Contacts of the strand formed by residues 79 - 86 (chain A) in PDB entry 1KRB
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ILE* 3.1 10.9 - - - +
78A PRO* 1.3 92.9 - - - +
80A ILE* 1.3 70.6 + - - +
81A GLN* 3.6 28.1 + - - +
94A THR* 4.6 5.2 - - + -
95A VAL 3.0 15.9 - - - +
96A HIS* 4.0 19.3 + - + +
98A PRO* 4.0 2.9 - - - -
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Residues in contact with ILE 80 (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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35A SER 4.9 0.2 - - - -
36A VAL* 3.8 31.0 - - + +
39A ILE* 3.8 39.3 - - + -
40A SER* 3.7 20.2 - - - +
43A ILE* 4.4 19.9 - - + +
77A ILE* 3.6 20.0 - - + -
79A ASP* 1.3 78.7 - - - +
81A GLN* 1.3 71.1 + - - +
82A VAL* 5.4 0.2 - - + -
93A VAL 3.6 1.4 - - - +
94A THR* 3.5 0.7 - - - -
95A VAL* 2.9 37.8 + - + +
98A PRO* 4.1 5.6 - - + -
469C GLN* 5.2 1.6 - - + -
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Residues in contact with GLN 81 (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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79A ASP* 3.6 19.8 + - - +
80A ILE* 1.3 81.8 - - - +
82A VAL* 1.3 65.3 + - - +
92A LEU* 3.9 10.3 - - + +
93A VAL 3.2 6.1 - - - +
94A THR* 3.1 30.2 + - + +
465C ILE* 3.6 18.2 - - - +
467C THR* 2.9 35.5 + - - +
468C PRO* 3.3 10.2 - - + +
469C GLN* 2.9 30.7 + - - +
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Residues in contact with VAL 82 (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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10A LYS* 4.9 0.7 - - - -
13A LEU* 3.9 28.7 - - + -
40A SER* 4.0 15.0 - - - +
43A ILE* 3.6 42.2 - - + -
44A MET* 4.0 12.1 - - + -
81A GLN* 1.3 76.8 - - - +
83A GLU* 1.3 75.7 + - - +
84A ALA* 5.9 0.2 - - + -
92A LEU* 4.2 0.6 - - - +
93A VAL* 3.0 29.7 + - - +
468C PRO* 4.1 6.9 - - - +
469C GLN* 3.9 11.4 - - + +
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Residues in contact with GLU 83 (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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10A LYS* 2.9 23.1 + - - +
44A MET* 4.4 1.6 - - - +
82A VAL* 1.3 86.6 - - - +
84A ALA* 1.3 63.1 + - - +
90A SER* 4.4 15.5 - - - -
91A LYS* 3.2 18.8 - - - +
92A LEU* 3.7 20.2 - - + +
93A VAL* 6.2 0.2 - - - -
460C ASP* 4.1 11.4 + - - +
462C ASN* 4.1 6.9 + - - +
463C ALA* 3.6 23.6 + - + +
464C SER* 2.7 34.5 + - - -
468C PRO* 4.3 11.0 - - + +
469C GLN 5.0 0.2 + - - -
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Residues in contact with ALA 84 (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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10A LYS* 4.6 4.5 - - - +
43A ILE* 4.9 2.7 - - + +
44A MET* 4.0 27.8 - - + +
47A ALA* 3.6 24.2 - - + -
82A VAL* 5.9 0.2 - - + -
83A GLU* 1.3 77.2 - - - +
85A THR* 1.3 59.9 + - - +
86A PHE* 3.3 9.2 - - + -
90A SER* 3.3 5.7 - - - -
91A LYS 3.3 25.5 + - - -
93A VAL* 6.0 0.4 - - + +
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Residues in contact with THR 85 (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 ALA* 3.8 14.7 - - - +
48A ARG* 4.4 5.7 + - - -
84A ALA* 1.3 73.5 - - - +
86A PHE* 1.3 71.3 + - - +
89A GLY* 4.0 11.9 - - - -
90A SER* 4.2 11.1 + - - +
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Residues in contact with PHE 86 (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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43A ILE* 5.4 0.2 - - + -
47A ALA* 3.5 30.1 - - + -
51A LYS 3.1 28.0 - - - -
52A SER* 4.7 1.1 - - - -
53A VAL* 3.8 18.6 - - + -
56A LEU* 3.7 10.5 - - + -
84A ALA* 3.3 19.3 - - + -
85A THR* 1.3 85.0 - - - +
87A PRO* 1.3 75.7 - - + +
88A ASP* 3.0 17.5 + - - +
89A GLY 2.9 20.7 + - - +
91A LYS* 3.5 35.4 - - + -
93A VAL* 3.6 26.5 - - + -
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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