Contacts of the strand formed by residues 88 - 93 (chain A) in PDB entry 1YC3
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 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE 3.9 0.6 - - - +
83A ASN* 2.7 41.1 + - - +
86A ASP* 2.6 42.1 + - - +
87A ARG* 1.3 81.5 - - - +
89A LEU* 1.3 57.8 + - - +
90A THR* 4.3 7.0 + - - -
187A ILE* 3.9 20.2 - - + +
188A LEU 3.1 8.3 - - - +
189A HIS* 3.7 27.6 - - + +
190A LEU* 4.7 0.4 - - - +
198A LEU* 3.4 6.8 - - - +
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Residues in contact with LEU 89 (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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44A PHE* 3.9 33.9 - - + -
45A LEU* 4.7 10.3 - - + -
80A LEU* 4.9 6.5 - - + -
81A ILE 3.8 3.4 - - - +
82A PRO* 3.9 26.9 - - + -
88A THR* 1.3 74.3 - - - +
90A THR* 1.3 68.9 + - - +
91A ILE* 3.8 13.3 - - + +
186A VAL 3.5 2.3 - - - +
188A LEU* 2.9 39.8 + - + +
190A LEU* 4.6 5.8 - - + +
197A TYR* 3.7 18.6 - - + +
198A LEU* 4.1 10.1 - - + -
203A ILE* 4.2 12.6 - - + -
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Residues in contact with THR 90 (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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79A ASN 3.7 0.5 - - - +
80A LEU* 3.4 4.2 - - - -
81A ILE* 2.8 54.6 + - + +
88A THR* 4.3 6.6 + - - -
89A LEU* 1.3 75.5 + - - +
91A ILE* 1.3 67.5 + - - +
92A VAL* 3.5 25.6 - - + -
185A LYS* 3.5 23.1 - - + -
186A VAL 3.3 5.4 - - - +
187A ILE* 3.8 20.8 - - + +
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Residues in contact with ILE 91 (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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45A LEU* 4.2 12.8 - - + -
48A LEU* 4.0 23.3 - - + -
49A ILE* 4.8 4.0 - - + -
52A SER* 4.0 15.5 - - - +
78A ILE* 4.0 15.0 - - + -
79A ASN 3.5 2.7 - - - -
80A LEU* 3.6 27.1 - - + -
89A LEU* 3.8 19.7 - - + +
90A THR* 1.3 79.0 - - - +
92A VAL* 1.3 62.4 + - - +
93A ASP* 5.4 0.2 - - - +
184A THR 3.8 1.4 - - - +
185A LYS* 3.2 1.7 - - - -
186A VAL* 2.7 51.5 + - + +
188A LEU* 4.0 20.0 - - + -
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Residues in contact with VAL 92 (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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77A HIS* 5.3 1.3 + - + -
78A ILE* 3.2 5.0 - - - +
79A ASN* 2.7 52.3 + - + +
81A ILE* 3.7 17.3 - - + -
90A THR* 3.5 27.6 - - + -
91A ILE* 1.3 76.1 - - - +
93A ASP* 1.3 73.4 + - - +
94A THR* 5.8 3.6 - - + -
180A MET* 5.2 7.2 - - - -
184A THR 3.5 6.7 - - - +
185A LYS* 3.5 22.2 - - + -
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Residues in contact with ASP 93 (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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52A SER* 2.8 36.8 + - - -
56A LEU* 4.2 4.0 - - + -
77A HIS* 3.3 12.1 - - - +
78A ILE* 4.2 3.1 - - + -
91A ILE 5.4 0.3 - - - +
92A VAL* 1.3 82.2 - - - +
94A THR* 1.3 61.9 + - - +
95A GLY* 2.8 27.1 + - - +
180A MET* 5.7 0.3 - - - +
182A ARG 3.9 1.0 - - - +
183A GLY* 3.3 2.8 - - - -
184A THR* 2.9 37.5 + - - +
237A 4BC 2.6 34.5 + - - -
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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