Contacts of the helix formed by residues 370 - 382 (chain E) in PDB entry 5UQ9
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 SER 370 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228E LEU 5.9 0.2 - - - -
229E ASP 3.5 16.4 - - - -
230E SER* 3.5 13.9 - - - +
331E LYS* 4.2 8.2 + - - -
335E TYR* 4.6 0.9 + - - -
363E ARG* 3.0 25.7 + - - +
368E ILE 3.4 10.7 + - - -
369E ARG* 1.3 77.2 - - - +
371E VAL* 1.3 60.3 + - - +
372E PHE* 3.7 14.3 - - - +
373E LEU* 2.9 36.2 + - - +
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Residues in contact with VAL 371 (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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226E THR 4.9 3.6 - - - +
227E GLU* 4.7 6.3 - - - +
229E ASP* 3.3 39.9 + - + +
363E ARG* 3.5 28.2 - - - +
370E SER* 1.3 71.1 - - - +
372E PHE* 1.3 61.2 + - - +
374E GLY* 2.8 17.8 + - - -
375E LYS* 3.1 27.2 + - - +
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Residues in contact with PHE 372 (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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227E GLU 4.0 14.8 - - - +
228E LEU* 6.0 0.2 - - - -
328E TYR* 3.6 26.2 - + - -
331E LYS* 3.8 25.6 - - + +
332E ILE* 3.6 37.7 - - + -
335E TYR* 3.6 31.4 - + + -
370E SER* 3.0 12.0 - - - +
371E VAL* 1.3 83.3 - - - +
373E LEU* 1.3 62.5 + - - +
375E LYS* 3.2 20.7 + - + +
376E ILE* 3.2 28.2 + - + +
389E LEU* 5.9 0.4 - - + -
395E PHE* 3.4 29.2 - + - -
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Residues in contact with LEU 373 (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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335E TYR* 3.5 31.0 - - + -
339E PHE* 5.4 0.9 - - + -
359E ALA* 3.8 22.6 - - + +
362E TRP* 3.2 54.1 - - + +
363E ARG* 4.2 6.1 - - - -
368E ILE* 3.2 29.6 - - + +
369E ARG* 3.8 4.5 - - - -
370E SER* 2.9 16.3 + - - +
372E PHE* 1.3 77.2 - - - +
374E GLY* 1.3 61.9 + - - +
376E ILE* 3.1 13.7 + - + +
377E LYS* 3.1 17.0 + - - +
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Residues in contact with GLY 374 (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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363E ARG* 3.7 18.8 - - - +
370E SER 3.6 2.2 + - - -
371E VAL* 2.8 12.1 + - - -
373E LEU* 1.3 78.6 - - - +
375E LYS* 1.3 60.9 + - - +
377E LYS* 3.1 10.5 + - - +
378E ASP* 2.9 32.6 + - - +
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Residues in contact with LYS 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328E TYR* 5.7 0.7 - - - +
371E VAL* 3.1 28.1 + - + +
372E PHE* 3.2 14.8 + - + +
374E GLY* 1.3 75.6 - - - +
376E ILE* 1.3 61.8 + - - +
378E ASP* 3.5 16.8 + - - +
379E ALA* 3.1 21.8 + - - +
382E ARG* 4.9 1.6 + - - -
394E PHE* 3.5 50.5 - - + -
395E PHE* 3.7 10.3 - - + -
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Residues in contact with ILE 376 (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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335E TYR* 3.5 41.5 - - + -
339E PHE* 4.0 14.6 - - + -
359E ALA* 4.3 5.2 - - + -
372E PHE* 3.2 26.4 + - + +
373E LEU* 3.1 14.2 + - + +
375E LYS* 1.3 74.0 - - - +
377E LYS* 1.3 64.7 + - - +
379E ALA* 3.2 1.9 + - - +
380E PHE* 3.1 47.9 + - + -
389E LEU* 3.8 11.9 - - + -
395E PHE* 3.5 22.7 - - + -
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Residues in contact with LYS 377 (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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168E GLU* 4.2 17.7 + - - -
356E GLY* 3.3 34.1 + - - +
357E GLY* 4.3 2.6 - - - +
359E ALA* 4.1 10.0 - - + +
360E LEU* 3.8 33.1 - - + +
363E ARG* 6.3 1.3 - - + -
373E LEU 3.1 11.6 + - - +
374E GLY* 3.1 13.0 + - - +
376E ILE* 1.3 76.9 - - - +
378E ASP* 1.3 61.7 + - - +
380E PHE* 3.1 2.9 + - - +
381E ASP* 2.8 54.6 + - - +
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Residues in contact with ASP 378 (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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76D LYS* 3.4 30.2 + - - +
374E GLY* 2.9 18.6 + - - +
375E LYS* 3.8 21.1 + - - +
376E ILE 3.3 0.2 - - - -
377E LYS* 1.3 82.7 - - - +
379E ALA* 1.3 63.0 + - - +
381E ASP* 4.0 7.3 - - - +
382E ARG* 3.0 47.1 + - - +
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Residues in contact with ALA 379 (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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375E LYS 3.1 5.8 + - - +
376E ILE 3.5 9.0 - - - +
377E LYS 3.2 0.4 - - - -
378E ASP* 1.3 78.4 - - - +
380E PHE* 1.3 58.4 + - - +
382E ARG* 3.2 34.3 - - - +
383E ASN* 3.5 7.3 + - - +
386E LEU* 3.7 14.2 - - + +
389E LEU* 4.0 11.0 - - + -
392E ASP* 3.8 9.9 - - - +
395E PHE* 3.6 29.2 - - + -
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Residues in contact with PHE 380 (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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339E PHE* 3.6 33.4 - + + -
343E ARG* 5.9 0.4 - - - -
355E TYR* 3.7 36.1 - + + -
356E GLY* 3.8 21.5 - - - +
376E ILE* 3.1 47.2 + - + +
377E LYS 3.8 0.2 - - - +
379E ALA* 1.3 77.7 - - - +
381E ASP* 1.3 60.4 + - - +
383E ASN 3.7 5.8 - - - -
384E PRO* 3.0 35.4 - - + +
386E LEU* 3.9 33.0 - - + -
388E ASN* 6.2 0.2 - - - -
389E LEU* 3.6 23.8 - - + -
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Residues in contact with ASP 381 (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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34D ARG* 5.5 1.2 - - - +
75D VAL* 6.1 0.3 - - - +
76D LYS* 4.7 20.9 + - + +
80D ALA* 4.9 3.3 - - - +
354E ASN* 5.5 1.2 - - - +
356E GLY* 4.8 5.8 - - - -
377E LYS* 2.8 60.3 + - - +
378E ASP* 4.0 7.4 + - - +
380E PHE* 1.3 70.7 - - - +
382E ARG* 1.3 64.6 + - - +
383E ASN 3.1 2.9 + - - -
384E PRO* 3.5 14.3 - - - +
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Residues in contact with ARG 382 (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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34D ARG* 4.8 3.8 + - - +
76D LYS* 5.3 3.0 - - + +
79D GLN* 4.4 28.0 - - - +
80D ALA* 3.7 33.4 - - + +
83D ASP* 3.3 21.9 - - - +
375E LYS 4.9 1.0 + - - -
378E ASP* 3.0 38.6 + - - +
379E ALA* 3.2 23.4 - - - +
381E ASP* 1.3 76.1 - - - +
383E ASN* 1.3 62.3 + - + +
384E PRO* 4.0 2.4 - - - +
392E ASP* 2.9 39.6 + - - +
394E PHE* 4.2 15.7 - - - +
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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