Contacts of the strand formed by residues 59 - 63 (chain A) in PDB entry 2F5Y
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 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MET* 5.7 1.2 - - - +
37A PRO* 3.3 36.3 - - + -
38A VAL 3.7 6.5 - - - +
39A ARG* 4.2 9.7 - - - +
57A LEU 3.2 8.5 + - - -
58A ASP* 1.3 72.1 - - - +
60A VAL* 1.3 63.8 + - - +
61A LEU* 3.7 9.8 + - + -
91A VAL* 3.2 5.6 - - - -
92A TRP* 2.8 56.8 + - + +
39B ARG* 4.9 4.5 + - - +
57B LEU* 5.2 4.5 - - + +
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 6.0 0.4 - - + -
32A ILE* 5.1 2.7 - - + -
37A PRO* 3.9 19.1 - - - +
38A VAL* 3.0 24.3 + - + +
39A ARG 4.8 1.1 - - - -
40A VAL* 4.2 24.5 - - + +
58A ASP 4.3 0.2 - - - +
59A THR* 1.3 73.1 - - - +
61A LEU* 1.3 63.6 + - - +
62A GLN 4.0 13.0 - - - +
68A VAL* 3.9 27.7 - - + +
69A GLU* 4.4 0.5 - - - -
76A LEU* 4.2 21.5 - - + -
89A LEU* 4.2 23.1 - - + -
90A LEU 4.0 4.3 - - - +
91A VAL* 4.4 5.8 - - + -
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.6 37.5 - - + -
37A PRO* 5.3 3.6 - - + -
59A THR* 4.0 16.8 - - + +
60A VAL* 1.3 80.3 - - - +
62A GLN* 1.3 60.5 + - + +
67A PRO* 3.5 2.4 - - - +
68A VAL* 2.8 24.2 + - - -
69A GLU* 3.3 35.5 + - + +
90A LEU* 3.0 23.5 + - + +
91A VAL 4.3 2.0 - - - -
92A TRP* 3.7 29.2 - - + +
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Residues in contact with GLN 62 (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 VAL* 3.7 2.3 - - - +
61A LEU* 1.3 81.1 - - + +
63A LEU* 1.3 60.3 + - - +
64A ASN 3.4 20.9 - - - +
65A GLU* 3.9 13.5 + - - -
66A ARG 3.3 18.2 - - - +
67A PRO* 4.0 16.6 - - - +
68A VAL* 3.8 4.5 - - - +
88A ILE 5.6 0.2 - - - +
89A LEU* 3.2 10.2 - - - +
90A LEU* 3.0 51.2 + - + +
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Residues in contact with LEU 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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62A GLN* 1.3 73.4 - - - +
64A ASN* 1.3 79.4 + - + +
66A ARG* 3.0 26.6 + - + +
68A VAL* 4.0 13.6 - - + +
71A TRP* 4.8 3.6 - - + -
76A LEU* 4.2 17.7 - - + -
79A GLU* 3.9 36.3 - - + +
80A ILE* 4.3 13.9 - - + +
83A CYS* 4.7 3.4 - - - -
87A ILE* 3.8 28.7 - - + -
88A ILE 3.7 0.9 - - - -
89A LEU* 3.4 23.8 - - + -
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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