Contacts of the strand formed by residues 46 - 58 (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 SER 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B ILE* 4.3 4.3 + - - +
42B LYS* 3.6 2.8 - - - +
43B ARG* 3.2 42.1 + - - +
44B GLY 3.7 4.3 - - - +
45B ARG* 1.3 79.2 - - - +
47B ASN* 1.3 62.8 + - - +
48B LEU* 4.3 16.5 - - - +
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Residues in contact with ASN 47 (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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40B LYS* 2.8 51.0 + - - +
41B ILE 3.6 2.9 - - - -
42B LYS* 3.4 33.7 - - - +
45B ARG 3.6 6.1 + - - +
46B SER* 1.3 78.1 + - - +
48B LEU* 1.3 63.0 + - - +
49B LEU 3.8 1.6 + - - -
87B GLN* 4.4 1.0 - - - +
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Residues in contact with LEU 48 (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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40B LYS* 3.1 6.9 - - - -
41B ILE* 2.9 50.7 + - + +
46B SER* 4.3 14.8 - - - +
47B ASN* 1.3 74.0 - - - +
49B LEU* 1.3 68.5 + - - +
50B TRP* 3.2 19.1 + - + +
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Residues in contact with LEU 49 (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* 3.8 32.1 - - + +
39B VAL 4.2 2.5 - - - +
40B LYS* 4.1 13.3 - - + +
47B ASN 3.8 4.2 + - - -
48B LEU* 1.3 72.5 - - - +
50B TRP* 1.3 69.4 + - - +
51B ASP 4.1 3.1 - - - +
52B THR* 3.5 35.9 - - + +
155B TYR* 5.5 1.3 - - - +
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Residues in contact with TRP 50 (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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39B VAL* 2.8 25.1 + - + +
41B ILE* 3.8 39.5 - - + +
48B LEU* 3.2 20.1 + - + +
49B LEU* 1.3 84.3 - - - +
51B ASP* 1.3 65.7 + - - +
79B GLN* 3.6 25.1 + - - -
86B PHE* 4.7 3.5 - + - -
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Residues in contact with ASP 51 (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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37B TYR* 4.2 2.1 + - - -
39B VAL* 2.7 41.6 + - + +
49B LEU* 3.9 1.3 - - - +
50B TRP* 1.3 82.2 - - - +
52B THR* 1.3 77.3 + - - +
74B TRP* 4.1 18.3 - - + -
79B GLN* 2.4 34.3 + - - +
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Residues in contact with THR 52 (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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9B MET 4.8 0.2 - - - +
10B GLU* 5.5 4.1 + - - +
37B TYR* 3.3 21.5 + - - -
38B GLU* 3.7 16.2 - - + +
49B LEU* 3.5 34.8 - - + -
51B ASP* 1.3 85.8 + - - +
53B GLY* 1.3 60.7 + - - +
159B ASN* 6.5 0.4 - - + -
160B PHE* 4.2 9.2 - - + -
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Residues in contact with GLY 53 (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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8B PRO* 4.8 0.2 - - - -
9B MET 3.2 13.5 - - - -
10B GLU* 4.3 8.1 - - - -
36B CYS* 3.5 0.5 - - - -
37B TYR* 3.0 45.4 + - - +
52B THR* 1.3 78.5 - - - +
54B VAL* 1.3 68.7 + - - +
160B PHE* 3.8 3.9 - - - -
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Residues in contact with VAL 54 (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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8B PRO* 3.4 4.4 - - - +
9B MET* 2.9 45.0 + - + +
10B GLU 3.8 18.6 - - - +
11B ARG* 4.2 6.3 - - - +
12B MET* 4.2 9.6 - - + -
34B TRP* 3.4 37.7 - - + -
35B LEU 3.3 9.4 - - - +
36B CYS* 4.1 4.7 - - - -
37B TYR* 3.7 1.4 - - - -
53B GLY* 1.3 81.2 - - - +
55B PHE* 1.3 67.1 + - - +
160B PHE* 3.9 25.1 - - + +
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Residues in contact with PHE 55 (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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7B ASN* 3.7 26.9 - - - -
8B PRO* 3.5 24.0 - - + -
9B MET* 5.9 0.2 - - - -
33B THR 3.9 0.3 - - - +
34B TRP* 3.5 3.0 - - - -
35B LEU* 2.8 42.1 + - + +
37B TYR* 3.3 34.1 - + - -
54B VAL* 1.3 78.8 - - - +
56B ARG* 1.3 61.5 + - - +
67B ALA* 4.4 13.0 - - + +
70B CYS* 3.7 27.8 - - + -
71B PHE* 3.8 25.8 - + + -
74B TRP* 3.5 29.2 - + + -
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Residues in contact with ARG 56 (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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9B MET* 5.6 4.7 - - - -
32B TYR* 3.5 59.7 + - + -
33B THR 3.4 3.6 - - - +
34B TRP* 3.3 51.1 - - + +
55B PHE* 1.3 76.8 - - - +
57B GLY* 1.3 60.5 + - - +
67B ALA* 4.4 2.9 - - - -
70B CYS* 4.4 11.4 - - - -
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Residues in contact with GLY 57 (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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32B TYR* 3.2 16.1 - - - +
33B THR* 2.9 29.1 + - - -
56B ARG* 1.3 74.5 - - - +
58B GLN* 1.3 64.0 + - - -
65B TYR 3.5 12.1 - - - -
67B ALA* 3.7 15.7 - - - +
70B CYS* 5.0 1.8 - - - -
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Residues in contact with GLN 58 (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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31B SER* 3.6 17.6 + - - +
32B TYR* 3.4 29.7 + - - -
33B THR* 4.3 4.7 + - - -
57B GLY* 1.3 75.6 - - - -
59B VAL* 1.3 62.5 + - - +
60B TYR 3.1 19.2 + - - +
61B PHE* 3.4 29.9 - - + -
65B TYR* 2.9 29.3 + - + +
66B HIS* 3.3 21.5 - - + +
67B ALA 4.3 1.7 + - - -
68B GLU* 5.2 0.2 - - - +
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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