Contacts of the helix formed by residues 60 - 64 (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 LEU 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B PRO* 2.8 28.6 + - + +
59B PRO* 1.3 77.7 - - - +
61B GLY* 1.3 70.7 + - - +
62B PRO* 3.1 3.9 - - - +
63B LEU* 2.9 19.3 + - - +
114B GLU* 3.4 48.5 - - + +
115B ASP* 4.1 5.6 - - + +
3384B SO4 5.0 2.2 - - - +
280C ALA* 3.8 16.4 - - + +
281C VAL* 4.7 6.7 - - + +
284C HIS* 3.8 39.3 - - + +
3385C SO4 4.0 10.1 + - - +
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 1.3 73.3 - - - +
62B PRO* 1.3 67.3 - - - +
63B LEU 3.0 5.7 + - - -
64B ARG* 3.2 23.0 + - - +
114B GLU* 4.8 3.6 + - - -
287B ARG* 4.1 16.1 - - - +
3384B SO4 5.3 2.7 + - - -
284C HIS* 3.6 21.6 + - - -
288C GLN* 5.7 0.9 - - - -
3385C SO4 4.8 0.4 - - - -
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Residues in contact with PRO 62 (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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60B LEU 3.6 4.0 - - - +
61B GLY* 1.3 81.1 - - - +
63B LEU* 1.3 66.4 + - + +
64B ARG 3.3 2.5 - - - -
66B THR* 3.4 8.0 - - - +
287B ARG* 3.4 25.6 + - - -
3284B SO4 4.3 16.6 + - - +
3385C SO4 4.6 12.3 - - - +
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Residues in contact with LEU 63 (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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57B LYS* 3.8 33.0 - - + +
58B PRO 3.5 20.9 - - - +
59B PRO* 3.8 15.6 - - + +
60B LEU 2.9 13.6 + - - +
62B PRO* 1.3 83.3 - - + +
64B ARG* 1.3 63.1 + - - +
65B PHE 3.5 1.6 + - - -
66B THR* 3.2 27.6 + - + +
67B PRO 5.2 1.1 - - - +
69B GLN* 3.2 35.9 - - + +
171B ARG* 3.9 5.7 + - - -
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Residues in contact with ARG 64 (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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59B PRO 4.0 14.3 + - - +
60B LEU 5.1 0.2 - - - -
61B GLY* 3.2 18.8 + - - +
63B LEU* 1.3 76.9 - - - +
65B PHE* 1.3 99.2 + - + +
66B THR* 3.2 0.9 - - - +
114B GLU* 2.7 40.0 + - - -
171B ARG* 5.0 2.2 - - - +
175B TRP* 4.1 13.3 - - + +
286B LEU 2.9 19.3 + - - -
287B ARG* 2.6 47.7 + - + +
289B LYS 2.7 31.3 + - - -
291B GLU* 4.0 5.3 - - - +
294B LEU* 3.8 13.8 - - - +
3384B SO4 3.8 12.3 + - - -
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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