Contacts of the strand formed by residues 17 - 24 (chain B) in PDB entry 3SHD
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 LYS 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B VAL 3.9 0.2 - - - +
13B HIS* 3.4 6.5 + - - -
14B ALA 2.9 33.5 + - - +
15B GLU 3.3 11.2 - - - +
16B GLY* 1.3 86.2 - - - +
18B PHE* 1.3 66.6 + - - +
91B ILE* 4.7 10.3 - - + -
106B TRP* 4.0 23.0 + - + +
107B VAL 3.5 12.8 - - - +
108B SER* 3.8 21.6 - - - +
111B GLU* 4.3 14.1 + - - -
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Residues in contact with PHE 18 (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 VAL* 3.7 23.1 - - + -
12B VAL 3.2 6.5 - - - +
13B HIS* 3.4 34.1 - + + -
16B GLY 4.9 2.5 - - - -
17B LYS* 1.3 77.9 - - - +
19B LEU* 1.3 64.4 + - - +
20B VAL* 3.5 1.8 + - - -
106B TRP* 3.3 7.0 - - - -
107B VAL* 2.7 44.5 + - - +
108B SER 4.1 0.4 - - - -
109B ALA* 3.6 38.1 - - + -
112B ILE* 4.1 14.6 - - + -
127B ILE* 4.1 14.4 - - + -
130B TYR* 3.6 33.0 - + - -
131B GLN* 4.6 8.5 - - + -
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Residues in contact with LEU 19 (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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10B CYS 4.9 1.0 - - - +
12B VAL* 2.9 29.0 + - + +
18B PHE* 1.3 73.6 - - - +
20B VAL* 1.3 68.0 + - - +
33B GLN* 4.4 5.7 - - - +
34B PRO* 3.6 26.5 - - + +
52B LEU* 4.6 1.8 - - + -
56B THR* 3.8 21.1 - - + -
58B ILE* 3.6 30.3 - - + -
94B THR* 4.4 1.3 - - + -
104B CYS* 3.8 25.6 - - + -
105B ARG 3.5 15.5 - - - +
106B TRP* 3.7 34.4 - - + +
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Residues in contact with VAL 20 (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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18B PHE 3.5 3.3 + - - +
19B LEU* 1.3 81.6 - - - +
21B VAL* 1.3 64.9 + - - +
22B GLU 4.3 0.2 + - - -
31B TRP* 3.7 39.0 - - + -
32B ASN* 3.4 20.4 - - - +
33B GLN* 4.6 3.4 - - - +
104B CYS* 3.5 4.3 - - - -
105B ARG* 2.8 55.7 + - + +
107B VAL* 4.7 4.9 - - + -
112B ILE* 4.0 26.2 - - + -
123B VAL* 5.0 5.6 - - + -
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Residues in contact with VAL 21 (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 LEU* 5.2 0.2 - - + -
20B VAL* 1.3 78.9 - - - +
22B GLU* 1.3 59.3 + - - +
23B GLU* 3.9 10.4 + - - +
30B LEU 3.4 3.8 - - - +
31B TRP* 3.4 2.5 - - - -
32B ASN* 2.7 54.2 + - + +
33B GLN 3.7 8.7 - - - +
34B PRO* 3.9 12.5 - - + +
55B GLU* 3.5 30.5 - - - +
56B THR* 3.9 28.0 - - + -
101B ILE* 4.2 13.5 - - + -
103B CYS 3.8 2.2 - - - -
104B CYS* 4.2 5.2 - - - -
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Residues in contact with GLU 22 (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* 4.2 0.8 - - - +
21B VAL* 1.3 70.5 - - - +
23B GLU* 1.3 55.1 + - - +
29B ALA* 3.9 28.3 - - + +
30B LEU 3.3 3.1 - - - +
31B TRP* 3.3 32.9 + - + +
101B ILE* 3.5 3.1 - - - -
102B ASP* 2.6 42.5 + - + +
103B CYS* 3.0 32.3 + - - +
105B ARG* 2.9 31.2 + - - -
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Residues in contact with GLU 23 (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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21B VAL* 4.3 9.3 - - - +
22B GLU* 1.3 75.6 - - - +
24B THR* 1.3 63.7 + - - +
25B ILE* 3.5 12.8 + - + +
28B LYS 3.5 0.3 - - - +
29B ALA* 4.2 0.7 - - - -
30B LEU* 2.8 32.7 + - - +
32B ASN* 4.3 3.8 - - - +
100B ASP* 3.0 32.7 - - + +
101B ILE* 3.6 17.6 - - + +
102B ASP* 3.8 1.1 - - - -
119B ARG* 2.7 34.1 + - - +
157B SO4 2.6 31.8 + - - -
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Residues in contact with THR 24 (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 GLU* 1.3 74.1 - - - +
25B ILE* 1.3 63.5 - - - +
26B ASN 4.1 0.9 + - - -
27B GLY* 4.5 10.7 + - - -
28B LYS 3.2 16.2 - - - -
29B ALA* 4.3 12.6 - - + +
100B ASP 4.5 2.5 + - - +
102B ASP* 2.4 41.7 + - - +
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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