Contacts of the helix formed by residues 684 - 692 (chain A) in PDB entry 2KFN
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 GLU 684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683A ASN* 1.3 79.0 + - - +
685A GLU* 1.3 72.7 + - + +
687A ARG* 3.2 35.2 - - + +
688A ARG* 3.4 16.8 + - + +
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Residues in contact with GLU 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A HIS* 2.8 30.2 + - - -
559A LEU* 3.5 6.6 - - - +
562A ARG* 3.0 35.5 + - - +
633A LEU* 3.4 22.9 - - + -
636A LEU* 3.4 21.1 - - + -
683A ASN* 3.0 15.2 + - - +
684A GLU* 1.3 83.2 - - + +
686A GLY* 1.3 66.5 + - - +
687A ARG 3.0 1.8 - - - -
688A ARG* 3.0 25.7 + - - +
689A ILE* 3.1 14.6 + - - +
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Residues in contact with GLY 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636A LEU* 4.8 1.4 - - - +
679A ILE* 3.8 5.0 - - - +
680A PRO* 3.5 36.3 - - - +
683A ASN* 3.6 9.9 + - - +
684A GLU 3.3 0.6 - - - -
685A GLU* 1.3 77.0 - - - +
687A ARG* 1.3 60.8 - - - +
689A ILE* 3.2 14.5 + - - +
690A ARG* 3.1 26.6 + - - +
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Residues in contact with ARG 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A VAL 4.6 2.9 - - - +
683A ASN 3.4 17.8 + - - +
684A GLU* 3.2 25.3 - - + +
686A GLY* 1.3 77.8 - - - +
688A ARG* 1.3 55.6 + - + +
690A ARG* 3.4 21.7 + - - +
691A GLN* 3.1 37.0 + - - +
925A ASP* 3.4 35.8 + - - +
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Residues in contact with ARG 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A VAL* 4.8 7.2 + - - +
552A LEU* 5.2 0.3 - - - +
554A ASN* 4.8 3.0 - - - +
555A HIS* 3.4 58.8 + - + +
558A GLU* 2.9 43.1 + - - +
562A ARG* 4.1 3.2 - - - +
684A GLU* 3.4 15.4 + - + +
685A GLU* 3.0 23.1 + - - +
687A ARG* 1.3 75.9 - - - +
689A ILE* 1.3 67.9 + - - +
691A GLN* 3.3 36.4 + - - +
692A ALA* 3.6 5.9 + - - +
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Residues in contact with ILE 689 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552A LEU* 4.8 7.2 - - + -
555A HIS* 3.9 14.1 - - + +
636A LEU* 4.2 17.3 - - + -
640A TYR* 4.0 20.2 - - + -
641A THR* 3.9 22.9 - - - +
644A LEU* 4.2 13.0 - - + -
679A ILE* 4.0 30.5 - - + -
685A GLU 3.1 13.3 + - - +
686A GLY* 3.3 13.0 - - - +
688A ARG* 1.3 74.6 - - - +
690A ARG* 1.3 59.3 + - - +
692A ALA* 2.9 29.3 + - - +
693A PHE* 3.4 14.8 - - + -
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Residues in contact with ARG 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A ILE* 4.3 10.6 + - + +
680A PRO 3.2 9.6 + - - -
681A VAL* 2.9 49.9 + - - +
686A GLY 3.1 8.0 + - - +
687A ARG* 3.6 26.1 - - - +
688A ARG 3.2 0.2 - - - -
689A ILE* 1.3 80.3 - - - +
691A GLN* 1.3 59.3 + - - +
692A ALA 3.0 0.4 - - - -
693A PHE* 3.1 19.0 + - - +
924A TRP* 3.4 60.0 + - + +
925A ASP* 3.0 41.1 + - + +
928A HIS* 3.7 32.2 + - - -
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Residues in contact with GLN 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A VAL* 4.9 10.7 - - + +
687A ARG* 3.1 28.6 + - - +
688A ARG* 3.6 28.4 + - - +
689A ILE 3.2 0.8 + - - -
690A ARG* 1.3 76.9 - - - +
692A ALA* 1.3 58.5 + - - +
693A PHE 3.2 0.9 - - - -
694A ILE* 3.5 8.5 - - - +
923A ASN* 3.3 32.3 + - - +
925A ASP* 3.3 28.0 + - + +
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Residues in contact with ALA 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ILE* 3.2 6.5 - - - -
548A ASP* 2.9 32.7 + - - +
551A VAL* 4.2 16.5 - - + +
552A LEU* 3.6 38.8 - - + -
688A ARG 3.6 1.9 + - - +
689A ILE 2.9 15.5 + - - +
691A GLN* 1.3 78.1 - - - +
693A PHE* 1.3 62.2 + - + +
694A ILE* 3.4 5.8 + - - -
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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