Contacts of the strand formed by residues 35 - 45 (chain B) in PDB entry 1TLY
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 THR 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B VAL* 5.9 3.1 - - - -
20B VAL 2.9 13.0 - - - +
21B GLY* 4.4 5.8 - - - -
34B ASP* 1.3 82.2 - - - +
36B TYR* 1.3 69.7 + - - +
57B PRO* 4.7 1.0 - - - +
58B VAL* 3.3 25.5 + - - +
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Residues in contact with TYR 36 (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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19B VAL* 3.5 4.9 - - - +
20B VAL* 2.7 74.6 + - + +
22B SER* 4.6 9.2 - - - -
34B ASP* 4.1 16.6 - - + -
35B THR* 1.3 85.2 - - - +
37B LEU* 1.3 74.5 + - - +
38B GLU* 4.5 2.3 + - - -
55B ASP* 3.0 38.9 + - + -
56B ALA 3.0 20.9 - - - +
57B PRO* 4.1 3.4 - - + -
58B VAL* 3.6 11.3 - - - +
265B TYR* 3.9 15.4 - - - -
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Residues in contact with LEU 37 (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 VAL* 5.1 11.4 - - + -
18B ASN 3.3 13.2 - - - +
19B VAL* 3.9 22.2 - - + -
36B TYR* 1.3 78.7 - - - +
38B GLU* 1.3 61.5 + - - +
55B ASP* 3.3 4.3 - - - -
56B ALA* 2.8 40.9 + - + +
57B PRO 3.9 4.3 - - - +
58B VAL* 3.6 37.9 - - + -
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Residues in contact with GLU 38 (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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16B SER 3.8 0.7 - - - +
17B VAL* 3.3 6.8 - - - +
18B ASN* 2.7 62.7 + - - +
20B VAL* 4.0 22.2 - - + +
36B TYR* 4.5 2.4 + - - -
37B LEU* 1.3 75.2 - - - +
39B TYR* 1.3 69.1 + - - +
40B GLU* 3.9 8.4 - - - +
51B TYR* 5.8 0.2 - - - -
53B TYR* 3.4 24.2 - - + -
54B ALA 3.0 9.0 - - - +
55B ASP* 3.0 27.1 - - - +
267B VAL* 4.7 4.9 - - - +
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Residues in contact with TYR 39 (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 TRP* 3.9 5.6 + + - -
15B GLN* 2.5 49.0 + - + +
16B SER 3.4 9.6 - - - -
17B VAL* 4.6 11.4 - - + +
38B GLU* 1.3 74.0 - - - +
40B GLU* 1.3 78.8 + - - +
41B ALA* 3.8 17.5 - - + +
52B GLY 5.8 0.2 - - - -
53B TYR* 3.0 7.5 - - - +
54B ALA* 2.8 49.5 + - + +
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Residues in contact with GLU 40 (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 HIS 4.4 0.2 - - - -
15B GLN* 3.4 4.6 - - - -
16B SER* 2.7 47.5 + - - +
18B ASN* 3.2 24.8 + - - +
38B GLU* 3.9 11.4 - - - +
39B TYR* 1.3 83.2 - - - +
41B ALA* 1.3 64.4 + - - +
51B TYR* 2.6 37.9 + - + +
52B GLY 3.6 2.7 - - - +
53B TYR* 4.0 7.0 - - + -
228B HIS* 4.6 5.7 + - - -
267B VAL* 5.7 1.4 - - - +
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Residues in contact with ALA 41 (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 TRP* 3.7 29.8 - - + -
14B HIS 3.2 8.5 - - - +
39B TYR* 3.8 15.0 - - + +
40B GLU* 1.3 78.8 - - - +
42B PHE* 1.3 59.4 + - - +
50B PHE* 3.5 13.2 - - + -
51B TYR* 3.3 8.3 - - - -
52B GLY 3.1 31.1 + - - +
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Residues in contact with PHE 42 (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 TRP 3.0 4.0 - - - +
13B TRP* 4.7 1.1 - - - -
14B HIS* 2.9 59.6 + + + -
41B ALA* 1.3 73.0 - - - +
43B ALA* 1.3 69.8 + - - +
44B LYS* 4.7 16.8 - - + -
49B ASP* 5.6 4.3 - - + -
50B PHE 3.3 15.5 - - - -
51B TYR* 4.4 20.4 - + + -
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Residues in contact with ALA 43 (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 TRP* 3.0 16.6 - - + +
13B TRP* 3.4 35.2 - - + -
41B ALA 4.2 0.4 - - - -
42B PHE* 1.3 80.7 - - - +
44B LYS* 1.3 63.9 + - - +
48B PHE* 4.4 6.5 - - + -
49B ASP* 3.3 4.5 - - - +
50B PHE* 2.7 47.5 + - + +
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Residues in contact with LYS 44 (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 ASP 4.4 3.1 - - - +
12B TRP* 3.3 26.7 + - - +
42B PHE* 4.7 16.8 - - + -
43B ALA* 1.3 76.6 - - - +
45B LYS* 1.3 62.9 + - - +
46B ASP* 4.3 1.7 + - - +
48B PHE 3.6 4.0 - - - +
49B ASP* 3.3 30.4 + - + +
101B GLU* 5.0 1.8 + - - -
103B TYR* 2.8 29.7 + - - -
130B ASP* 4.2 3.8 + - - -
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Residues in contact with LYS 45 (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 TRP* 3.8 42.4 - - + -
44B LYS* 1.3 78.4 - - - +
46B ASP* 1.3 65.8 + - - +
47B TRP* 2.4 54.5 + - + +
48B PHE* 2.5 42.2 + - + +
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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