Contacts of the helix formed by residues 302 - 311 (chain E) in PDB entry 1QK1
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 302 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300E ASP* 2.6 44.4 + - - +
301E SER* 1.3 77.9 + - - +
303E PHE* 1.3 56.1 + - - +
304E PRO 3.3 1.6 - - - -
305E LYS* 2.7 30.2 + - + +
306E ILE* 3.0 19.6 + - + +
362E LEU* 4.9 4.0 - - - +
367E ASP* 3.6 20.0 + - - -
368E ILE* 3.4 42.8 + - - +
370E ILE* 4.0 33.0 - - + -
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Residues in contact with PHE 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E LEU* 4.0 22.0 - - + -
297E LEU* 3.6 49.6 - - + +
298E SER* 4.0 23.1 - - - +
300E ASP* 3.7 10.1 + - - +
302E ARG* 1.3 77.2 - - - +
304E PRO* 1.3 72.6 - - + +
305E LYS 2.9 1.2 + - - -
306E ILE* 3.2 5.1 + - + +
307E LEU* 3.2 51.2 + - + +
314E LYS* 3.3 37.9 - - + -
329E PHE* 4.5 10.1 - + - -
331E ILE* 4.6 6.7 - - + -
355E LEU* 4.7 1.8 - - + -
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Residues in contact with PRO 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E ASP 4.3 2.0 - - - +
301E SER* 3.7 15.0 - - - +
302E ARG 3.5 3.1 - - - -
303E PHE* 1.3 99.7 - - + +
305E LYS* 1.3 58.8 + - - +
307E LEU* 3.9 9.4 - - + +
308E GLU* 3.3 23.1 + - - +
314E LYS* 5.5 8.1 - - - -
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Residues in contact with LYS 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301E SER 5.2 0.4 + - - +
302E ARG* 2.7 20.3 + - - +
304E PRO* 1.3 72.7 - - - +
306E ILE* 1.3 65.1 + - - +
307E LEU 3.1 1.6 - - - -
308E GLU* 2.6 48.5 + - - +
309E ASN* 3.0 28.8 + - - +
370E ILE* 3.9 29.8 - - + -
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Residues in contact with ILE 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E LEU* 4.3 11.2 - - + -
302E ARG* 3.0 19.1 + - + +
303E PHE* 3.9 6.7 - - + +
305E LYS* 1.3 73.9 - - - +
307E LEU* 1.3 63.2 + - - +
309E ASN* 3.4 2.1 + - - +
310E LEU* 3.1 30.0 + - + +
354E TYR* 4.3 6.3 - - + -
355E LEU* 3.6 28.0 - - + -
358E CYS* 3.9 15.3 - - - -
368E ILE* 3.8 29.4 - - + -
369E ARG 4.4 6.7 - - - +
370E ILE* 4.0 13.9 - - + -
371E PRO* 3.8 30.0 - - + +
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Residues in contact with LEU 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E PHE* 3.2 52.9 + - + +
304E PRO* 3.9 7.6 - - + +
305E LYS 3.1 0.2 - - - -
306E ILE* 1.3 78.9 - - - +
308E GLU* 1.3 64.0 + - - +
310E LEU* 3.1 5.1 + - - -
311E ARG 3.0 17.2 + - - -
312E LEU* 3.0 38.3 + - + +
313E GLN* 4.9 0.9 - - - +
314E LYS* 4.1 23.6 - - + +
331E ILE* 4.7 5.8 - - + -
355E LEU* 3.5 36.8 - - + -
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Residues in contact with GLU 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E PRO 3.3 12.9 + - - +
305E LYS* 2.6 46.3 + - + +
307E LEU* 1.3 78.7 - - - +
309E ASN* 1.3 65.8 + - - +
311E ARG* 3.1 20.1 + - - +
312E LEU 4.4 3.8 + - - -
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Residues in contact with ASN 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305E LYS* 3.0 35.2 + - - +
306E ILE 3.9 4.0 - - - +
308E GLU* 1.3 78.7 - - - +
310E LEU* 1.3 59.6 + - - +
311E ARG* 3.2 1.9 + - - +
370E ILE* 3.8 12.6 - - - +
371E PRO* 2.3 43.3 + - + +
372E THR* 3.8 1.0 - - - +
373E PRO* 3.1 39.5 - - + +
374E VAL* 3.2 31.9 + - - +
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Residues in contact with LEU 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E ILE* 3.1 24.5 + - + +
307E LEU 3.1 5.8 + - - +
309E ASN* 1.3 76.2 - - - +
311E ARG* 1.3 72.3 + - - +
312E LEU* 3.3 16.2 + - + +
347E LEU* 3.6 17.8 - - - +
350E ASP 5.7 0.7 - - - -
351E GLY* 3.7 34.5 - - - +
354E TYR* 4.0 15.5 - - + -
355E LEU* 3.9 20.4 - - + -
371E PRO* 4.0 20.6 - - + -
372E THR 5.9 0.4 - - - +
374E VAL* 4.4 12.9 - - + +
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Residues in contact with ARG 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ASN* 3.6 27.3 + - - +
307E LEU 3.0 2.8 + - - -
308E GLU* 3.1 13.4 + - - +
309E ASN 4.0 2.9 - - - +
310E LEU* 1.3 79.6 - - - +
312E LEU* 1.3 62.6 + - - +
334E LEU* 3.2 46.5 + - + +
335E ASP* 3.2 41.3 + - - +
339E LYS* 4.1 8.1 - - - +
347E LEU* 4.0 11.4 - - + +
374E VAL* 3.0 40.5 + - + -
376E HIS* 6.4 0.4 - - - -
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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