Contacts of the helix formed by residues 366 - 379 (chain E) in PDB entry 1RHQ
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 PHE 366 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D PHE* 6.2 2.0 - + - -
279D LEU* 4.0 11.0 - - + -
281D ILE* 5.9 8.1 - - + -
328E LEU* 3.0 34.5 - - + -
330E ALA* 5.9 1.1 - - + -
357E LEU* 5.5 7.6 - - + -
365E GLU* 1.3 89.7 - - - +
367E MET* 1.3 70.3 + - + +
368E HIS 3.1 1.1 - - - +
369E ILE* 2.9 17.0 + - + +
370E LEU* 2.5 58.7 + - + +
394E LEU* 5.1 1.8 - - + -
398E LEU* 3.3 24.2 - - + +
400E PHE* 3.2 38.8 - + - -
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Residues in contact with MET 367 (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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367B MET* 4.7 28.9 - - + +
368B HIS* 5.1 1.6 - - + -
371B THR* 5.3 8.7 - - - +
389B ILE* 6.1 1.3 - - - -
328E LEU* 3.7 20.6 - - + -
365E GLU* 3.3 17.4 + - - +
366E PHE* 1.3 106.8 - - + +
368E HIS* 1.3 59.9 + - + +
370E LEU* 2.7 37.3 + - + +
371E THR* 2.9 18.0 + - - +
389E ILE* 4.0 15.3 - - + +
392E SER* 3.9 27.8 - - - +
394E LEU* 4.1 7.2 - - + -
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Residues in contact with HIS 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B GLU* 2.7 44.9 + - + +
367B MET* 5.2 0.9 - - + -
368B HIS* 3.1 39.5 + + - -
397B GLU* 3.3 31.1 + - + +
399B TYR* 4.0 9.2 - - - -
364E LEU* 4.3 16.8 - - + +
365E GLU* 3.8 19.7 + - + +
366E PHE 3.8 0.2 - - - +
367E MET* 1.3 84.1 - - + +
369E ILE* 1.3 59.8 + - - +
371E THR* 3.6 17.0 + - - -
372E ARG* 4.0 13.7 + - - +
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Residues in contact with ILE 369 (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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353E LEU* 6.0 2.0 - - + -
356E MET* 4.4 21.5 - - + +
357E LEU* 4.5 22.7 - - + +
360E TYR* 3.7 24.2 - - + +
361E ALA* 3.9 14.4 - - - -
364E LEU* 3.6 22.7 - - + -
365E GLU 2.9 31.9 - - - +
366E PHE* 2.9 18.0 + - + +
368E HIS* 1.3 75.8 - - - +
370E LEU* 1.3 64.2 + - + +
371E THR 3.1 1.4 + - - -
372E ARG* 3.3 14.2 + - - +
373E VAL* 3.4 15.4 + - + +
400E PHE* 5.1 2.0 - - + -
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Residues in contact with LEU 370 (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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328E LEU* 4.2 1.3 - - + -
330E ALA* 3.8 25.8 - - + -
349E PHE* 5.0 4.5 - - + -
353E LEU* 4.4 22.0 - - + -
366E PHE* 2.5 51.2 + - + +
367E MET* 2.7 21.8 + - + +
369E ILE* 1.3 72.5 - - + +
371E THR* 1.3 54.1 + - - -
373E VAL* 3.2 16.1 - - + +
374E ASN* 3.1 26.0 + - - +
389E ILE* 3.2 38.4 - - + -
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Residues in contact with THR 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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367B MET* 5.3 9.2 - - - +
392B SER* 5.6 1.8 + - - +
394B LEU* 4.1 9.9 - - + +
395B THR 3.6 3.3 - - - +
396B LYS* 3.4 43.1 - - - +
397B GLU* 4.3 6.6 - - + +
367E MET 2.9 13.8 + - - -
368E HIS* 3.8 12.7 + - - -
369E ILE 3.1 0.8 + - - -
370E LEU* 1.3 75.5 - - - +
372E ARG* 1.3 60.1 + - - +
374E ASN* 3.4 9.9 - - - +
375E ARG* 2.8 26.3 + - - +
389E ILE* 4.3 6.9 - - - +
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Residues in contact with ARG 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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151A ASN* 2.8 48.5 + - - +
397B GLU* 5.0 7.3 + - - +
356E MET* 4.0 15.9 - - - -
360E TYR* 3.7 39.9 + - - -
364E LEU* 3.8 35.6 - - - +
368E HIS 4.0 11.1 + - - +
369E ILE 3.3 5.2 + - - +
371E THR* 1.3 75.7 - - - +
373E VAL* 1.3 57.6 + - - +
374E ASN 3.2 0.2 - - - -
375E ARG* 3.3 32.3 - - + +
376E LYS* 2.3 41.5 + - + +
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Residues in contact with VAL 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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349E PHE* 3.4 46.2 - - + +
352E SER* 4.4 3.1 - - - +
353E LEU* 3.6 29.8 - - + +
356E MET* 4.1 22.6 - - + +
369E ILE* 3.4 17.9 - - + +
370E LEU* 3.2 15.0 - - + +
372E ARG* 1.3 80.2 - - - +
374E ASN* 1.3 64.3 + - - +
376E LYS* 3.1 5.3 + - - +
377E VAL* 2.8 26.0 - - - +
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Residues in contact with ASN 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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392B SER 4.1 4.0 - - - +
394B LEU 3.6 21.3 - - - +
395B THR* 4.8 1.1 - - - -
349E PHE* 5.0 1.4 - - - -
370E LEU* 3.1 15.0 + - - +
371E THR* 3.4 7.1 - - - +
373E VAL* 1.3 78.6 - - - +
375E ARG* 1.3 63.4 + - - +
377E VAL* 3.0 2.8 + - - +
378E ALA* 2.9 26.2 + - - +
386E ILE* 4.3 7.9 - - + -
387E PRO* 3.3 45.9 - - + +
389E ILE* 2.9 34.6 - - - +
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Residues in contact with ARG 375 (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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150A ASP 4.1 4.4 + - - -
151A ASN* 3.0 41.0 + - - +
395B THR* 2.6 51.0 + - - +
396B LYS* 3.7 27.8 - - - +
371E THR* 2.8 17.7 + - - +
372E ARG* 3.3 37.0 - - + +
374E ASN* 1.3 76.7 - - - +
376E LYS* 1.3 54.1 + - + +
377E VAL 2.8 6.1 + - - -
378E ALA* 3.8 0.4 - - - -
379E THR* 2.3 50.3 + - + +
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Residues in contact with LYS 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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351E GLN* 6.4 0.4 - - - +
352E SER* 3.9 19.2 - - - +
355E ALA* 2.8 36.6 - - - +
356E MET* 3.5 27.4 - - + +
372E ARG* 2.3 32.4 + - + +
373E VAL* 3.7 3.6 - - - +
375E ARG* 1.3 67.4 - - + +
377E VAL* 1.3 59.7 + - - +
379E THR* 3.4 45.1 - - + +
380E PHE* 3.2 22.4 - - + -
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Residues in contact with VAL 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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348E TRP* 4.0 32.8 - - + -
349E PHE* 4.2 7.2 - - - -
352E SER* 3.1 26.9 - - - +
373E VAL* 2.8 26.2 - - + +
374E ASN 3.0 3.6 + - - +
375E ARG 3.0 1.0 - - - -
376E LYS* 1.3 79.7 - - - +
378E ALA* 1.3 65.0 + - - +
379E THR 3.3 1.1 - - - -
380E PHE* 3.5 19.5 - - + +
384E LYS* 3.4 13.2 + - - -
385E GLN* 3.8 24.2 - - + +
387E PRO* 4.2 13.2 - - + -
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Residues in contact with ALA 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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320B LYS 4.4 0.3 - - - +
321B ILE* 4.2 7.6 - - + +
322B PRO* 3.3 34.4 - - + +
325B ALA* 4.8 0.9 - - + -
395B THR* 4.1 20.9 - - + -
374E ASN 2.9 15.9 + - - +
375E ARG 3.9 2.0 - - - +
377E VAL* 1.3 79.3 - - - +
379E THR* 1.3 63.6 + - + +
384E LYS* 3.2 23.4 + - - -
385E GLN 3.9 3.3 + - - +
386E ILE* 4.4 5.6 - - + -
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Residues in contact with THR 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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320B LYS 5.1 3.3 - - - +
321B ILE* 5.2 11.7 - - + -
395B THR* 6.3 2.0 - - - -
396B LYS* 6.2 0.4 - - - +
375E ARG* 2.3 48.5 + - + +
376E LYS* 3.6 4.9 - - - -
378E ALA* 1.3 86.2 - - + +
379E GLU* 1.3 68.3 + - - +
380E PHE 3.4 6.6 + - - +
384E LYS* 4.9 1.6 - - - -
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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