Contacts of the strand formed by residues 37 - 48 (chain B) in PDB entry 4AAE
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 HIS 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ILE* 3.6 32.8 - - + -
28B LYS 3.2 5.4 - - - +
29B PRO* 3.8 20.7 - - + +
30B ASN 3.7 1.9 + - - +
33B TYR* 3.5 19.8 - - - +
35B PHE* 3.0 25.2 + - - +
36B LYS* 1.3 89.2 + - + +
38B GLN* 1.3 60.2 + - - +
39B LEU 4.2 0.3 + - - -
122B PHE* 4.1 23.6 - - + -
143B THR* 3.9 14.6 - - + +
147B THR* 4.5 4.4 - - - +
148B VAL* 4.0 17.8 - - + +
151B VAL* 3.8 36.5 - - + +
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Residues in contact with GLN 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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26B GLN 3.5 0.3 - - - +
27B ILE* 3.4 5.9 - - - -
28B LYS* 2.8 58.9 + - + +
30B ASN* 4.6 3.0 - - + +
33B TYR* 3.0 39.3 + - + +
37B HIS* 1.3 72.8 - - - +
39B LEU* 1.3 76.6 + - - +
40B SER* 3.6 12.1 + - - +
503E A 3.6 10.4 - - - +
504E A 2.7 50.3 + - - +
505E A 4.6 0.6 - - - +
620G T 4.4 3.0 + - - -
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Residues in contact with LEU 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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26B GLN 4.0 4.0 - - - +
27B ILE* 3.9 26.9 - - + -
37B HIS 4.2 0.8 + - - -
38B GLN* 1.3 82.2 - - - +
40B SER* 1.3 59.2 + - - +
41B LEU* 4.3 6.0 + - + +
81B ILE* 5.4 6.2 - - - +
108B ILE* 4.8 5.2 - - + -
112B LEU* 3.5 41.9 - - + +
115B ALA* 5.0 0.9 - - + -
122B PHE* 3.9 31.1 - - + -
125B VAL* 3.6 19.7 - - + -
126B CYS* 4.2 11.2 - - - -
129B VAL* 4.1 16.2 - - + -
503E A 4.8 8.4 + - - +
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Residues in contact with SER 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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24B ILE 3.7 1.1 - - - +
25B ALA* 3.3 4.3 - - - -
26B GLN* 2.7 44.8 + - - +
28B LYS* 3.7 41.7 + - - +
38B GLN* 3.6 11.5 + - - -
39B LEU* 1.3 74.4 - - - +
41B LEU* 1.3 66.1 + - - +
42B THR* 4.5 7.7 + - - -
79B SER* 5.4 2.1 + - - -
504E A 5.3 3.3 + - - -
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Residues in contact with LEU 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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24B ILE 3.4 3.1 - - - +
25B ALA* 3.8 21.1 - - + -
26B GLN 5.1 0.4 - - - +
39B LEU* 4.3 6.0 + - + +
40B SER* 1.3 88.6 + - - +
42B THR* 1.3 65.0 + - - +
79B SER* 3.4 27.1 + - - +
81B ILE* 5.0 12.2 - - + +
84B LEU* 3.9 16.5 - - + +
105B VAL* 4.3 15.9 - - + +
108B ILE* 4.3 31.6 - - + -
109B ILE* 3.4 37.7 - - + -
112B LEU* 5.5 5.6 - - + -
129B VAL* 5.5 2.0 - - + -
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Residues in contact with THR 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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22B SER 3.6 1.4 - - - +
23B ILE* 3.7 3.2 - - - +
24B ILE* 2.8 56.1 + - + +
26B GLN* 4.7 8.4 + - - -
28B LYS* 5.7 1.0 + - - -
40B SER* 4.5 6.4 + - - -
41B LEU* 1.3 77.6 + - - +
43B PHE* 1.3 72.8 + - - +
44B GLN* 4.3 15.7 - - + +
77B ILE* 4.4 12.3 - - + -
78B LEU 3.7 3.4 - - - -
79B SER* 3.1 18.3 + - - +
84B LEU* 4.8 2.6 - - - +
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Residues in contact with PHE 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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16B PHE* 6.0 0.2 - + - -
17B VAL* 3.6 42.4 - - + -
21B GLY* 4.4 11.0 - - - -
22B SER 3.5 8.7 - - - -
23B ILE* 4.1 16.2 - - + +
42B THR* 1.3 75.2 - - - +
44B GLN* 1.3 65.5 + - - +
45B VAL* 3.7 20.9 - - + -
58B LEU* 5.7 1.1 - - + -
62B ILE* 5.1 2.7 - - + -
76B TYR* 3.7 31.6 - + - -
77B ILE* 3.5 4.2 - - - -
78B LEU* 2.8 38.0 + - + +
84B LEU* 3.8 23.4 - - + +
87B PHE* 4.3 25.8 - + - -
88B LEU* 5.3 3.8 - - + -
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Residues in contact with GLN 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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20B ASP 4.4 0.3 - - - +
21B GLY* 3.6 0.7 - - - -
22B SER* 2.9 48.2 + - - +
24B ILE* 3.6 20.1 - - + +
42B THR* 4.3 7.8 - - + +
43B PHE* 1.3 78.2 - - - +
45B VAL* 1.3 70.0 + - - +
46B THR* 4.5 4.0 + - - +
70B ARG* 5.1 2.8 + - - -
75B ASN* 4.2 25.9 - - + +
76B TYR 3.4 10.5 - - - +
77B ILE* 4.5 10.2 - - + +
615G G 4.0 15.6 + - - +
616G A 3.3 32.9 + - - +
617G C 4.8 6.8 + - - -
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Residues in contact with VAL 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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16B PHE* 3.7 37.0 - - + -
20B ASP* 4.2 15.0 - - - +
21B GLY* 4.2 3.4 - - - -
43B PHE* 3.7 26.0 - - + -
44B GLN* 1.3 78.7 - - - +
46B THR* 1.3 73.9 + - - +
47B GLN* 4.6 0.9 - - - +
55B LEU* 3.6 21.0 - - + +
58B LEU* 5.0 3.6 - - + -
75B ASN* 3.1 7.8 - - - +
76B TYR* 2.9 41.3 + - + +
615G G 4.7 0.4 - - - -
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Residues in contact with THR 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 ASP* 3.7 14.5 + - - +
44B GLN* 4.5 6.1 + - - +
45B VAL* 1.3 78.2 - - - +
47B GLN* 1.3 85.3 + - - +
55B LEU* 4.8 0.2 - - - -
73B VAL* 3.8 20.2 - - + -
74B SER 3.4 8.5 - - - +
75B ASN* 2.8 21.3 + - - +
614G T 4.0 23.8 + - + +
615G G 3.0 28.9 + - - -
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Residues in contact with GLN 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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18A ASP 5.7 0.4 + - - -
19A GLY* 6.3 0.2 - - - -
97A LEU* 4.0 26.5 - - - +
16B PHE* 4.4 12.1 - - - -
20B ASP* 4.5 3.6 + - - -
45B VAL* 4.6 0.2 - - - +
46B THR* 1.3 90.4 + - - +
48B LYS* 1.3 66.5 + - - +
51B ARG* 3.5 47.0 + - + +
54B PHE* 4.2 12.6 - - + -
55B LEU* 3.6 25.7 - - + +
73B VAL* 3.3 4.9 - - - +
74B SER 2.8 28.3 + - - -
614G T 5.2 0.4 - - - -
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Residues in contact with LYS 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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137A ASP* 3.6 40.3 + - - +
139A LYS* 5.9 2.6 - - - +
47B GLN* 1.3 79.3 + - - +
49B THR* 1.3 60.9 + - - +
50B GLN* 3.2 22.2 - - + +
51B ARG* 2.8 33.8 + - - +
52B ARG* 3.6 3.1 + - - -
72B SER 3.5 10.1 - - - +
73B VAL* 4.2 1.3 - - - +
74B SER* 5.2 0.2 - - - -
612G G 4.4 5.0 + - - -
613G C 2.9 36.2 + - - +
614G T 3.1 34.4 + - - +
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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