Contacts of the strand formed by residues 350 - 354 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167K GLU* 3.5 13.9 - - - -
168K LEU 3.2 12.3 + - - -
348K THR* 3.1 22.7 + - - -
349K ASP* 1.3 75.1 - - - +
351K GLN* 1.3 72.4 + - - +
373K VAL* 3.3 16.4 - - - -
375K ARG* 4.2 5.5 - - - +
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Residues in contact with GLN 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159K VAL* 4.4 0.7 - - - +
167K GLU* 3.3 4.6 + - - +
168K LEU* 3.4 13.2 - - + +
170K ILE* 4.5 13.2 - - + -
345K ILE* 3.2 52.8 + - + +
348K THR* 4.1 1.5 + - - +
350K GLY* 1.3 92.1 - - - +
352K ILE* 1.3 65.5 + - - +
353K PHE* 3.9 2.2 - - + +
371K LEU 3.9 17.7 - - - +
372K SER* 3.3 5.0 - - - -
373K VAL* 3.1 39.0 + - - +
375K ARG* 5.8 3.8 - - - +
160O GLY* 4.5 12.1 - - - +
190O ARG* 5.5 0.4 - - - +
611O PO4 5.4 1.8 + - - -
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Residues in contact with ILE 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K VAL* 4.3 25.6 - - + -
159K VAL* 4.3 13.5 - - + -
161K ILE* 4.6 9.0 - - + -
167K GLU* 3.8 27.6 - - + +
168K LEU 2.7 13.1 + - - +
169K ILE* 3.9 19.7 - - + +
170K ILE* 3.0 24.2 + - - +
180K VAL* 5.3 10.8 - - + -
351K GLN* 1.3 76.0 - - - +
353K PHE* 1.3 60.0 + - - +
354K LEU* 3.7 9.9 + - + +
367K ILE* 3.7 31.2 - - + -
372K SER* 3.7 4.3 - - - +
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Residues in contact with PHE 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K ILE* 3.3 18.6 - - + -
171K GLY* 4.9 5.6 - - - -
172K ASP* 5.2 0.7 - - - -
331K THR* 5.0 2.5 - - - -
334K GLY* 4.4 22.4 - - - -
336K VAL* 3.5 32.1 - - + -
351K GLN* 3.9 2.6 - - + -
352K ILE* 1.3 73.8 - - - +
354K LEU* 1.3 70.7 + - - +
355K GLU* 3.5 40.8 - - + -
366K ALA 3.2 12.5 - - - +
367K ILE* 3.7 2.4 - - - -
368K ASN* 3.4 36.6 + - + -
371K LEU* 4.4 25.4 - - + -
372K SER* 2.7 19.8 + - - +
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Residues in contact with LEU 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K ILE* 4.1 13.0 - - + -
170K ILE 2.9 11.9 + - - +
171K GLY* 3.5 16.0 - - - -
172K ASP* 3.7 9.2 + - - +
175K THR* 3.6 19.8 + - - +
176K GLY 3.5 33.4 - - - +
177K LYS* 3.7 15.3 - - + +
180K VAL* 4.3 6.1 - - + -
352K ILE* 4.2 7.4 - - + +
353K PHE* 1.3 82.1 - - - +
355K GLU* 1.3 62.7 + - - +
365K PRO* 4.2 6.5 - - + -
366K ALA* 3.4 33.0 - - + +
367K ILE* 3.9 16.2 - - + -
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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