Contacts of the strand formed by residues 40 - 51 (chain B) in PDB entry 5A72
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 TYR 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ILE* 3.6 22.7 - - + -
31B VAL 3.4 16.2 - - - +
32B SER* 3.7 19.6 - - - -
33B ARG* 4.3 1.6 - - - +
36B TYR* 3.4 19.0 - - - +
38B LEU* 2.9 13.8 + - - +
39B LYS* 1.3 96.1 - - + +
41B GLN* 1.3 60.5 + - - +
125B LEU* 3.9 25.7 - - + +
146B ILE* 3.7 22.3 - - + +
150B ASN* 4.2 23.5 + - + +
151B VAL* 4.2 17.9 - - + -
154B CYS* 4.0 25.3 - - + +
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Residues in contact with GLN 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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29B GLN 3.4 0.2 - - - +
30B ILE* 3.4 6.8 - - - +
31B VAL* 2.9 39.8 + - + +
33B ARG* 2.9 37.3 + - + +
36B TYR* 3.7 26.9 + - + +
40B TYR* 1.3 75.4 - - - +
42B VAL* 1.3 70.5 + - - +
43B ARG* 3.6 17.9 + - - +
116B LEU* 6.4 0.2 - - + -
125B LEU* 4.8 0.9 - - - -
503C A 3.3 17.1 + - - +
504C G 2.9 28.9 + - - -
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Residues in contact with VAL 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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28B ALA* 4.8 0.2 - - + -
29B GLN 3.3 9.9 - - - +
30B ILE* 5.0 4.0 - - + -
41B GLN* 1.3 82.8 + - - +
43B ARG* 1.3 64.8 + - - +
44B VAL* 3.8 1.4 + - - +
112B ILE* 3.8 25.4 - - + -
116B LEU* 3.9 27.2 - - + +
119B THR* 5.4 0.4 - - + +
125B LEU* 3.8 24.0 - - + +
128B ALA* 3.8 22.2 - - + +
129B ALA* 4.0 15.3 - - + +
132B ALA* 4.0 20.4 - - + -
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Residues in contact with ARG 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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28B ALA* 3.2 4.9 - - - +
29B GLN* 2.9 49.2 + - + +
31B VAL* 3.7 30.2 - - + +
33B ARG* 3.3 31.1 - - - +
41B GLN* 3.6 18.2 + - - +
42B VAL* 1.3 74.0 - - - +
44B VAL* 1.3 67.2 + - - +
45B SER* 4.8 5.4 - - - +
83B VAL* 3.8 28.4 - - + +
504C G 4.8 5.2 + - - +
505C A 3.5 14.3 - - - +
506C A 4.0 6.2 - - - +
618D G 4.3 9.3 + - - -
619D T 2.6 41.0 + - - +
620D T 4.4 0.6 + - - -
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Residues in contact with VAL 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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27B ASN 3.6 3.4 - - - -
28B ALA* 4.1 10.5 - - + -
42B VAL* 4.6 2.0 - - + +
43B ARG* 1.3 80.9 - - - +
45B SER* 1.3 64.1 + - - +
83B VAL* 3.6 3.3 - - - +
84B GLY* 3.0 29.4 + - - +
85B GLY 3.9 22.4 - - - +
88B LEU* 3.4 19.4 - - + +
109B VAL* 3.8 18.2 - - + -
112B ILE* 3.7 30.3 - - + -
113B ILE* 4.2 7.9 - - + -
116B LEU* 4.1 12.1 - - + -
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Residues in contact with SER 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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25B CYS 3.6 1.3 + - - +
26B ILE* 3.5 5.4 - - - +
27B ASN* 2.9 45.7 + - - +
28B ALA* 5.6 0.2 - - - -
29B GLN* 4.6 12.0 + - - +
43B ARG* 4.8 5.7 - - - +
44B VAL* 1.3 78.3 - - - +
46B LEU* 1.3 60.6 + - - +
47B THR* 4.3 6.3 + - - -
81B CYS* 4.2 17.3 - - - -
82B VAL 3.2 11.2 - - - -
83B VAL* 4.5 7.4 - - - -
88B LEU* 3.4 8.2 - - - +
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Residues in contact with LEU 46 (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 VAL* 4.1 13.7 - - + -
25B CYS 3.5 3.8 - - - -
26B ILE* 3.9 24.5 - - + +
45B SER* 1.3 74.6 - - - +
47B THR* 1.3 71.7 + - - +
48B VAL* 4.5 9.9 - - + -
61B ILE* 6.0 0.2 - - + -
65B LEU* 4.9 2.5 - - + -
80B PHE* 4.0 25.6 - - + -
81B CYS* 3.4 1.4 - - - -
82B VAL* 3.0 38.8 + - + +
88B LEU* 3.7 16.7 - - + +
91B THR* 4.4 8.7 - - + -
92B LEU* 3.9 11.4 - - + -
95B LEU* 3.8 27.6 - - + -
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Residues in contact with THR 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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24B GLY* 3.1 4.5 - - - -
25B CYS* 2.8 43.5 + - - -
45B SER* 4.3 7.6 + - - -
46B LEU* 1.3 80.8 + - - +
48B VAL* 1.3 69.8 + - - +
49B PHE* 3.4 37.9 - - + -
79B GLU* 4.1 12.8 - - - +
80B PHE 3.1 14.4 - - - +
81B CYS* 3.5 16.9 - - + -
616D A 5.6 0.2 - - - +
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Residues in contact with VAL 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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19B PHE* 3.3 35.4 - - + -
20B VAL* 4.0 26.5 - - + -
23B ASP 3.8 5.4 - - - +
24B GLY* 4.6 2.9 - - - -
46B LEU* 4.5 4.3 - - + -
47B THR* 1.3 78.8 - - - +
49B PHE* 1.3 66.0 + - - +
58B LEU* 3.7 20.6 - - + +
61B ILE* 4.0 13.5 - - + -
78B SER 4.0 0.2 - - - +
79B GLU* 3.5 4.5 - - - -
80B PHE* 3.0 47.3 + - + +
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Residues in contact with PHE 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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23B ASP* 3.2 21.9 + - - +
24B GLY 4.3 0.2 - - - -
25B CYS* 3.6 16.4 - - + -
47B THR* 3.4 30.1 - - + -
48B VAL* 1.3 79.9 - - - +
50B GLN* 1.3 75.7 + - - +
58B LEU* 4.7 0.4 - - - -
73B ARG* 3.8 2.5 - - - -
77B MET* 3.7 13.9 - - + -
78B SER 3.6 3.1 - - - -
79B GLU* 3.1 35.4 - - + -
614D C 3.5 17.2 - - + +
615D G 3.5 44.4 - + + -
616D A 3.4 30.7 - + - -
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Residues in contact with GLN 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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21A ASP 5.0 1.8 + - - -
22A ALA 5.8 0.2 + - - -
101A LEU* 3.4 21.8 - - - +
19B PHE* 3.6 7.7 - - + -
23B ASP* 3.0 17.4 + - - +
49B PHE* 1.3 84.9 - - - +
51B SER* 1.3 66.9 + - - +
54B GLN* 2.7 31.7 + - + +
57B ILE* 4.0 15.5 - - + -
58B LEU* 4.1 22.2 - - + +
77B MET* 3.3 7.4 - - - +
78B SER* 2.6 40.4 + - - +
614D C 3.3 22.3 + - - -
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Residues in contact with SER 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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140A ASP* 5.8 4.0 - - - -
50B GLN* 1.3 74.7 - - - +
52B THR* 1.3 55.4 + - - +
53B THR* 3.0 25.4 + - - +
54B GLN* 2.7 37.4 + - - +
55B HIS* 3.5 0.3 + - - -
76B GLY 3.6 10.6 + - - -
77B MET* 3.8 7.1 - - - -
78B SER* 4.7 0.2 - - - -
613D A 4.3 19.1 + - - -
614D C 2.8 23.0 + - - -
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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