Contacts of the strand formed by residues 61 - 65 (chain A) in PDB entry 2F5O
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 PHE 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ARG* 3.3 7.4 - - - +
58A ARG* 2.9 39.9 + - + +
60A LYS* 1.3 80.9 - - - +
62A LEU* 1.3 60.5 + - - +
63A LYS* 6.2 0.7 - - + -
72A ILE* 3.9 11.0 - - + -
73A SER 3.5 4.7 - - - +
74A HIS* 3.4 38.4 - + + -
76A ARG* 5.0 0.7 - - - -
116A THR* 4.9 2.9 - - - -
130A PRO* 3.4 51.8 - - + -
131A LEU* 3.8 23.1 - - + -
134A LEU* 4.3 18.6 - - + -
166A CYS* 6.2 0.9 - - + -
9C A 4.0 21.8 - - - -
10C T 4.2 5.8 - - - -
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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
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7A VAL* 3.6 29.4 - - + +
10A ILE* 3.9 22.9 - - + -
11A ARG* 3.8 30.5 - - + -
55A LEU* 4.1 12.6 - - + -
56A GLU 3.4 7.9 - - - +
57A ARG* 4.5 1.6 - - + -
60A LYS 3.9 1.7 + - - +
61A PHE* 1.3 74.1 - - - +
63A LYS* 1.3 60.1 + - - +
64A PHE* 4.0 14.5 - - + -
71A LEU 3.5 1.2 - - - +
72A ILE* 3.4 3.6 - - - +
73A SER* 2.9 37.5 + - - +
75A LEU* 4.4 14.1 - - + -
81A TYR* 4.2 22.4 - - + -
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Residues in contact with LYS 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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55A LEU* 3.4 4.8 - - - -
56A GLU* 2.7 56.5 + - + +
57A ARG* 5.1 1.8 - - - +
58A ARG* 4.7 13.7 - - + +
61A PHE* 4.1 1.3 + - + +
62A LEU* 1.3 74.1 - - - +
64A PHE* 1.3 61.2 + - - +
65A LEU* 3.5 24.6 + - + +
70A ALA* 4.1 19.7 - - + -
71A LEU 3.5 2.9 - - - -
72A ILE* 4.5 9.0 - - + +
122A LYS 5.5 2.4 + - - -
125A ALA* 4.8 7.6 - - - +
126A ASP* 2.6 38.4 + - - -
131A LEU* 3.7 18.6 - - + -
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Residues in contact with PHE 64 (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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14A LEU* 3.8 14.4 - - + -
18A ILE* 3.6 32.1 - - + -
52A VAL* 5.2 4.7 - - + -
54A GLY 3.7 5.2 - - - +
55A LEU* 3.5 22.4 - - + -
62A LEU* 4.1 16.2 - - + -
63A LYS* 1.3 73.2 - - - +
65A LEU* 1.3 59.0 + - - +
66A LEU* 3.4 12.9 - - + +
70A ALA* 3.2 7.1 - - - +
71A LEU* 2.8 64.9 + - + +
73A SER* 4.1 4.0 - - - -
81A TYR* 3.7 38.6 - + - -
106A LEU* 3.7 16.8 - - + -
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Residues in contact with LEU 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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52A VAL* 3.6 0.7 - - - +
53A ARG* 2.7 35.7 + - + -
54A GLY* 2.9 31.6 + - - +
56A GLU* 3.5 32.8 - - + +
63A LYS* 3.8 31.4 - - + +
64A PHE* 1.3 72.8 - - - +
66A LEU* 1.3 61.3 + - - +
69A ASP 4.1 1.6 - - - -
70A ALA* 4.5 4.3 - - + -
122A LYS* 4.0 22.7 - - + +
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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