Contacts of the helix formed by residues 392 - 407 (chain B) in PDB entry 3DRW
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 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B TYR* 3.5 56.0 + - + -
390B ASN* 2.6 19.4 + - - +
391B GLU* 1.3 76.3 - - + +
393B SER* 1.3 56.8 + - - +
394B GLU 3.3 2.9 - - - -
395B TYR* 3.1 26.8 + - + +
396B VAL* 2.8 38.8 + - + +
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Residues in contact with SER 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PHE* 3.7 10.2 - - - +
390B ASN* 2.7 22.5 + - - -
391B GLU 3.3 2.2 - - - -
392B ARG* 1.3 76.5 - - - +
394B GLU* 1.3 64.8 + - - +
396B VAL* 3.2 4.0 + - - +
397B LYS* 3.0 24.7 + - - +
418B PRO* 3.1 42.0 - - - +
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Residues in contact with GLU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B GLU 4.8 3.9 + - - +
392B ARG 3.3 0.2 - - - -
393B SER* 1.3 79.8 - - - +
395B TYR* 1.3 63.9 + - - +
397B LYS* 3.4 17.1 + - + +
398B LEU* 3.0 35.2 + - + +
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ARG* 3.4 32.0 - - + +
394B GLU* 1.3 76.0 - - - +
396B VAL* 1.3 70.7 + - + +
398B LEU* 3.2 11.3 + - + +
399B ARG* 2.9 75.4 + - + +
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 3.7 6.2 - - + +
338B TYR* 4.2 29.4 - - + +
339B TYR* 3.8 21.3 - - + -
392B ARG* 2.8 26.1 + - + +
393B SER* 3.2 7.6 + - - +
395B TYR* 1.3 82.8 - - + +
397B LYS* 1.3 52.2 + - - +
399B ARG* 3.2 6.7 + - - +
400B PHE* 2.8 35.5 + - - +
416B VAL* 3.6 30.5 - - + -
417B ILE 5.2 4.9 - - - -
418B PRO* 5.2 3.1 - - + -
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Residues in contact with LYS 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B SER 3.0 16.3 + - - +
394B GLU* 3.5 18.4 - - + +
396B VAL* 1.3 79.1 - - - +
398B LEU* 1.4 63.9 + - + +
400B PHE* 3.1 12.7 + - + +
401B GLU* 3.0 37.5 + - + +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B GLU* 3.0 30.2 + - + +
395B TYR* 3.2 11.2 + - + +
397B LYS* 1.4 76.0 - - + +
399B ARG* 1.3 83.5 + - - +
401B GLU* 3.1 8.5 + - + +
402B GLU* 2.9 23.9 + - - +
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Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 3.9 19.3 - - + +
314B GLU* 5.4 1.8 + - - +
395B TYR* 2.9 76.7 + - + +
396B VAL* 3.6 5.4 - - - +
398B LEU* 1.3 96.5 + - - +
400B PHE* 1.3 57.2 + - - +
402B GLU* 2.6 44.8 + - - +
403B ALA* 2.9 29.6 + - - +
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Residues in contact with PHE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LEU* 3.6 9.4 - - + +
317B ILE* 3.7 13.7 - - + -
396B VAL 2.8 17.5 + - - +
397B LYS* 3.4 12.1 - - + +
398B LEU 3.1 0.2 - - - -
399B ARG* 1.3 74.9 - - - +
401B GLU* 1.3 69.3 + - - +
403B ALA* 3.3 2.9 + - - +
404B LYS* 3.1 60.2 + - + +
414B VAL* 3.6 37.2 - - + -
415B VAL* 4.9 0.9 - - - -
416B VAL* 3.6 47.6 - - + -
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Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LYS* 3.0 31.2 + - + +
398B LEU* 3.7 9.2 - - + +
400B PHE* 1.3 82.0 - - + +
402B GLU* 1.3 63.8 + - - +
404B LYS* 3.1 34.6 + - - +
405B SER* 3.2 21.5 + - - -
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Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 5.1 1.7 - - + +
398B LEU 2.9 15.3 + - - +
399B ARG* 2.6 46.9 + - - +
401B GLU* 1.3 74.2 - - - +
403B ALA* 1.3 64.5 + - - +
405B SER* 3.1 17.2 + - - -
406B ARG* 3.2 56.7 + - - +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LEU* 5.1 0.2 - - + -
314B GLU* 3.9 34.1 - - + +
317B ILE* 3.8 25.8 - - + -
399B ARG 2.9 18.4 + - - +
400B PHE 3.3 5.6 + - - +
402B GLU* 1.3 75.8 - - - +
404B LYS* 1.3 58.8 + - - +
406B ARG* 3.1 1.7 + - - -
407B LEU* 2.9 37.8 + - + +
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Residues in contact with LYS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ILE* 5.7 0.7 - - + -
400B PHE* 3.1 55.1 + - + +
401B GLU* 3.1 41.4 + - - +
403B ALA* 1.3 77.2 - - + +
405B SER* 1.3 61.8 + - - +
407B LEU 3.2 16.5 - - - +
409B MET* 3.8 36.8 - - + +
414B VAL* 5.5 1.1 - - + +
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Residues in contact with SER 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B GLU 3.2 12.4 + - - -
402B GLU* 3.1 13.8 + - - -
404B LYS* 1.3 78.6 - - - +
406B ARG* 1.3 61.0 + - - +
407B LEU 4.8 0.7 - - - +
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Residues in contact with ARG 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 2.8 39.3 + - - +
402B GLU* 3.2 50.2 + - - +
403B ALA 3.1 6.7 + - - +
405B SER* 1.3 79.8 - - - +
407B LEU* 1.3 64.3 + - - +
408B ARG 4.2 0.5 + - - -
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 3.5 45.3 - - + +
317B ILE* 3.7 25.8 - - + -
318B LEU* 4.0 30.5 - - + +
321B MET* 3.9 11.0 - - + -
403B ALA 2.9 21.3 + - - +
404B LYS 3.2 14.6 - - - +
405B SER 4.8 0.3 - - - +
406B ARG* 1.3 83.4 - - - +
408B ARG* 1.3 61.1 - - - +
409B MET* 3.0 19.6 + - - +
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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