Contacts of the strand formed by residues 83 - 91 (chain A) in PDB entry 2K9U
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 GLY 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A PRO* 4.2 10.1 - - - -
82A PRO* 1.3 78.3 - - - +
84A ASP* 1.3 69.8 + - - +
85A TYR* 3.8 3.1 + - - -
104A PRO* 3.4 6.1 - - - +
105A VAL 3.3 24.2 + - - +
112A ALA* 5.2 2.8 - - - +
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Residues in contact with ASP 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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56A GLU 4.1 0.9 - - - +
57A GLY* 4.4 2.8 - - - -
58A PRO* 4.7 5.4 - - - +
83A GLY* 1.3 78.6 - - - +
85A TYR* 1.3 53.9 + - - +
86A GLU* 2.4 43.7 - - - +
102A VAL* 4.8 11.9 - - + -
103A VAL 4.7 1.1 - - - -
104A PRO* 4.7 7.7 - - + +
8B ARG* 4.4 10.5 + - - +
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Residues in contact with TYR 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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55A VAL* 5.4 5.4 - - + -
56A GLU 3.3 17.9 - - - -
57A GLY* 3.9 5.4 - - - -
58A PRO* 3.7 17.5 - - + -
59A SER* 2.3 58.2 + - - -
61A ALA* 3.9 23.8 + - + -
79A VAL* 4.2 18.2 - - + -
80A GLN 4.0 3.6 + - - -
81A GLU 3.8 16.3 + - - -
83A GLY 5.0 2.0 - - - -
84A ASP* 1.3 70.3 - - - +
86A GLU* 1.3 67.9 + - - +
102A VAL* 3.3 4.3 - - - -
103A VAL* 2.8 53.2 + - + +
105A VAL* 4.0 17.5 - - + -
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Residues in contact with GLU 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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54A ALA 3.4 2.3 - - - +
55A VAL* 3.3 4.0 - - - -
56A GLU* 2.8 64.4 + - + +
84A ASP* 2.4 38.6 - - - +
85A TYR* 1.3 83.6 - - - +
87A VAL* 1.3 61.1 + - - +
100A PRO* 4.5 13.2 - - + -
101A PHE 3.2 11.9 - - - +
102A VAL* 4.7 4.0 - - - +
103A VAL* 6.1 0.2 - - - -
8B ARG* 3.0 29.9 + - - -
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Residues in contact with VAL 87 (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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28A LEU* 5.6 4.7 - - + -
39A PHE* 6.2 5.8 - - + -
53A ILE* 3.5 29.8 - - + -
54A ALA 3.4 3.6 - - - +
55A VAL* 3.7 16.4 - - + -
86A GLU* 1.3 76.5 - - - +
88A SER* 1.3 63.9 + - - +
89A ILE* 3.9 15.6 + - + -
99A SER* 3.9 1.4 - - - -
100A PRO* 3.3 3.2 - - - +
101A PHE* 2.8 51.2 + - + +
103A VAL* 5.1 11.8 - - + +
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Residues in contact with SER 88 (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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52A SER 3.0 13.2 - - - +
53A ILE* 3.5 0.8 - - - -
54A ALA* 3.1 38.6 + - - +
87A VAL* 1.3 76.6 - - - +
89A ILE* 1.3 61.7 + - - +
90A LYS* 3.7 18.7 + - - -
99A SER* 3.1 20.2 - - - -
100A PRO* 4.6 7.2 - - - -
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Residues in contact with ILE 89 (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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21A VAL* 4.6 12.8 - - + -
23A ALA* 4.3 19.1 - - + -
39A PHE* 5.4 7.4 - - + -
41A ILE* 4.8 17.5 - - + -
51A LEU* 4.6 15.3 - - + -
52A SER 3.4 7.0 - - - +
53A ILE* 4.4 9.9 - - + -
87A VAL* 3.9 26.9 - - + -
88A SER* 1.3 75.8 - - - +
90A LYS* 1.3 61.7 + - - +
94A GLU 3.9 0.3 - - - +
95A HIS* 3.6 12.5 - - - -
96A ILE* 3.4 38.4 + - + +
99A SER* 3.8 4.5 - - - -
101A PHE* 5.5 3.4 - - + -
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Residues in contact with LYS 90 (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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21A VAL* 6.3 0.2 - - - -
50A GLY 3.2 6.2 - - - +
51A LEU* 3.3 13.1 - - - +
52A SER* 3.4 36.3 + - - +
54A ALA* 5.7 0.9 - - - +
88A SER* 3.7 34.8 + - - -
89A ILE* 1.3 75.2 - - - +
91A PHE* 1.3 60.1 + - - +
92A ASN 3.1 5.9 + - - -
93A ASP* 3.5 22.9 - - - +
94A GLU 3.3 10.3 - - - +
95A HIS* 3.3 39.2 - - + +
99A SER* 4.5 0.2 + - - -
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Residues in contact with PHE 91 (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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20A LYS* 2.9 29.2 - - - -
21A VAL* 3.5 22.4 - - + +
43A THR* 4.4 9.0 - - - -
46A ALA* 4.2 7.6 - - + -
47A GLY 3.0 28.7 - - - -
48A ALA 4.1 5.6 - - - -
49A GLY* 4.0 12.1 - - - -
50A GLY 3.2 14.4 - - - -
51A LEU* 4.0 17.1 - - + +
90A LYS* 1.3 67.4 - - - +
92A ASN* 1.3 64.5 + - + +
93A ASP 3.3 0.2 - - - -
94A GLU* 2.6 60.2 + - + +
17B LEU* 3.5 35.0 - - + -
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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