Contacts of the strand formed by residues 53 - 58 (chain A) in PDB entry 4M75
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 LYS 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ARG* 1.3 76.3 - - - +
54A ILE* 1.3 63.2 + - - +
65A PHE* 4.3 21.1 - - + +
66A GLY* 3.1 24.9 - - - +
67A VAL* 4.1 11.8 - - + +
81A ASP 5.9 0.4 + - - -
83A VAL* 5.7 5.3 - - - +
85A ARG* 4.9 6.3 - - - +
114A GLU* 3.5 6.4 - - - +
115A VAL* 2.9 39.5 + - + -
117A ILE* 5.8 10.1 - - + -
120A GLU* 3.8 24.8 + - - -
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Residues in contact with ILE 54 (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 SER* 3.6 36.8 - - - +
52A ARG* 5.1 0.2 - - + -
53A LYS* 1.3 80.5 - - - +
55A PHE* 1.3 61.4 + - - +
56A VAL* 3.9 22.8 - - + +
64A LEU 3.8 0.5 - - - +
65A PHE* 3.6 5.2 - - - -
66A GLY 2.7 35.8 + - - +
68A LEU* 3.9 37.2 - - + -
77A LEU* 4.8 3.4 - - + -
79A LEU* 4.0 8.5 - - + +
112A LEU* 4.5 13.0 - - + -
113A GLY 2.8 19.3 - - - +
114A GLU* 4.0 0.9 - - - -
115A VAL* 4.2 6.1 - - - +
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Residues in contact with PHE 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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54A ILE* 1.3 71.4 - - - +
56A VAL* 1.3 75.7 + - - +
57A LEU* 4.7 1.8 - - + -
63A MSE 5.3 0.2 - - - -
64A LEU 3.5 4.5 - - - +
65A PHE* 3.7 27.8 - - + -
111A MSE 3.8 32.5 - - + -
112A LEU* 3.0 28.3 - - - +
113A GLY* 2.5 42.9 + - - -
115A VAL* 4.2 3.6 - - + +
53B HIS* 3.6 26.9 - + + -
54B LEU* 3.7 16.8 - - + -
57B VAL* 3.7 25.6 - - + -
60B ILE* 3.7 22.0 - - + -
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Residues in contact with VAL 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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54A ILE* 3.9 21.1 - - + -
55A PHE* 1.3 84.3 - - - +
57A LEU* 1.3 62.0 + - - +
58A LEU* 3.8 24.2 + - + -
62A ARG 3.6 4.7 - - - +
63A MSE 3.7 2.5 - - - +
64A LEU* 2.8 42.2 + - + +
77A LEU* 4.7 4.0 - - + -
79A LEU* 4.2 19.7 - - + -
104A ILE* 3.9 12.3 - - + -
109A VAL* 3.9 23.6 - - + -
111A MSE 3.5 3.1 - - - +
112A LEU* 4.4 4.0 - - + -
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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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55A PHE* 4.7 3.4 - - + -
56A VAL* 1.3 73.0 - - - +
58A LEU* 1.3 77.8 + - - +
61A GLY* 4.0 15.9 - - - +
62A ARG 3.9 9.2 - - - +
63A MSE 4.8 9.2 - - - +
109A VAL* 3.5 5.2 - - - +
110A VAL* 2.7 57.2 + - + -
111A MSE 2.9 49.8 + - + +
172A TYR* 4.1 7.0 - - + -
19B LEU* 5.7 0.9 - - + -
51B TYR* 3.7 28.9 - - + +
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Residues in contact with LEU 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 VAL* 3.8 24.2 - - + -
57A LEU* 1.3 84.7 - - - +
59A ARG* 1.3 60.4 + - - +
60A ASP* 3.1 26.0 - - - +
61A GLY* 2.7 20.4 + - - -
62A ARG* 3.2 20.6 + - + +
64A LEU* 4.7 8.3 - - + -
104A ILE* 4.4 13.0 - - + -
108A ASN* 3.3 16.6 - - + +
109A VAL* 4.3 7.4 - - + -
110A VAL* 3.9 2.9 - - - -
172A TYR* 3.3 3.6 - - - +
77G LYS* 4.5 9.2 - - + -
78G PHE* 3.7 36.1 - - + -
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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