Contacts of the strand formed by residues 59 - 68 (chain B) in PDB entry 3TSO
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 ALA 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.0 17.9 - - + -
55B MET* 3.4 4.0 - - - -
56B LEU* 2.8 40.1 + - - +
57B GLY 3.5 0.4 - - - -
58B THR* 1.3 79.3 - - + +
60B ALA* 1.3 61.6 + - - +
61B VAL* 3.5 3.4 + - + +
174B PHE* 3.6 31.9 - - + -
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Residues in contact with ALA 60 (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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11B PHE* 3.8 21.2 + - - +
53B THR* 4.4 14.6 - - + -
54B VAL 3.7 4.7 - - - -
55B MET* 3.8 16.7 - - + +
58B THR 4.0 0.8 + - - -
59B ALA* 1.3 70.9 - - - +
61B VAL* 1.3 61.6 + - - +
62B LYS 4.2 0.4 - - - -
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Residues in contact with VAL 61 (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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11B PHE* 3.7 12.3 - - + +
13B PHE* 3.5 33.7 - - + -
52B ARG 3.9 0.2 - - - +
53B THR* 3.2 4.5 - - - +
54B VAL* 2.8 45.8 + - + +
56B LEU* 3.8 28.7 - - + -
59B ALA* 3.9 9.9 - - + +
60B ALA* 1.3 77.3 - - - +
62B LYS* 1.3 68.3 + - - +
63B ALA* 3.8 1.2 + - - +
170B LEU* 4.6 7.6 - - + -
174B PHE* 3.9 20.9 - - + -
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Residues in contact with LYS 62 (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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11B PHE 3.0 13.5 + - - +
12B VAL* 3.4 27.3 - - + +
13B PHE* 3.0 28.9 + - - +
51B THR* 4.1 26.5 - - + -
52B ARG 4.4 0.4 - - - +
53B THR* 3.4 25.0 + - + +
60B ALA 4.2 0.8 - - - -
61B VAL* 1.3 73.2 - - - +
63B ALA* 1.3 71.2 + - - +
64B GLN* 3.9 1.9 + - + +
497C ARG* 4.7 16.7 - - - +
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Residues in contact with ALA 63 (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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13B PHE 3.7 4.9 - - - +
15B VAL* 5.1 0.4 - - + -
32B PHE* 4.7 2.2 - - + -
50B SER 3.9 0.5 - - - +
51B THR* 3.2 26.7 - - - -
52B ARG 2.8 18.4 + - - +
61B VAL 3.8 1.2 + - - -
62B LYS* 1.3 74.7 - - - +
64B GLN* 1.3 60.3 + - - +
65B ILE* 3.8 23.0 - - + +
170B LEU* 3.6 35.9 - - + -
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Residues in contact with GLN 64 (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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12B VAL* 4.3 21.4 - - + +
13B PHE 2.9 11.2 + - - +
14B LYS* 3.5 20.7 - - - +
15B VAL 2.9 24.8 + - - +
49B PHE* 3.5 35.8 - - + -
50B SER 3.9 3.1 - - - -
51B THR* 4.1 6.7 - - + -
62B LYS* 3.9 2.2 + - + +
63B ALA* 1.3 71.4 - - - +
65B ILE* 1.3 60.1 + - - +
66B TRP* 3.0 36.2 - - - +
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Residues in contact with ILE 65 (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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15B VAL* 3.2 21.3 - - + +
17B LEU* 3.7 22.0 - - + -
29B LEU* 3.4 23.2 - - + +
32B PHE* 3.5 36.8 - - + -
33B THR* 4.0 14.8 - - + -
49B PHE* 3.2 2.3 - - - -
50B SER 3.0 31.6 + - - +
63B ALA* 4.0 19.1 - - + +
64B GLN* 1.3 76.5 - - - +
66B TRP* 1.3 62.5 + - - +
166B PHE* 3.8 22.9 - - + -
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Residues in contact with TRP 66 (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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14B LYS* 3.8 28.9 - - + +
15B VAL 2.8 13.7 + - - +
16B VAL* 4.3 5.4 - - + -
17B LEU* 3.1 23.0 + - - +
47B VAL* 3.5 31.4 - - + -
48B GLU 3.4 9.4 - - - -
49B PHE* 3.4 36.1 - + + -
64B GLN* 3.0 48.2 - - - +
65B ILE* 1.3 72.8 - - - +
67B ASP* 1.3 63.3 + - - +
81B TYR* 3.1 28.6 + + + -
489C MET* 4.0 22.2 - - + -
493C PRO* 4.1 22.0 - - + -
496C LEU* 4.0 6.5 - - + -
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Residues in contact with ASP 67 (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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17B LEU* 4.3 5.5 - - + +
25B LYS* 3.7 17.7 - - - +
26B THR* 2.7 42.6 + - - +
29B LEU* 3.7 22.5 - - + +
44B THR* 3.9 8.4 + - - +
47B VAL* 3.5 1.4 - - - -
48B GLU* 2.8 41.4 + - + +
66B TRP* 1.3 76.4 - - - +
68B THR* 1.3 79.5 + - - +
81B TYR* 3.2 8.4 + - - -
200B MG 4.2 1.0 - - - -
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Residues in contact with THR 68 (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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17B LEU 4.9 1.4 - - - +
25B LYS* 3.5 11.8 - - - +
44B THR* 4.0 8.3 - - - -
46B GLY 2.6 24.5 + - - -
47B VAL* 3.6 11.7 - - - +
67B ASP* 1.3 86.7 + - - +
69B ALA* 1.3 79.0 + - - +
70B GLY 3.5 1.4 + - - -
75B ARG* 3.1 23.2 + - - +
77B ILE* 4.4 2.2 - - + -
81B TYR* 3.5 29.9 + - + +
201B GNP 4.2 0.7 + - - -
203B GOL 3.9 14.6 - - - +
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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