Contacts of the strand formed by residues 350 - 354 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167U GLU* 3.1 10.5 - - - +
168U LEU 3.0 23.0 + - - -
348U THR* 3.2 12.7 + - - -
349U ASP* 1.3 76.8 - - - +
351U GLN* 1.3 68.7 + - - +
373U VAL* 3.2 19.5 - - - -
374U SER* 4.0 0.7 - - - -
375U ARG* 4.1 5.8 - - - +
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Residues in contact with GLN 351 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167U GLU* 3.3 7.4 - - - +
168U LEU* 3.7 25.1 - - + -
170U ILE* 4.4 9.6 - - + -
345U ILE* 2.8 53.1 + - + +
348U THR* 3.1 15.6 + - - -
350U GLY* 1.3 78.9 - - - +
352U ILE* 1.3 62.8 + - - +
353U PHE* 3.8 4.0 - - + +
371U LEU 4.6 13.2 - - - +
372U SER* 3.3 3.5 - - - -
373U VAL* 2.8 42.7 + - - +
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Residues in contact with ILE 352 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155U VAL* 4.9 7.9 - - + -
159U VAL* 3.4 34.3 - - + +
161U ILE* 5.3 1.1 - - + -
167U GLU* 3.3 26.7 - - + +
168U LEU 2.8 19.2 + - - +
169U ILE* 4.1 11.0 - - + -
170U ILE* 3.1 22.6 + - - +
180U VAL* 5.0 13.2 - - + -
351U GLN* 1.3 83.6 - - - +
353U PHE* 1.3 60.1 + - - +
354U LEU* 3.6 11.9 + - + +
367U ILE* 4.2 29.6 - - + -
372U SER* 3.8 3.4 - - - -
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Residues in contact with PHE 353 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170U ILE* 3.1 29.8 - - + +
171U GLY* 4.3 11.4 - - - -
172U ASP* 4.8 2.0 - - - -
331U THR* 4.7 6.5 - - - -
334U GLY* 4.6 16.2 - - - -
336U VAL* 3.7 28.5 - - + -
351U GLN* 3.8 1.9 - - + -
352U ILE* 1.3 73.7 - - - +
354U LEU* 1.3 63.9 + - - +
355U GLU* 3.3 34.5 - - + -
366U ALA 3.5 2.4 - - - +
367U ILE* 3.6 6.2 - - - +
368U ASN* 3.5 26.3 + - + -
371U LEU* 3.8 43.7 - - + +
372U SER* 3.4 13.8 - - - +
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Residues in contact with LEU 354 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169U ILE* 4.3 8.7 - - + -
170U ILE 2.9 12.3 + - - +
171U GLY* 3.5 15.0 - - - -
172U ASP* 3.8 9.7 + - - +
175U THR* 3.8 19.2 - - - +
176U GLY 3.9 6.7 - - - +
177U LYS* 3.5 45.3 - - + +
180U VAL* 4.2 16.4 - - + -
352U ILE* 4.0 9.6 - - + +
353U PHE* 1.3 78.7 - - - +
355U GLU* 1.3 64.6 + - - +
356U ALA 3.8 1.2 + - - -
365U PRO* 4.8 0.4 - - + -
366U ALA* 3.0 38.1 - - + +
367U ILE* 3.8 17.5 - - + -
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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
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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