Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 2L89
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 ASP 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ARG 3.7 22.6 - - - +
50A LEU* 4.6 2.9 - - - -
51A ASN* 3.1 35.6 + - - +
52A PHE 3.2 1.0 - - - +
53A GLY* 1.3 76.1 - - - +
55A ARG* 1.3 75.0 + - - +
56A ILE* 3.1 8.9 + - + +
69A LEU* 3.6 2.9 - - - +
70A LEU* 3.0 21.4 + - - +
111A LEU 4.5 5.7 + - - +
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Residues in contact with ARG 55 (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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53A GLY 4.0 1.5 + - - +
54A ASP* 1.3 73.1 + - - +
56A ILE* 1.3 61.5 + - - +
68A ALA 3.6 9.0 - - - +
69A LEU* 3.6 25.7 - - + +
111A LEU* 2.9 37.0 + - + +
112A LEU* 4.5 1.6 - - - +
113A ASP* 2.9 47.0 + - - +
116A ILE* 3.5 31.2 - - + +
137A SER* 3.5 20.8 + - - +
138A LYS* 3.9 5.7 + - - +
140A PRO* 3.5 38.1 - - + +
144A LYS* 6.1 1.0 - - - +
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Residues in contact with ILE 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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49A ARG 4.8 0.4 - - - +
50A LEU* 3.8 24.9 - - + -
54A ASP* 3.5 20.0 - - + +
55A ARG* 1.3 79.5 - - - +
57A LEU* 1.3 60.7 + - - +
68A ALA* 2.7 40.3 + - + +
70A LEU* 3.3 28.3 - - + +
90A TYR* 4.8 1.1 - - + -
92A VAL* 3.2 32.1 - - + -
108A VAL* 3.1 25.8 - - + -
109A LYS 3.5 11.9 - - - +
110A PRO* 4.4 4.3 - - + -
111A LEU* 3.9 6.1 - - - -
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Residues in contact with LEU 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 ILE* 1.3 73.0 - - - +
58A VAL* 1.3 60.8 + - - +
65A TRP* 3.2 34.5 - - + +
66A TRP 3.7 2.2 - - - +
67A PRO* 3.6 16.6 - - + -
108A VAL* 3.0 10.6 - - - +
109A LYS* 2.7 72.7 + - + +
111A LEU* 3.5 22.1 - - + +
134A TYR* 2.8 34.1 - - + +
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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
----------------------------------------------------------
57A LEU* 1.3 76.6 - - - +
59A LYS* 1.3 69.7 + - - +
60A ALA 3.4 1.0 + - - -
65A TRP* 3.9 3.6 - - - -
66A TRP* 2.7 39.9 + - - +
68A ALA* 3.6 11.9 - - + -
92A VAL* 4.1 7.2 - - + -
94A PHE* 3.2 38.1 - - + -
101A ALA* 5.3 2.0 - - + -
103A VAL* 3.2 36.3 - - + -
107A SER 3.2 8.5 - - - +
108A VAL* 3.8 6.5 - - + -
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Residues in contact with LYS 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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58A VAL* 1.3 78.4 - - - +
60A ALA* 1.3 67.0 + - - +
61A PRO* 4.0 1.9 - - - +
63A TYR 3.8 12.6 - - - +
64A PRO* 3.9 10.3 - - + -
65A TRP* 3.5 45.6 - - + +
103A VAL* 5.1 6.1 - - - +
107A SER* 3.0 27.3 + - - +
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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