Contacts of the strand formed by residues 17 - 24 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13K HIS* 3.4 5.6 - - - -
14K ALA 2.8 33.3 + - - +
15K GLU 3.7 8.7 - - - +
16K GLY* 1.3 86.2 + - - +
18K PHE* 1.3 65.7 + - - +
91K ILE* 4.3 14.8 - - + -
106K TRP* 3.7 32.1 - - + +
107K VAL* 3.2 20.0 - - - +
108K SER* 4.3 16.9 - - - +
111K GLU* 4.5 4.9 + - - -
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Residues in contact with PHE 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K VAL* 3.5 33.7 - - + -
12K VAL 3.4 4.3 - - - +
13K HIS* 3.2 37.9 - + + -
16K GLY 5.1 2.0 - - - -
17K LYS* 1.3 75.7 - - - +
19K LEU* 1.3 64.8 + - - +
20K VAL* 5.3 0.4 - - + -
106K TRP* 3.5 4.9 - - - -
107K VAL* 2.7 38.3 + - - +
108K SER 4.3 0.4 - - - -
109K ALA* 3.7 43.5 - - + -
112K ILE* 4.1 14.4 - - + -
127K ILE* 3.7 21.3 - - + -
130K TYR* 3.7 24.5 - + - -
131K GLN* 5.5 1.8 - - + -
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Residues in contact with LEU 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K CYS 4.8 2.4 - - - +
11K VAL* 5.9 0.2 - - - -
12K VAL* 3.1 29.0 + - + +
18K PHE* 1.3 73.3 - - - +
20K VAL* 1.3 74.7 + - - +
33K GLN* 4.5 2.3 - - - +
34K PRO* 3.5 27.0 - - + +
52K LEU* 4.7 1.1 - - + -
56K THR* 3.6 17.3 - - + -
58K ILE* 3.4 32.5 - - + -
94K THR* 4.3 8.3 - - + -
104K CYS* 3.7 33.4 - - + -
105K ARG 3.9 4.9 - - - +
106K TRP* 3.6 27.5 - - + -
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Residues in contact with VAL 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K PHE* 5.3 0.4 - - + -
19K LEU* 1.3 80.6 - - - +
21K VAL* 1.3 65.7 + - - +
31K TRP* 3.7 42.6 - - + -
32K ASN 3.4 15.0 - - - +
33K GLN* 4.7 4.9 - - + +
34K PRO* 4.7 0.9 - - - -
104K CYS* 3.6 2.6 - - - -
105K ARG* 3.1 41.5 + - + +
107K VAL* 4.2 6.5 - - + -
112K ILE* 3.6 31.9 - - + -
123K VAL* 5.1 5.4 - - + -
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Residues in contact with VAL 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K VAL* 1.3 75.6 - - - +
22K GLU* 1.3 59.8 + - - +
23K GLU* 4.5 8.0 - - - +
30K LEU 3.5 1.2 - - - +
31K TRP* 3.4 3.8 - - - -
32K ASN* 2.8 51.6 + - + +
33K GLN 3.6 16.3 - - - +
34K PRO* 4.5 4.5 - - + -
55K GLU* 3.4 50.0 - - + +
56K THR* 4.3 8.3 - - + -
101K ILE* 4.3 13.5 - - + -
103K CYS 3.8 2.7 - - - -
104K CYS* 3.9 12.8 - - - +
157K SO4 4.8 0.2 - - - +
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Residues in contact with GLU 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K VAL 4.1 0.4 + - - -
21K VAL* 1.3 73.4 - - - +
23K GLU* 1.3 64.6 + - - +
29K ALA* 3.4 32.5 - - + +
30K LEU 3.5 4.0 - - - +
31K TRP* 3.3 27.7 + - + +
101K ILE* 3.6 6.2 - - - +
102K ASP* 3.0 31.1 + - + +
103K CYS* 2.9 32.7 + - - +
105K ARG* 2.7 33.9 + - - +
117K ASN* 4.3 2.4 + - - -
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Residues in contact with GLU 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K VAL* 4.5 4.5 - - - +
22K GLU* 1.3 76.2 - - - +
24K THR* 1.3 59.9 + - - +
25K ILE* 5.0 4.9 - - + -
29K ALA* 4.4 0.4 - - - -
30K LEU* 2.7 51.5 + - + +
32K ASN* 4.0 12.3 - - + +
100K ASP* 3.1 28.9 - - + +
101K ILE* 3.2 23.0 - - + +
102K ASP* 4.0 4.3 - - - -
119K ARG* 2.8 34.9 + - - +
157K SO4 3.2 27.0 + - - -
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Residues in contact with THR 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K GLU* 1.3 74.6 - - - +
25K ILE* 1.3 74.5 + - - +
27K GLY* 3.3 24.7 - - - +
28K LYS 3.2 17.0 - - - +
29K ALA* 4.0 6.4 - - + +
100K ASP 4.4 1.9 + - - +
102K ASP* 2.6 31.4 + - - -
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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