Contacts of the strand formed by residues 979 - 982 (chain A) in PDB entry 1YO8
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 TRP 979 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962A PHE* 3.6 39.6 - + + -
964A MSE 4.0 22.8 - - + +
977A PRO* 3.5 18.6 - - + +
978A ASN* 1.3 77.6 + - - +
980A VAL* 1.3 61.4 + - - +
981A ILE* 4.2 6.7 + - - +
988A LEU* 3.8 22.9 - - + -
989A VAL 3.6 2.7 - - - -
990A GLN* 3.7 23.3 - - + -
997A GLY 4.4 2.5 - - - -
998A ILE 4.3 5.2 + - - -
999A ALA* 3.6 27.8 - - + +
1152A LEU* 3.7 25.6 - - + -
1154A VAL* 3.5 30.5 - - + -
1162A PHE* 3.6 26.9 - + - -
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Residues in contact with VAL 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978A ASN* 4.4 9.6 - - - +
979A TRP* 1.3 74.0 - - - +
981A ILE* 1.3 64.6 + - - +
982A ARG* 3.8 28.8 + - - +
987A GLU 3.8 0.2 - - - +
988A LEU* 3.3 5.6 - - - -
989A VAL* 2.9 49.0 + - + +
991A THR* 4.1 16.6 - - - +
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Residues in contact with ILE 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960A ARG* 3.8 27.4 - - + +
962A PHE* 3.5 34.5 - - + -
979A TRP 4.6 4.9 - - - +
980A VAL* 1.3 80.2 - - - +
982A ARG* 1.3 69.1 + - - +
984A GLN* 5.5 0.2 - - - -
985A GLY* 3.7 30.7 - - - +
987A GLU 3.5 2.2 - - - -
988A LEU* 3.8 15.7 - - + -
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Residues in contact with ARG 982 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A PRO 3.9 4.6 + - - -
725A ASN* 4.0 2.6 - - - +
729A GLU* 3.5 23.2 + - + +
738A ASP* 6.5 0.4 - - - -
739A ALA* 3.4 34.1 - - - +
980A VAL* 3.8 25.5 - - + +
981A ILE* 1.3 76.8 - - - +
983A HIS* 1.3 73.5 + - - +
984A GLN* 3.0 4.8 + - - -
985A GLY 3.0 11.7 + - - -
987A GLU* 2.7 52.3 + - - +
989A VAL* 4.1 17.6 - - - +
1161A TYR* 3.5 25.1 + - - -
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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