Contacts of the helix formed by residues 687 - 696 (chain F) in PDB entry 1K7L
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 HIS 687 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306E VAL* 3.6 24.6 - - + +
310E LYS* 2.6 47.8 + - + +
462E GLU* 3.1 43.1 + - + +
463E ILE* 4.5 0.7 - - - -
465E ARG* 6.2 0.7 - - + -
466E ASP* 6.4 0.2 - - + -
685F GLU* 2.6 51.5 + - + +
686F ARG* 1.3 71.1 - - - +
688F LYS* 1.3 53.7 + - - +
690F LEU* 3.3 21.6 + - + -
691F HIS* 2.8 35.1 + - + -
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Residues in contact with LYS 688 (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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371C ASP* 4.9 4.0 - - + +
415C ASN* 5.3 0.9 - - - +
462E GLU* 3.8 3.4 + - - +
686F ARG* 3.1 32.0 + - + +
687F HIS* 1.3 75.7 - - - +
689F ILE* 1.3 59.1 + - + +
691F HIS* 3.3 7.3 + - - +
692F ARG* 2.9 60.0 + - - +
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Residues in contact with ILE 689 (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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414C SER 3.6 22.2 - - - +
415C ASN* 3.6 28.5 - - - +
417C PRO* 4.3 18.4 - - + -
457E HIS* 5.3 0.2 - - - +
458E PRO* 3.6 33.9 - - + -
459E LEU* 3.6 31.2 - - + +
462E GLU* 3.3 16.4 + - - +
688F LYS* 1.3 72.8 - - + +
690F LEU* 1.3 67.8 - - - +
692F ARG* 3.2 8.9 + - - +
693F LEU* 3.1 24.2 + - + +
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Residues in contact with LEU 690 (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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284E VAL* 5.1 4.9 - - + -
288E THR* 4.3 11.4 - - - +
306E VAL* 3.8 36.6 - - + +
309E LEU* 4.1 31.9 - - + -
310E LYS* 4.4 4.9 - - - +
459E LEU* 4.3 13.2 - - + +
462E GLU* 2.8 18.4 + - - +
463E ILE* 4.6 13.2 - - + -
687F HIS* 3.6 20.0 - - + +
689F ILE* 1.3 72.4 - - - +
691F HIS* 1.3 62.4 + - - +
693F LEU* 3.3 12.9 + - + +
694F LEU* 3.1 32.4 + - + +
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Residues in contact with HIS 691 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E LEU* 4.1 17.6 - - + +
303E ASN* 3.8 21.6 + - - -
306E VAL* 3.6 25.5 - - + +
685F GLU* 4.3 7.3 + - - -
686F ARG* 2.9 31.4 + - - +
687F HIS* 2.8 18.2 + - + +
688F LYS* 3.3 9.2 - - - +
690F LEU* 1.3 77.4 - - - +
692F ARG* 1.3 57.8 + - + +
694F LEU* 3.2 7.8 + - - +
695F GLN* 2.9 50.4 + - - +
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Residues in contact with ARG 692 (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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369C GLU* 4.3 11.4 + - - +
371C ASP* 2.7 36.2 + - - +
415C ASN* 2.6 55.0 + - - +
416C HIS* 3.6 28.6 + - - -
417C PRO* 5.8 1.8 - - + -
418C ASP* 3.8 35.5 - - + +
686F ARG* 6.1 0.4 - - - +
688F LYS* 2.9 38.3 + - - +
689F ILE* 3.2 9.4 + - + +
691F HIS* 1.3 74.0 - - + +
693F LEU* 1.3 66.2 + - + +
694F LEU 3.4 0.3 + - - -
695F GLN* 3.6 14.7 + - + +
696F GLU 3.8 8.1 + - - -
697F GLY 4.3 0.5 + - - -
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Residues in contact with LEU 693 (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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417C PRO* 4.1 23.3 - - + -
418C ASP* 4.9 2.2 - - + +
284E VAL* 5.0 1.1 - - + -
285E THR* 4.5 26.7 - - + +
288E THR* 3.8 26.8 - - + +
289E GLU* 4.3 0.9 - - - +
292E LYS* 2.7 27.2 + - - -
459E LEU* 3.8 32.8 - - + -
689F ILE* 3.1 22.9 + - + +
690F LEU* 3.5 13.7 - - + +
691F HIS 3.2 0.2 - - - -
692F ARG* 1.3 78.2 - - + +
694F LEU* 1.3 49.7 + - - +
697F GLY 3.8 29.4 + - - +
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Residues in contact with LEU 694 (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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288E THR* 3.5 13.2 - - + -
292E LYS* 2.8 27.1 + - + +
297E PHE* 4.2 6.5 - - + -
302E LEU* 4.0 15.3 - - + +
305E GLN* 3.5 34.4 + - + +
306E VAL* 3.5 36.6 - - + +
309E LEU* 3.3 29.4 - - + -
690F LEU* 3.1 17.1 + - + +
691F HIS* 3.7 5.8 - - - +
692F ARG 3.2 0.6 - - - -
693F LEU* 1.3 76.7 - - - +
695F GLN* 1.3 63.7 + - - +
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Residues in contact with GLN 695 (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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369C GLU* 5.9 2.5 - - - +
292E LYS* 4.6 0.2 + - - -
302E LEU* 3.9 24.3 - - - +
691F HIS* 2.9 43.5 + - - +
692F ARG* 4.1 8.1 - - + +
693F LEU 3.5 0.4 - - - -
694F LEU* 1.3 79.3 + - - +
696F GLU* 1.3 82.0 + - - +
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Residues in contact with GLU 696 (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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369C GLU* 4.6 9.4 - - - +
418C ASP* 2.9 25.8 - - + +
289E GLU* 4.2 5.4 - - - +
292E LYS* 2.7 22.2 + - - +
692F ARG* 3.8 2.8 + - - -
693F LEU 4.0 0.2 - - - -
695F GLN* 1.3 97.7 - - - +
697F GLY* 1.3 59.0 + - - +
234G SER* 3.8 22.8 + - - +
236G ASN* 3.5 30.7 + - + +
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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