Contacts of the helix formed by residues 331 - 336 (chain B) in PDB entry 1YA8
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 THR 331 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B LYS* 3.5 37.2 - - + -
323B ILE* 3.3 17.8 - - + +
330B LYS* 1.3 79.5 - - - +
332B PRO* 1.3 65.4 - - - +
333B GLU* 3.3 13.4 - - - +
334B GLU* 2.7 41.5 + - - +
335B LEU* 3.0 21.7 + - - +
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Residues in contact with PRO 332 (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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229B VAL* 6.0 0.7 - - + -
232B LEU* 3.9 20.4 - - + +
250B ALA* 3.7 42.6 - - + +
251B LEU* 4.1 4.9 - - + -
256B VAL* 4.3 12.3 - - + -
258B LYS* 4.2 7.2 - - - -
323B ILE* 4.2 9.2 - - + -
328B LEU* 4.9 10.8 - - + -
330B LYS 3.5 1.3 - - - +
331B THR* 1.3 80.6 - - - +
333B GLU* 1.3 78.7 + - - +
334B GLU 3.1 1.8 - - - -
335B LEU* 4.3 1.3 - - + -
336B GLN* 3.0 29.8 + - - +
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Residues in contact with GLU 333 (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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250B ALA 4.0 2.8 - - - +
251B LEU* 3.3 44.5 - - + +
253B SER* 4.5 1.3 + - - -
258B LYS* 2.7 42.0 + - - +
331B THR* 3.3 12.2 - - - +
332B PRO* 1.3 74.4 - - - +
334B GLU* 1.3 63.8 + - + +
336B GLN* 3.2 17.3 + - - +
337B ALA* 4.0 6.1 + - - +
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Residues in contact with GLU 334 (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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330B LYS* 3.9 31.6 + - + +
331B THR* 2.7 32.2 + - - +
332B PRO 3.1 0.4 - - - -
333B GLU* 1.3 76.1 - - + +
335B LEU* 1.3 56.4 + - - +
337B ALA* 2.7 37.5 + - - +
338B GLU* 4.7 1.6 - - - +
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Residues in contact with LEU 335 (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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232B LEU* 4.1 36.7 - - + +
234B PRO* 6.2 0.7 - - + -
328B LEU* 3.4 25.4 - - + -
329B LEU* 4.7 9.6 - - + +
330B LYS* 3.2 51.6 - - + +
331B THR 3.0 6.3 + - - +
332B PRO* 3.4 4.5 + - + +
334B GLU* 1.3 78.1 - - - +
336B GLN* 1.3 58.0 + - - +
338B GLU* 3.0 46.9 + - - +
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Residues in contact with GLN 336 (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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232B LEU* 4.5 13.6 - - + +
251B LEU* 3.2 40.8 - - - +
332B PRO 3.0 18.7 + - - +
333B GLU* 3.2 13.2 + - - +
334B GLU 3.0 0.2 + - - -
335B LEU* 1.3 75.5 - - - +
337B ALA* 1.3 56.3 + - + +
338B GLU 3.1 3.5 + - - -
339B ARG* 3.2 22.0 + - - -
432B ILE* 3.9 3.8 - - - +
433B VAL* 4.3 9.9 - - + +
436B ASN* 2.8 50.5 + - + +
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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