Contacts of the strand formed by residues 86 - 94 (chain B) in PDB entry 5TKM
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 PHE 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 3.7 23.1 - - + -
40B LYS 3.3 1.8 - - - +
41B ILE* 3.4 29.4 - - + -
42B LYS* 5.2 0.9 - - - -
50B TRP* 4.7 2.5 - + - -
75B PHE* 4.0 17.9 - + + -
79B GLN* 3.8 30.3 - - + -
80B LEU* 3.9 20.4 - - + -
82B ALA* 3.8 16.6 - - + -
84B LYS* 3.5 28.0 - - + -
85B CYS* 1.3 73.8 - - - +
87B GLN* 1.3 59.6 + - - +
88B ILE* 4.0 5.2 - - + -
113B ASN* 2.9 10.6 + - - +
114B VAL* 3.5 23.1 - - + -
115B THR* 3.0 27.9 + - - +
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLU 3.6 2.6 - - - +
40B LYS* 2.8 66.0 + - + +
42B LYS* 3.1 48.9 - - + +
47B ASN* 4.4 1.2 - - - +
85B CYS 4.1 0.6 + - - -
86B PHE* 1.3 73.8 - - - +
88B ILE* 1.3 63.0 + - - +
89B THR* 3.5 22.1 + - - +
115B THR* 3.6 16.8 - - - +
117B THR* 5.3 7.4 - - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLU 3.5 7.6 - - - +
39B VAL* 4.6 5.4 - - + -
71B PHE* 3.7 23.3 - - + -
75B PHE* 3.9 31.9 - - + -
86B PHE* 4.6 3.8 - - + -
87B GLN* 1.3 77.7 - - - +
89B THR* 1.3 59.3 + - - +
90B TRP* 3.5 31.4 - - + +
107B PHE* 4.8 5.4 - - + -
114B VAL* 3.6 26.0 - - + -
115B THR 2.8 15.8 + - - +
116B LEU* 3.3 13.0 - - + -
117B THR* 2.8 32.4 + - - +
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B CYS 3.7 0.2 - - - +
37B TYR* 3.2 5.2 - - - -
38B GLU* 2.9 46.9 + - + +
40B LYS* 5.5 1.0 - - - +
87B GLN* 3.5 23.5 + - - -
88B ILE* 1.3 73.0 + - - +
90B TRP* 1.3 69.6 + - - +
91B PHE* 3.6 36.0 - - + -
117B THR* 3.5 17.3 - - + +
119B SER* 5.7 0.7 - - - +
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Residues in contact with TRP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.6 29.1 - - + +
36B CYS 3.2 3.1 - - - +
37B TYR* 3.8 4.0 - - + -
68B GLU* 3.5 32.1 - - + -
71B PHE* 3.5 36.8 - + - -
72B LEU* 5.8 0.2 - - + -
88B ILE* 3.5 21.6 - - + +
89B THR* 1.3 84.2 - - - +
91B PHE* 1.3 67.9 + - - +
92B VAL* 3.8 18.6 - - + -
96B PRO* 4.5 2.0 - - + -
104B LEU* 3.8 31.4 - - + -
116B LEU* 3.9 15.3 - - + -
117B THR 2.8 14.5 + - - +
118B ILE* 3.7 32.5 - - + -
119B SER* 3.0 25.8 + - - +
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 3.9 7.8 - - + -
34B TRP 3.7 1.0 - - - +
35B LEU* 3.7 1.2 - - - -
36B CYS* 2.7 44.6 + - + +
38B GLU* 5.0 4.3 - - + -
89B THR* 3.6 29.6 - - + -
90B TRP* 1.3 74.6 - - - +
92B VAL* 1.3 59.9 + - - +
119B SER* 3.3 14.6 - - - -
148B MET* 4.2 7.6 - - + -
152B GLU* 3.9 37.9 - - + -
155B TYR* 4.1 23.1 - + - -
156B CYS* 3.4 31.9 - - - -
160B PHE* 3.8 25.6 - + - -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 3.7 5.3 - - - -
33B THR* 4.7 3.8 - - + -
34B TRP 3.3 4.9 - - - +
35B LEU* 3.6 31.4 - - + -
68B GLU* 5.5 1.8 - - - +
90B TRP* 3.8 23.1 - - + -
91B PHE* 1.3 77.8 - - - +
93B SER* 1.3 59.5 + - - +
94B TRP 3.1 23.1 - - - +
95B THR* 4.5 0.7 - - - -
96B PRO* 5.6 0.7 - - + -
118B ILE* 3.7 16.8 - - + -
119B SER 2.9 16.7 + - - +
120B ALA* 3.7 11.7 - - + -
121B ALA* 2.8 26.0 + - - +
148B MET* 4.1 0.7 - - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASN* 3.2 30.0 - - - +
21B PHE* 3.8 14.1 - - - -
32B TYR 3.9 2.6 + - - -
33B THR* 3.5 6.4 - - - -
34B TRP* 3.0 36.1 + - - +
92B VAL* 1.3 74.7 - - - +
94B TRP* 1.3 63.7 + - - +
121B ALA* 3.8 5.1 - - - +
122B ARG* 3.2 38.5 + - - +
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Residues in contact with TRP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PRO 4.9 0.2 - - - -
27B LEU* 3.8 11.2 - - + -
30B ARG* 3.0 35.3 + - + +
32B TYR 3.3 18.4 + - - -
33B THR* 3.4 26.2 - - - +
59B VAL* 3.4 16.9 - - + +
68B GLU* 4.2 1.9 - - - +
92B VAL* 3.1 22.0 - - - +
93B SER* 1.3 76.5 + - - +
95B THR* 1.3 70.0 + - - +
96B PRO* 4.6 0.2 - - - +
122B ARG* 3.2 61.1 - - + +
123B LEU 3.4 28.3 - - - -
124B TYR* 4.1 7.4 - + + +
125B TYR* 3.5 40.6 - + - -
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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