LEU* 3.4 22.4 - - + +
170L ILE* 4.3 10.8 - - + -
345L ILE* 3.6 41.1 + - + +
348L THR* 4.5 1.1 - - - +
350L GLY* 1.3 87.6 - - - +
352L ILE* 1.3 59.7 - - - +
353L PHE 4.0 0.7 - - - +
371L LEU 2.9 25.2 - - - +
372L SER* 3.1 20.1 - - - -
373L VAL* 3.1 27.3 + - - +
375L ARG* 5.4 0.6 - - - +
159M ALA 4.9 0.4 + - - -
160M GLY* 4.2 17.0 + - - -
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Residues in contact with ILE 352 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L VAL* 4.3 23.6 - - + -
159L VAL* 4.0 23.8 - - + -
161L ILE* 4.5 3.4 - - + -
167L GLU* 4.0 23.6 - - + +
168L LEU 2.7 13.3 + - - +
169L ILE* 3.7 14.9 - - + +
170L ILE* 3.0 28.8 + - - +
180L VAL* 4.9 14.8 - - + -
326L LEU* 6.1 1.6 - - + -
351L GLN* 1.3 75.6 - - - +
353L PHE* 1.3 59.9 + - - +
354L LEU* 3.9 14.4 + - + +
367L ILE* 4.0 27.8 - - + -
372L SER* 3.8 3.1 - - - -
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Residues in contact with PHE 353 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170L ILE* 3.2 24.9 - - + -
171L GLY* 3.8 17.7 - - - -
172L ASP* 4.7 5.4 - - - -
331L THR* 4.7 0.9 - - - -
334L GLY* 4.5 17.3 - - - -
336L VAL* 3.5 26.0 - - + -
351L GLN* 4.0 0.8 - - + -
352L ILE* 1.3 72.8 - - - +
354L LEU* 1.3 70.9 + - - +
355L GLU* 3.5 27.4 - - + -
366L ALA 3.4 2.4 - - - +
367L ILE* 3.4 5.0 - - - -
368L ASN* 3.1 39.2 + - + -
371L LEU* 3.7 48.7 - - + +
372L SER* 3.7 7.7 - - - -
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Residues in contact with LEU 354 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L ILE* 4.4 8.5 - - + -
170L ILE 3.0 12.9 + - - +
171L GLY* 3.7 14.6 - - - -
172L ASP* 4.0 2.4 + - - +
175L THR* 3.7 30.0 - - - +
176L GLY 3.8 4.0 - - - +
177L LYS* 3.6 43.3 - - + +
180L VAL* 4.4 13.0 - - + -
352L ILE* 4.3 10.1 - - + +
353L PHE* 1.3 83.7 - - - +
355L GLU* 1.3 63.1 + - - +
356L ALA 3.8 1.4 + - - -
365L PRO* 4.9 0.4 - - + -
366L ALA* 3.2 32.3 - - + +
367L ILE* 4.0 12.8 - - + +
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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