Contacts of the strand formed by residues 46 - 58 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ILE 4.3 4.1 + - - -
42A LYS* 3.6 2.6 - - - +
43A ARG* 3.2 43.4 + - - +
44A GLY 3.7 4.2 - - - +
45A ARG* 1.3 79.4 - - - +
47A ASN* 1.3 63.5 + - - +
48A LEU* 4.3 16.6 - - - +
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Residues in contact with ASN 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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40A LYS* 2.8 50.1 + - - +
41A ILE 3.6 2.9 - - - -
42A LYS* 3.4 33.3 - - - +
45A ARG 3.6 6.8 + - - +
46A SER* 1.3 77.2 + - - +
48A LEU* 1.3 64.6 + - - +
49A LEU 3.8 2.4 + - - -
87A GLN* 4.4 1.2 - - - +
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Residues in contact with LEU 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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40A LYS* 3.1 6.6 - - - -
41A ILE* 2.9 49.6 + - + +
46A SER* 4.3 13.7 - - - +
47A ASN* 1.3 75.3 - - - +
49A LEU* 1.3 68.4 + - - +
50A TRP* 3.2 20.1 + - + +
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Residues in contact with LEU 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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38A GLU* 3.8 31.4 - - + +
39A VAL 4.2 2.7 - - - +
40A LYS* 4.1 13.5 - - + +
47A ASN 3.8 3.6 + - - -
48A LEU* 1.3 72.7 - - - +
50A TRP* 1.3 69.7 + - - +
51A ASP 4.1 3.8 - - - +
52A THR* 3.5 34.3 - - + +
155A TYR* 5.5 1.3 - - - +
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Residues in contact with TRP 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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39A VAL* 2.8 25.1 + - + +
41A ILE* 3.8 39.7 - - + +
48A LEU* 4.1 19.3 - - + +
49A LEU* 1.3 84.2 - - - +
51A ASP* 1.3 64.9 + - - +
79A GLN* 3.6 25.6 + - - -
86A PHE* 4.7 3.1 - + - -
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Residues in contact with ASP 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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37A TYR* 4.2 1.5 + - - -
38A GLU* 3.4 0.2 - - - -
39A VAL* 2.7 42.5 + - + +
49A LEU* 3.9 0.6 - - - +
50A TRP* 1.3 81.0 - - - +
52A THR* 1.3 76.8 + - - +
74A TRP* 4.1 18.7 - - + -
79A GLN* 2.4 33.9 + - - +
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Residues in contact with THR 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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8A PRO* 5.7 0.2 - - - +
10A GLU* 5.5 3.9 + - - +
37A TYR* 3.3 22.0 + - - -
38A GLU* 3.7 16.2 - - + +
49A LEU* 3.5 35.2 - - + -
51A ASP* 1.3 86.6 + - - +
53A GLY* 1.3 60.0 + - - +
159A ASN* 6.5 0.2 - - + -
160A PHE* 4.2 9.0 - - + -
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Residues in contact with GLY 53 (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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8A PRO* 4.8 0.4 - - - -
9A MET 3.2 14.1 - - - -
10A GLU* 4.3 7.6 - - - -
36A CYS* 3.5 0.7 - - - -
37A TYR* 3.0 46.4 + - - +
52A THR* 1.3 77.9 - - - +
54A VAL* 1.3 69.2 + - - +
160A PHE* 3.8 4.1 - - - -
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Residues in contact with VAL 54 (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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8A PRO* 3.4 4.3 - - - +
9A MET* 2.9 44.2 + - + +
10A GLU 3.8 18.6 - - - +
11A ARG* 4.2 5.8 - - - +
12A MET* 4.2 9.2 - - + -
34A TRP* 3.4 38.1 - - + -
35A LEU 3.3 10.1 - - - +
36A CYS* 4.1 4.0 - - - -
37A TYR* 3.7 2.2 - - - -
53A GLY* 1.3 79.9 - - - +
55A PHE* 1.3 67.2 + - - +
160A PHE* 3.9 25.8 - - + +
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASN* 3.7 26.5 - - - -
8A PRO* 3.5 24.2 - - + -
9A MET* 5.9 0.4 - - - -
33A THR 3.9 0.4 - - - +
34A TRP* 3.5 3.4 - - - -
35A LEU* 2.8 41.2 + - + +
37A TYR* 3.3 34.5 - + - -
54A VAL* 1.3 79.3 - - - +
56A ARG* 1.3 61.2 + - - +
67A ALA* 4.4 13.7 - - + +
70A CYS* 3.7 27.4 - - + -
71A PHE* 3.8 26.0 - + + -
74A TRP* 3.5 29.6 - + + -
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A MET* 5.6 4.5 - - - -
32A TYR* 3.5 58.6 + - + -
33A THR 3.4 4.7 - - - +
34A TRP* 3.3 49.8 - - + +
55A PHE* 1.3 74.4 - - - +
57A GLY* 1.3 63.0 + - - +
67A ALA* 4.4 3.6 - - - -
70A CYS* 4.4 11.3 - - - -
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Residues in contact with GLY 57 (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 TYR* 3.2 15.9 - - - -
33A THR* 2.9 29.1 + - - -
56A ARG* 1.3 74.8 - - - +
58A GLN* 1.3 64.8 + - - -
65A TYR 3.5 11.9 - - - -
66A HIS 4.2 0.4 - - - -
67A ALA* 3.7 15.2 - - - +
70A CYS* 5.0 1.3 - - - -
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Residues in contact with GLN 58 (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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31A SER* 3.6 17.5 + - - +
32A TYR* 3.4 28.5 + - - -
33A THR* 4.3 4.8 + - - -
57A GLY* 1.3 74.6 - - - -
59A VAL* 1.3 62.1 + - - +
60A TYR 3.1 19.9 + - - +
61A PHE* 3.4 29.8 - - + -
65A TYR* 2.9 30.0 + - + +
66A HIS* 3.3 21.1 - - - +
67A ALA 4.3 1.4 + - - -
68A GLU* 5.2 0.5 - - - +
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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