Contacts of the strand formed by residues 46 - 52 (chain A) in PDB entry 3KCC
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 SER 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ILE* 5.1 0.2 - - - -
45A GLY* 1.3 75.2 + - - -
47A VAL* 1.3 64.8 + - - +
64A LEU 3.3 5.8 - - - -
65A ASN* 2.7 24.7 + - - +
89A LYS* 2.8 45.1 + - - +
90A THR* 3.3 15.9 + - - +
92A CYS* 3.4 10.2 - - - -
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Residues in contact with VAL 47 (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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29A LEU* 4.2 14.8 - - + -
42A ILE* 3.9 16.2 - - + -
46A SER* 1.3 80.8 - - - +
48A ALA* 1.3 61.7 + - - +
49A VAL* 4.9 0.2 - - + -
63A TYR* 3.3 5.7 - - - +
64A LEU* 2.8 58.8 + - + +
70A ILE* 4.7 1.3 - - + -
86A VAL* 3.5 28.5 - - + -
87A ARG 3.2 12.8 - - - +
88A ALA* 4.1 4.5 - - - -
89A LYS* 3.5 11.3 - - - +
92A CYS* 3.9 16.2 - - - -
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Residues in contact with ALA 48 (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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47A VAL* 1.3 74.3 - - - +
49A VAL* 1.3 63.3 + - - +
50A LEU* 3.9 23.7 + - + +
60A ILE* 4.7 4.0 - - + -
62A SER 3.6 4.7 - - - +
63A TYR* 4.1 12.6 - - + -
85A TRP 3.7 0.7 - - - +
86A VAL* 3.3 4.4 - - - -
87A ARG* 2.9 36.0 + - + +
89A LYS* 3.8 18.1 - - + +
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Residues in contact with VAL 49 (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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47A VAL* 4.9 0.4 - - + -
48A ALA* 1.3 74.0 - - - +
50A LEU* 1.3 56.2 + - - +
60A ILE* 3.4 5.4 - - - -
61A LEU* 2.7 38.1 + - + -
62A SER* 2.8 23.8 + - - +
64A LEU* 3.7 31.9 - - + -
84A ALA* 3.8 13.2 - - + -
85A TRP 3.4 4.7 - - - +
86A VAL* 4.2 9.6 - - + -
301A CMP 3.5 51.8 - - + +
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Residues in contact with LEU 50 (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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48A ALA* 3.9 15.9 - - + +
49A VAL* 1.3 77.9 - - - +
51A ILE* 1.3 66.6 + - - +
52A LYS* 5.8 0.7 - - + -
58A GLU* 4.4 14.6 - - + +
59A MET 3.3 8.3 - - - +
60A ILE* 3.4 34.3 - - + +
61A LEU* 5.1 0.4 - - - -
84A ALA* 3.3 6.3 - - - +
85A TRP* 2.8 43.6 + - + +
87A ARG* 3.2 61.5 - - + +
174A GLN* 5.0 2.7 - - - +
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Residues in contact with ILE 51 (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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32A GLN* 4.2 7.2 - - - +
50A LEU* 1.3 78.7 - - - +
52A LYS* 1.3 65.5 + - - +
58A GLU* 3.3 5.7 - - - +
59A MET* 2.9 44.6 + - + +
61A LEU* 3.7 31.4 - - + -
83A SER 4.1 9.9 - - - +
84A ALA* 3.9 10.3 - - + -
85A TRP* 4.3 4.5 - - - -
128B SER* 3.8 17.5 - - - +
129B GLU* 5.5 1.3 - - - -
132B GLY* 3.7 31.6 - - - +
136B PHE* 4.2 4.9 - - + -
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Residues in contact with LYS 52 (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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32A GLN* 5.3 0.8 - - - +
50A LEU* 5.6 1.3 - - - -
51A ILE* 1.3 82.9 - - - +
53A ASP* 1.3 67.1 + - - +
56A GLY* 4.5 11.7 - - - +
57A LYS 3.0 8.5 - - - +
58A GLU* 3.7 19.4 + - + -
85A TRP* 3.6 53.5 - - + +
87A ARG* 3.7 27.2 - - - +
136B PHE* 3.6 11.6 - - - -
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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