Contacts of the strand formed by residues 61 - 65 (chain A) in PDB entry 1ESQ
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 ALA 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU 3.4 3.1 + - - +
20A VAL* 3.6 10.6 - - + +
21A HIS* 2.8 30.7 + - - +
59A ALA* 3.3 2.8 - - - +
60A GLY* 1.3 83.3 - - - +
62A LEU* 1.3 61.3 + - - +
89A VAL* 3.6 8.5 - - - -
90A PRO* 3.7 8.7 - - + +
205A GLY* 3.1 39.9 - - - +
206A ALA 4.4 0.7 - - - +
209A ALA* 3.9 4.5 - - + +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 3.4 43.7 - - + +
23A ILE* 4.2 4.7 - - + -
56A ALA* 4.5 4.5 - - + -
61A ALA* 1.3 73.8 - - - +
63A VAL* 1.3 65.9 + - - +
64A LEU* 3.8 25.4 - - + -
80A ALA* 3.5 33.7 - - + +
81A GLY* 3.6 12.6 - - - +
84A ALA* 3.8 15.3 - - + -
89A VAL* 3.7 3.8 - - + +
90A PRO 2.9 12.0 + - - +
91A VAL* 3.2 11.2 - - + -
92A ILE* 2.9 25.5 + - - +
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Residues in contact with VAL 63 (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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20A VAL* 4.0 15.5 - - + -
21A HIS 2.9 7.3 + - - +
22A SER* 3.5 13.3 - - - +
23A ILE 3.1 25.6 + - - +
24A THR* 6.2 0.9 - - - -
62A LEU* 1.3 79.3 - - - +
64A LEU* 1.3 73.0 + - - +
65A ASN* 5.0 5.6 - - + +
92A ILE* 3.3 12.8 - - + +
198A SER 5.4 0.2 - - - +
201A THR* 3.9 23.8 - - + +
202A SER* 3.9 33.2 - - - +
205A GLY* 4.1 16.2 - - - -
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.6 11.9 - - + -
62A LEU* 3.8 23.8 - - + -
63A VAL* 1.3 83.1 - - - +
65A ASN* 1.3 57.1 + - - +
77A MET* 3.9 45.3 - - + +
81A GLY* 5.0 2.5 - - - -
91A VAL* 4.0 22.4 - - + -
92A ILE 2.8 14.2 + - - +
93A LEU* 3.5 13.2 - - + +
94A ASP* 2.7 34.0 + - - +
111A ILE* 3.9 26.0 - - + -
115A VAL* 5.0 1.3 - - + -
117A LEU* 5.0 2.0 - - + -
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Residues in contact with ASN 65 (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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23A ILE 3.0 9.3 + - - +
24A THR* 3.1 36.9 + - - +
25A ASN* 3.0 12.1 + - - -
63A VAL* 5.2 5.2 - - + -
64A LEU* 1.3 75.4 - - - +
66A ILE* 1.3 62.5 + - - +
67A GLY 2.8 18.2 + - - -
69A LEU 5.6 0.2 + - - -
77A MET* 3.2 15.1 - - - +
94A ASP* 3.6 16.2 + - + +
96A VAL* 3.5 15.0 - - - +
198A SER* 3.0 33.9 + - - +
201A THR* 5.7 0.4 - - - -
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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