Contacts of the helix formed by residues 397 - 410 (chain B) in PDB entry 1Y8X
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 VAL 397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.5 29.8 - - + +
41A LEU* 4.4 13.5 - - + -
49A ILE* 3.7 25.4 - - + +
51A PHE* 4.2 9.2 - - + -
394B MSE 3.0 26.3 - - + +
395B GLN 3.2 3.1 - - - -
396B SER* 1.3 80.6 + - - +
398B THR* 1.3 62.6 + - - +
399B SER* 3.9 15.7 - - - +
400B ILE* 3.0 7.9 + - - +
401B GLU* 2.8 25.5 + - - +
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Residues in contact with THR 398 (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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48A ASP* 5.1 6.6 + - - -
49A ILE 5.6 0.5 + - - -
395B GLN 5.0 3.8 - - - +
396B SER 3.8 4.0 + - - +
397B VAL* 1.3 68.6 - - - +
399B SER* 1.3 69.0 + - - +
400B ILE 2.9 3.3 + - - -
401B GLU* 4.0 15.3 - - + -
402B GLU* 2.9 40.7 + - + +
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Residues in contact with SER 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE 3.8 22.4 + - - -
50A SER* 3.6 10.2 - - - -
51A PHE* 3.1 30.9 + - - +
54A PRO* 5.0 0.5 - - - +
397B VAL* 3.3 8.7 - - - +
398B THR* 1.3 82.1 + - - +
400B ILE* 1.3 59.1 + - - +
402B GLU* 4.4 4.8 - - - +
403B ARG* 4.1 29.1 + - - +
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Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 4.7 0.2 - - + -
51A PHE* 3.7 39.7 - - + -
54A PRO* 4.5 15.7 - - + +
57A LEU* 3.7 28.5 - - + -
391B THR* 4.3 9.2 - - + -
394B MSE 3.2 46.0 - - + -
397B VAL* 3.0 2.3 + - + -
398B THR 2.9 0.6 + - - -
399B SER* 1.3 78.8 - - - +
401B GLU* 1.3 60.4 + - - +
402B GLU 3.1 1.8 - - - -
403B ARG* 3.0 12.0 + - - +
404B THR* 2.7 40.6 + - + +
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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
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393B TYR* 2.7 29.1 + - - +
394B MSE 3.1 21.9 + - - +
395B GLN* 3.8 18.2 - - + +
397B VAL 2.8 14.8 + - - +
398B THR* 3.9 18.8 - - + +
400B ILE* 1.3 72.6 - - - +
402B GLU* 1.3 72.4 + - + +
404B THR* 3.3 4.5 - - - -
405B ARG* 2.5 65.6 + - - +
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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
----------------------------------------------------------
398B THR* 2.9 30.2 + - - +
399B SER* 4.4 6.2 - - - +
401B GLU* 1.3 94.4 - - + +
403B ARG* 1.3 62.6 + - + +
405B ARG* 4.3 13.1 + - - +
406B PRO* 4.3 10.4 - - - +
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Residues in contact with ARG 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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51A PHE 3.1 20.3 + - - -
52A SER* 2.8 32.1 + - - +
54A PRO* 3.4 33.5 - - + +
399B SER* 4.1 17.1 + - - +
400B ILE 3.0 5.4 + - - +
402B GLU* 1.3 81.7 - - + +
404B THR* 1.3 62.7 + - - +
405B ARG 3.6 0.2 - - - -
406B PRO* 4.1 9.8 - - - +
407B ASN* 4.3 4.2 + - - -
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Residues in contact with THR 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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54A PRO* 4.4 11.4 - - + -
390B ARG* 5.7 1.8 - - - +
391B THR 3.4 26.2 - - - +
392B LEU 3.3 11.4 - - - +
393B TYR* 3.2 21.3 - - - -
394B MSE 3.9 4.3 + - - -
400B ILE* 2.7 36.0 + - + +
401B GLU* 3.3 12.1 - - - -
403B ARG* 1.3 80.9 - - - +
405B ARG* 1.3 65.2 + - - +
406B PRO* 3.4 2.7 - - - -
407B ASN* 3.2 26.2 + - - +
408B LEU 4.0 0.2 + - - -
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Residues in contact with ARG 405 (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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393B TYR* 3.6 10.1 - - + +
401B GLU* 2.5 44.4 + - - +
402B GLU* 4.3 18.2 - - - +
404B THR* 1.3 74.4 - - - +
406B PRO* 1.3 72.5 - - + +
407B ASN 3.0 3.5 + - - -
408B LEU* 3.0 32.2 + - + +
409B SER* 3.8 3.1 + - - -
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Residues in contact with PRO 406 (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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402B GLU 4.3 6.5 - - - +
403B ARG* 4.1 9.2 - - - +
404B THR 3.4 9.0 - - - +
405B ARG* 1.3 96.3 - - + +
407B ASN* 1.3 59.0 + - - +
409B SER* 3.1 13.3 + - - -
410B LYS* 3.0 38.7 + - - +
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Residues in contact with ASN 407 (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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361B LEU* 3.0 34.3 - - + +
390B ARG* 5.3 12.8 + - - +
391B THR 4.4 3.4 + - - -
392B LEU* 3.0 22.0 + - - +
403B ARG 4.3 3.2 + - - -
404B THR* 3.2 28.6 + - - +
405B ARG 3.0 0.6 - - - -
406B PRO* 1.3 76.2 - - - +
408B LEU* 1.3 66.2 + - - +
409B SER 3.0 2.0 - - - -
410B LYS* 2.8 26.6 + - - +
415B LEU* 3.9 18.3 - - + +
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Residues in contact with LEU 408 (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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360B LYS* 3.7 4.9 - - - +
361B LEU* 3.2 21.7 + - + +
362B GLN* 3.0 54.9 + - + +
365B LEU* 3.7 20.4 - - + -
393B TYR* 3.5 63.0 - - + +
405B ARG* 3.0 24.4 + - + +
407B ASN* 1.3 78.8 - - - +
409B SER* 1.3 59.2 + - - +
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Residues in contact with SER 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LYS* 3.0 36.8 + - - +
362B GLN* 5.3 1.8 - - - -
405B ARG 4.6 2.7 - - - -
406B PRO* 3.1 15.8 + - - -
407B ASN 3.0 0.2 - - - -
408B LEU* 1.3 79.2 - - - +
410B LYS* 1.3 60.6 + - - +
411B THR* 5.4 0.3 - - - +
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Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LYS* 3.3 22.0 - - - +
361B LEU* 3.4 5.9 + - - +
406B PRO* 3.0 26.7 + - + +
407B ASN* 2.8 24.9 + - - +
409B SER* 1.3 82.5 - - - +
411B THR* 1.3 69.1 + - - +
414B GLU* 3.5 32.7 + - + +
415B LEU* 3.9 10.7 - - + +
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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