Contacts of the strand formed by residues 57 - 63 (chain A) in PDB entry 6R4E
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 ILE 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE 3.5 9.4 - - - +
43A ASP* 4.3 4.3 - - - +
54A ALA 5.5 0.9 - - - +
55A CYS 4.1 0.8 + - - -
56A LYS* 1.3 71.6 - - - +
58A GLN* 1.3 67.2 + - - +
59A LEU* 4.2 4.5 - - + -
115A ASN 5.0 2.5 + - - +
116A ASN* 3.0 59.5 + - + +
117A GLU 4.5 0.4 - - - +
119A ILE* 3.7 27.6 - - + -
190A LYS* 4.1 29.8 - - + +
191A SER* 4.0 11.7 - - - -
192A VAL* 3.6 32.1 - - + +
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Residues in contact with GLN 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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41A GLY* 3.5 3.5 - - - -
42A PHE* 2.6 70.4 + - + +
44A GLY* 4.1 13.9 - - - -
56A LYS 3.7 1.2 + - - -
57A ILE* 1.3 75.4 - - - +
59A LEU* 1.3 82.4 + - - +
60A ILE* 4.2 8.1 - - + +
76A GLN* 5.4 4.9 + - - -
79A MET* 4.8 6.0 - - + +
116A ASN* 4.8 1.3 + - - +
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Residues in contact with LEU 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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40A VAL 3.5 1.8 - - - +
41A GLY* 3.7 17.9 - - - -
57A ILE* 4.2 2.2 + - + -
58A GLN* 1.3 102.0 + - - +
60A ILE* 1.3 64.8 + - - +
61A LYS* 4.1 16.2 - - + -
109A PRO* 3.8 31.2 - - + +
111A ARG* 4.3 12.8 - - + +
116A ASN* 4.0 29.6 - - - +
119A ILE* 3.8 30.1 - - + -
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Residues in contact with ILE 60 (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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39A GLY* 3.2 3.3 - - - -
40A VAL* 3.0 38.5 + - + +
42A PHE* 3.9 13.9 - - + -
58A GLN* 4.2 7.6 - - - +
59A LEU* 1.3 80.1 - - - +
61A LYS* 1.3 62.2 + - - +
69A LEU* 3.4 17.1 - - + +
72A GLU* 3.8 28.7 - - + -
73A VAL* 4.4 17.0 - - + -
76A GLN* 4.0 20.9 - - + +
79A MET* 3.6 31.0 - - + -
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Residues in contact with LYS 61 (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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38A ALA 3.6 4.9 - - - -
59A LEU* 4.1 14.9 - - + +
60A ILE* 1.3 84.9 - - - +
62A LYS* 1.3 65.3 + - - +
72A GLU* 5.9 0.7 - - - +
104A PRO* 3.3 24.7 + - - +
105A VAL* 3.6 15.9 + - - +
107A SER* 2.7 41.4 + - - +
108A HIS 3.3 19.7 - - - +
109A PRO* 3.2 28.4 + - + +
110A GLN* 3.9 5.7 + - - +
111A ARG* 5.4 4.2 - - - +
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Residues in contact with LYS 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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37A SER* 3.4 1.6 - - - -
38A ALA 3.0 31.7 + - - +
61A LYS* 1.3 78.8 - - - +
63A LYS* 1.3 75.1 + - - +
64A GLY* 3.7 1.8 + - - +
68A ALA* 3.8 40.8 + - + +
69A LEU* 4.1 14.5 - - + +
71A GLU* 5.8 2.0 + - - +
72A GLU* 3.4 33.3 + - + +
104A PRO* 4.7 8.3 - - + -
107A SER* 4.1 6.3 + - - -
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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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36A ASP* 3.5 12.1 - - - +
37A SER* 3.7 7.4 - - - -
62A LYS* 1.3 89.5 - - - +
64A GLY* 1.3 61.4 + - - +
68A ALA* 5.3 0.7 - - - +
102A PRO* 3.5 41.2 + - + +
103A SER* 4.2 17.5 - - - +
104A PRO* 4.6 10.4 - - + +
107A SER* 4.5 1.2 + - - -
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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