Contacts of the helix formed by residues 313 - 324 (chain F) in PDB entry 1K9V
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 ILE 313 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305F ILE* 4.8 6.5 - - + +
306F ILE 4.0 4.7 - - - +
307F SER* 3.8 27.8 - - - +
309F GLY* 4.8 6.7 - - - +
310F PRO 5.0 2.5 - - - +
311F GLY 3.7 11.2 - - - +
312F ASN* 1.3 78.0 + - - +
314F MET* 1.3 80.4 + - + +
315F ASN 3.2 2.7 - - - -
316F LEU* 3.2 10.7 + - + +
317F TYR* 2.9 18.7 + - + -
334F LEU* 3.7 31.6 - - + -
349F PRO* 3.7 33.9 - - + -
350F GLY* 5.0 1.8 - - - +
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Residues in contact with MET 314 (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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312F ASN* 3.0 17.9 + - - +
313F ILE* 1.3 91.8 - - + +
315F ASN* 1.3 56.5 + - - +
317F TYR* 3.1 35.0 + - + +
318F ARG* 2.8 71.3 + - + +
334F LEU* 4.7 12.8 - - - -
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Residues in contact with ASN 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F ASN* 4.4 15.6 + - - +
313F ILE* 3.2 0.8 - - - +
314F MET* 1.3 78.3 - - - +
316F LEU* 1.3 62.8 + - - +
318F ARG* 3.2 19.8 + - - +
319F GLY 2.9 19.2 + - - -
480F GLU* 3.6 23.9 - - + +
481F LYS* 4.3 22.3 + - - +
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Residues in contact with LEU 316 (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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305F ILE* 3.8 27.1 - - + -
313F ILE* 3.2 14.2 + - + +
315F ASN* 1.3 78.8 - - - +
317F TYR* 1.3 56.2 + - - +
320F VAL* 2.9 57.7 + - + +
347F PHE* 4.3 14.1 - - + -
349F PRO* 4.6 18.4 - - + -
383F VAL* 4.8 15.0 - - + -
479F PRO* 4.9 1.1 - - + -
480F GLU* 3.6 33.5 - - + +
490F LEU* 4.4 15.0 - - + -
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Residues in contact with TYR 317 (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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305F ILE* 3.8 15.9 - - + -
313F ILE* 2.9 16.4 + - + +
314F MET* 3.2 39.7 - - + +
315F ASN 3.1 0.2 - - - -
316F LEU* 1.3 76.1 - - - +
318F ARG* 1.3 65.8 + - + +
320F VAL* 3.3 1.4 + - - +
321F LYS* 2.8 60.8 + - + +
332F ILE* 3.3 46.2 + - + +
333F GLU* 5.6 0.2 - - - -
334F LEU* 4.2 17.0 - - + -
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Residues in contact with ARG 318 (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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314F MET* 2.8 76.8 + - + +
315F ASN* 3.3 21.8 + - - +
317F TYR* 1.3 79.0 - - + +
319F GLY* 1.3 64.1 + - - +
321F LYS* 3.1 9.5 + - + +
322F ARG* 2.9 28.2 + - - +
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Residues in contact with GLY 319 (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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315F ASN 2.9 14.3 + - - -
316F LEU 3.8 3.1 - - - -
318F ARG* 1.3 77.8 - - - +
320F VAL* 1.3 60.9 + - - +
322F ARG* 3.5 4.6 + - - +
323F ALA* 3.0 24.8 + - - +
480F GLU* 4.6 7.9 - - - -
487F ARG* 5.7 1.7 - - - +
490F LEU* 3.5 18.6 - - - +
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Residues in contact with VAL 320 (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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303F ILE* 4.1 36.8 - - + -
305F ILE* 4.1 8.3 - - + -
316F LEU* 2.9 49.8 + - + +
317F TYR 3.8 2.9 - - - +
319F GLY* 1.3 70.0 - - - +
321F LYS* 1.3 65.6 + - - +
323F ALA* 3.4 4.5 + - - +
324F SER* 3.0 22.0 + - - -
332F ILE* 4.1 8.1 - - + -
347F PHE* 3.9 23.8 - - + -
490F LEU* 3.8 9.4 - - + +
494F ILE* 4.0 4.2 - - + +
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Residues in contact with LYS 321 (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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317F TYR* 2.8 46.7 + - + +
318F ARG* 3.1 9.2 + - + +
320F VAL* 1.3 75.8 - - - +
322F ARG* 1.3 64.6 + - - +
324F SER* 2.7 20.0 + - - +
325F GLU* 3.3 7.1 + - - +
332F ILE* 3.3 21.5 - - + +
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Residues in contact with ARG 322 (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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318F ARG 2.9 19.1 + - - +
319F GLY* 4.0 4.3 - - - +
321F LYS* 1.3 73.6 - - - +
323F ALA* 1.3 57.6 + - - +
325F GLU* 3.1 25.4 - - - +
326F ASN 4.6 0.3 + - - -
487F ARG* 6.5 1.1 - - + -
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Residues in contact with ALA 323 (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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319F GLY 3.0 18.4 + - - +
320F VAL 3.7 4.9 - - - +
322F ARG* 1.3 76.1 - - - +
324F SER* 1.3 56.1 + - - +
325F GLU 3.1 8.4 + - - -
326F ASN* 4.1 3.1 + - - +
327F PHE* 3.3 23.6 - - - -
487F ARG* 4.1 8.0 - - + +
490F LEU* 3.8 26.2 - - + -
491F GLU* 3.7 24.1 - - + +
494F ILE* 3.7 8.3 - - + -
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Residues in contact with SER 324 (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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303F ILE* 4.5 0.7 - - - -
320F VAL 3.0 13.9 + - - -
321F LYS 2.7 18.6 + - - -
323F ALA* 1.3 74.6 - - - +
325F GLU* 1.3 66.0 + - - +
326F ASN 3.5 0.2 - - - -
327F PHE* 3.4 22.5 + - - +
328F GLU* 5.1 0.2 - - - -
330F VAL* 3.5 35.6 + - - +
332F ILE* 3.3 16.0 - - - +
494F ILE* 3.5 14.3 - - - +
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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