Contacts of the helix formed by residues 554 - 561 (chain F) in PDB entry 6K4Y
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 ARG 554 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552F THR* 2.9 15.7 + - - +
553F ALA* 1.3 78.1 - - - +
555F GLU* 1.3 62.6 + - - +
557F LYS* 3.2 13.3 + - + +
558F VAL* 3.0 33.2 + - + +
9I ARG* 3.2 48.6 - - - +
12I ILE* 5.6 0.6 - - - +
13I THR* 4.2 22.1 + - + +
72I GLU* 3.2 46.1 + - - +
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Residues in contact with GLU 555 (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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550F GLY 4.2 2.7 - - - +
551F LEU* 3.2 20.3 - - + -
552F THR* 2.4 55.8 + - - +
553F ALA 3.0 4.9 + - - -
554F ARG* 1.3 80.6 - - - +
556F ALA* 1.3 55.9 + - - +
558F VAL* 3.2 8.0 + - - +
559F LEU* 2.8 32.4 + - + +
13I THR* 4.3 10.4 - - + +
16I SER* 5.1 9.2 - - - -
17I ILE* 3.3 30.2 - - + +
20I LYS* 4.5 11.0 + - - +
72I GLU 5.8 0.2 - - - +
76I GLY* 4.6 3.5 + - - -
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Residues in contact with ALA 556 (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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551F LEU* 3.8 22.8 - - + +
553F ALA* 4.3 10.5 - - - +
555F GLU* 1.3 76.7 - - - +
557F LYS* 1.3 60.0 + - - +
559F LEU* 3.5 12.0 - - - +
560F ARG* 2.9 36.9 + - - +
565F ILE 4.3 0.9 - - - +
567F MET* 4.5 23.6 - - + +
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Residues in contact with LYS 557 (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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553F ALA 3.3 17.9 + - - +
554F ARG* 3.2 16.6 + - + +
555F GLU 3.2 0.4 - - - -
556F ALA* 1.3 78.4 - - - +
558F VAL* 1.3 63.4 + - + +
560F ARG* 3.6 15.0 - - - +
561F MET* 2.9 69.8 + - + +
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Residues in contact with VAL 558 (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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554F ARG* 3.0 12.9 + - + +
555F GLU 3.3 11.9 - - - +
557F LYS* 1.3 82.4 - - + +
559F LEU* 1.3 58.4 + - - +
560F ARG 3.4 0.4 - - - -
561F MET* 4.3 6.5 - - + +
562F ARG* 3.2 45.2 + - - +
563F PHE* 3.6 6.4 + - - -
10I GLU* 4.7 21.3 - - + -
13I THR* 4.0 15.3 - - + -
14I VAL* 4.8 11.4 - - + +
17I ILE* 3.7 18.7 - - + +
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Residues in contact with LEU 559 (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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551F LEU* 4.5 14.8 - - + -
555F GLU 2.8 24.1 + - - +
556F ALA* 3.1 15.2 + - + +
558F VAL* 1.3 78.9 - - - +
560F ARG* 1.3 49.9 + - - +
563F PHE* 3.1 35.6 - - + +
564F GLY 2.8 8.8 + - - -
565F ILE* 2.6 44.6 + - + +
567F MET* 5.0 8.7 - - - -
580F PHE* 6.1 1.8 - - + -
583F THR* 4.3 16.4 - - + +
17I ILE* 3.8 23.6 - - + -
21I PHE* 4.6 15.9 - - + -
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Residues in contact with ARG 560 (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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556F ALA* 2.9 19.7 + - - +
557F LYS* 3.6 17.4 + - - +
559F LEU* 1.3 77.7 - - - +
561F MET* 1.3 74.2 + - + +
562F ARG 3.3 1.1 - - - -
564F GLY* 3.6 16.6 - - - +
565F ILE 3.3 7.2 - - - +
566F ASP* 3.3 29.3 - - - +
567F MET 4.8 13.4 + - - +
568F ASN* 5.8 4.9 + - - +
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Residues in contact with MET 561 (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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557F LYS* 2.9 56.1 + - + +
558F VAL* 4.5 5.2 - - + -
560F ARG* 1.3 90.3 - - + +
562F ARG* 1.3 66.3 + - + +
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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