Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 2Y1Z
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 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 4.1 17.5 - - + -
84A PHE* 3.9 17.0 - - + +
85A SER 3.7 15.3 - - - +
86A PRO* 3.3 16.6 + - + +
87A GLU 3.4 2.6 - - - +
88A GLU* 1.3 79.2 - - - +
90A LYS* 1.3 62.7 + - - +
101A HIS 3.5 5.4 - - - +
102A GLY* 4.1 2.9 - - - -
118A PHE* 3.8 33.4 - - + -
137A MET* 3.6 32.1 - - + -
143A LEU* 4.6 18.2 - - + -
1152A MRD 4.1 15.6 + - - +
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Residues in contact with LYS 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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89A LEU* 1.3 75.8 - - - +
91A VAL* 1.3 65.4 + - - +
92A LYS* 4.3 6.1 - - + -
99A GLU 3.7 0.7 - - - +
100A VAL* 3.5 5.7 - - - +
101A HIS* 3.0 40.7 + - + +
143A LEU* 5.8 0.2 - - - +
1152A MRD 5.3 0.7 - - - -
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Residues in contact with VAL 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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89A LEU 5.7 0.2 - - - -
90A LYS* 1.3 78.9 - - - +
92A LYS* 1.3 74.8 + - - +
93A VAL* 5.2 4.7 - - + -
98A ILE* 4.7 2.2 - - + -
99A GLU 3.4 6.3 - - - +
100A VAL* 4.0 15.7 - - + -
133A ILE* 5.9 0.7 - - + -
134A THR 5.9 0.2 - - - -
135A SER* 3.8 37.2 - - - +
143A LEU* 4.0 18.2 - - + -
145A VAL* 4.2 18.8 - - + -
1152A MRD 4.4 14.7 + - + +
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Residues in contact with LYS 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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90A LYS* 5.5 5.2 - - + -
91A VAL* 1.3 80.4 - - - +
93A VAL* 1.3 69.4 + - - +
94A LEU* 4.3 1.1 - - + -
98A ILE* 3.6 1.7 - - - +
99A GLU* 2.8 54.1 + - + +
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Residues in contact with VAL 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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91A VAL* 5.2 6.3 - - + -
92A LYS* 1.3 81.9 - - - +
94A LEU* 1.3 64.1 - - - +
95A GLY 4.3 4.5 - - - +
97A VAL 3.4 8.7 - - - +
98A ILE* 4.5 8.7 - - + -
124A ILE* 3.9 17.9 - - + -
130A PRO* 3.8 26.9 - - + +
133A ILE* 3.7 29.2 - - + -
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Residues in contact with LEU 94 (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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92A LYS* 4.3 1.7 - - + -
93A VAL* 1.3 74.3 - - - +
95A GLY* 1.3 65.7 + - - +
96A ASP 3.2 0.5 + - - -
97A VAL* 3.1 30.0 + - + +
99A GLU* 5.9 3.5 - - - +
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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