Contacts of the strand formed by residues 97 - 101 (chain A) in PDB entry 1YI8
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 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLN* 3.2 23.7 + - - +
56A LEU* 3.5 35.4 - - + +
58A VAL* 3.9 23.8 - - + -
92A LEU* 3.9 15.1 - - + +
93A ASP 3.0 10.1 + - - -
94A PRO 3.6 10.2 - - - +
96A LYS* 1.3 80.8 + - - +
98A THR* 1.3 60.8 + - - +
99A CYS 3.8 3.0 + - - +
323A PHE* 4.2 12.0 - - + -
330A ARG* 2.7 23.9 + - - -
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Residues in contact with THR 98 (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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56A LEU 3.1 13.9 + - - -
57A PHE* 3.5 35.6 - - + -
58A VAL 3.0 24.6 + - - +
96A LYS 5.4 0.2 + - - -
97A THR* 1.3 75.2 - - - +
99A CYS* 1.3 59.7 + - - +
100A VAL* 3.5 5.9 + - + +
327A GLY* 3.4 18.8 - - - +
330A ARG* 2.4 48.5 + - + +
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Residues in contact with CYS 99 (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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58A VAL* 3.5 14.8 - - + +
60A LEU* 3.7 22.9 - - - -
84A ALA* 4.9 0.2 - - - -
87A TYR* 4.7 3.8 - - - -
97A THR 3.8 3.4 + - - -
98A THR* 1.3 72.4 - - - +
100A VAL* 1.3 62.3 + - - +
323A PHE* 3.4 43.8 + - + +
324A VAL* 3.3 33.8 - - - +
327A GLY* 3.0 26.0 - - - -
328A THR 3.1 3.1 + - - -
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Residues in contact with VAL 100 (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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26A LEU* 6.4 0.2 - - + -
57A PHE* 4.2 9.9 - - + -
58A VAL 2.8 14.1 + - - +
59A LEU* 3.4 13.8 - - + -
60A LEU* 2.6 36.3 + - - +
98A THR* 3.6 19.7 - - + +
99A CYS* 1.3 80.3 - - - +
101A VAL* 1.3 67.2 + - - +
102A GLN 3.4 1.9 + - - -
105A VAL* 4.2 9.6 - - + -
161A PHE* 3.9 23.8 - - + -
327A GLY 3.6 13.2 - - - +
328A THR* 3.9 16.8 - - + +
331A GLY* 4.1 8.3 - - - -
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Residues in contact with VAL 101 (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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60A LEU* 4.3 16.6 - - + +
62A ASP* 3.5 25.4 - - - +
80A VAL* 4.4 15.0 - - + -
100A VAL* 1.3 74.4 - - - +
102A GLN* 1.3 55.3 + - - +
103A SER* 4.7 0.2 - - - -
104A ALA* 2.7 44.9 + - + +
105A VAL* 3.6 5.0 + - - +
324A VAL* 4.1 24.2 - - + -
328A THR* 3.0 21.4 + - - +
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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