Contacts of the helix formed by residues 377 - 381 (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 377 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K PRO* 3.5 17.1 - - - +
374K SER 4.1 2.9 - - - -
375K ARG 3.8 0.2 + - - -
376K VAL* 1.3 77.4 - - - +
378K SER* 1.3 66.4 + - - +
379K ALA 3.3 0.2 - - - -
380K ALA 3.3 6.1 + - - -
381K GLN* 3.5 14.2 - - - +
423O VAL* 3.6 12.7 + - - +
424O PHE* 3.6 22.5 - - - +
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Residues in contact with SER 378 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377K GLY* 1.3 71.2 - - - +
379K ALA* 1.3 62.0 + - - +
381K GLN* 3.1 32.9 + - - +
383K LYS* 5.8 1.9 - - - +
386K LYS* 3.3 47.6 + - - +
422O GLU 5.2 1.0 + - - -
423O VAL* 3.0 20.7 + - - -
426O GLY* 6.1 1.2 - - - -
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Residues in contact with ALA 379 (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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143K SER* 5.6 3.1 - - - +
144K VAL* 3.4 21.0 - - + +
145K HIS* 3.3 20.1 - - - +
376K VAL* 5.2 9.6 - - + -
377K GLY 3.3 0.8 - - - -
378K SER* 1.3 78.5 - - - +
380K ALA* 1.3 57.6 + - - +
381K GLN 3.4 1.5 + - - +
423O VAL* 4.3 17.8 - - + +
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Residues in contact with ALA 380 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144K VAL* 4.1 15.9 - - + -
145K HIS 4.7 4.3 - - - -
147K PRO* 3.4 20.2 - - - +
160K PRO* 3.7 9.8 - - - +
161K ILE 3.5 9.6 - - - +
162K GLY* 3.6 28.7 - - - +
165K GLN* 4.4 0.4 - - - +
376K VAL* 3.6 21.3 + - + +
377K GLY 3.3 4.3 + - - -
378K SER 3.2 0.8 - - - -
379K ALA* 1.3 76.6 - - - +
381K GLN* 1.3 59.0 + - - +
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Residues in contact with GLN 381 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145K HIS 5.3 0.7 - - - +
147K PRO* 3.8 11.8 - - - +
156K ASP 3.0 23.3 + - - +
157K ALA* 3.1 24.7 + - - +
160K PRO* 3.7 19.5 - - + +
377K GLY 3.5 11.6 - - - +
378K SER* 3.1 21.5 + - - +
379K ALA 3.4 2.0 + - - +
380K ALA* 1.3 78.5 - - - +
382K VAL* 1.3 67.7 + - - +
383K LYS* 3.3 6.9 + - - +
385K LEU* 4.0 22.8 - - + +
386K LYS* 3.7 21.9 - - + +
389K ALA* 5.9 2.2 - - - +
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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