Contacts of the strand formed by residues 55 - 59 (chain A) in PDB entry 2Y96
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 VAL 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A THR* 3.0 15.3 + - - -
54A HIS* 1.3 77.6 - - - +
56A ASN* 1.3 67.5 + - - +
63A TYR* 3.8 31.9 - - + -
64A ILE 3.4 13.2 - - - +
65A GLY* 3.8 7.9 - - - -
69A THR* 3.6 29.2 - - + +
81A PHE* 5.3 2.9 - - + -
144A LEU* 3.9 3.4 - - + -
181A ARG* 3.5 0.2 - - - +
1208A SO4 3.1 17.7 + - - +
1211A SO4 3.9 7.1 + - - +
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Residues in contact with ASN 56 (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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51A GLN* 3.6 18.8 + - - +
53A THR* 2.9 20.1 + - - +
55A VAL* 1.3 72.2 - - - +
57A GLU* 1.3 66.0 + - - +
58A VAL* 3.5 2.1 + - - +
63A TYR* 3.2 6.8 - - - -
64A ILE 3.0 30.9 + - - +
151A ARG* 4.7 0.2 + - - -
180A ASN 3.1 27.0 + - - +
181A ARG* 2.8 44.4 + - + +
1211A SO4 2.8 27.0 + - - +
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Residues in contact with GLU 57 (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 ASN* 1.3 71.3 - - - +
58A VAL* 1.3 57.7 + - - +
59A TRP 3.3 18.6 - - - +
60A PRO* 3.7 6.1 - - - +
61A LYS* 3.0 28.2 + - - +
62A LEU 3.6 6.5 - - - +
63A TYR* 3.5 32.2 + - + -
180A ASN* 3.3 21.8 - - - +
1211A SO4 3.1 24.3 + - - +
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Residues in contact with VAL 58 (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 ASN 3.7 10.5 - - - +
57A GLU* 1.3 76.4 - - - +
59A TRP* 1.3 64.1 - - + +
62A LEU* 2.9 25.8 + - + +
64A ILE* 3.8 34.5 - - + +
158A VAL* 4.1 10.5 - - + -
162A LEU* 5.4 0.2 - - - +
176A GLN* 3.0 27.3 + - - +
177A VAL* 4.4 14.1 - - + +
180A ASN* 3.4 27.0 + - + +
181A ARG* 3.9 21.3 - - + -
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Residues in contact with TRP 59 (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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57A GLU* 3.3 8.6 - - - +
58A VAL* 1.3 77.2 - - + +
60A PRO* 1.3 103.1 - - + +
61A LYS 3.1 1.0 + - - -
62A LEU* 2.9 37.4 + - + +
136A LEU* 4.2 17.3 - - + +
158A VAL* 5.9 0.2 - - + -
161A TYR* 4.5 4.5 + + - -
162A LEU* 3.9 15.5 - - + -
166A LYS* 3.7 40.7 - - + +
168A MET* 3.4 29.6 - - + -
176A GLN* 3.6 32.5 - - + +
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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