Contacts of the strand formed by residues 17 - 22 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L HIS* 3.4 5.0 + - - -
14L ALA 3.0 36.2 + - - +
15L GLU* 2.9 24.9 + - - +
16L GLY* 1.3 88.8 - - - +
18L PHE* 1.3 61.8 + - - +
19L LEU 4.0 0.2 - - - -
91L ILE* 4.0 10.8 - - + +
106L TRP* 3.4 44.1 - - + +
107L VAL* 3.4 12.1 - - - +
108L SER* 4.2 5.8 - - - +
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Residues in contact with PHE 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L VAL* 4.0 13.0 - - + -
12L VAL 3.4 4.3 - - - +
13L HIS* 3.4 34.1 - + + -
16L GLY 4.5 8.7 - - - -
17L LYS* 1.3 72.4 - - - +
19L LEU* 1.3 68.6 + - - +
20L VAL* 3.2 5.5 + - - +
106L TRP* 4.1 0.9 - - - -
107L VAL* 2.9 42.1 + - - +
108L SER 4.0 0.7 - - - -
109L ALA* 3.4 27.6 - - - -
112L ILE* 4.7 6.1 - - + -
127L ILE* 3.9 28.7 - - + -
130L TYR* 4.0 22.0 - + - -
131L GLN* 3.2 31.0 - - + -
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Residues in contact with LEU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L CYS 4.8 0.9 - - - +
11L VAL* 5.6 0.3 - - - -
12L VAL* 3.0 33.1 + - + +
18L PHE* 1.3 72.0 - - - +
20L VAL* 1.3 71.3 + - - +
21L VAL* 4.6 2.2 - - + -
33L GLN* 4.5 6.2 - - - +
34L PRO* 3.8 37.1 - - + +
52L LEU* 4.4 1.6 - - + -
56L THR* 4.1 18.6 - - + +
58L ILE* 4.3 9.4 - - + -
94L THR* 6.0 0.2 - - - -
104L CYS* 4.3 19.7 - - + -
105L ARG 3.5 14.1 - - - +
106L TRP* 3.5 40.6 - - + +
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Residues in contact with VAL 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L PHE 3.2 3.3 + - - +
19L LEU* 1.3 75.0 - - - +
21L VAL* 1.3 68.1 + - - +
31L TRP* 4.0 30.1 - - + +
32L ASN* 3.6 30.7 - - - +
33L GLN* 4.0 4.0 - - + +
104L CYS* 3.6 4.0 - - - +
105L ARG* 3.0 33.3 + - + +
107L VAL* 3.6 28.7 - - + -
112L ILE* 4.2 18.4 - - + -
123L VAL* 4.5 8.3 - - + -
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Residues in contact with VAL 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L LEU* 4.6 1.8 - - + -
20L VAL* 1.3 78.8 - - - +
22L GLU* 1.3 67.3 + - - +
23L GLU* 5.0 7.0 - - + -
31L TRP* 3.1 35.2 - - - -
32L ASN* 2.7 38.6 + - + +
33L GLN 4.7 1.1 - - - +
34L PRO* 4.2 13.2 - - + -
55L GLU* 4.6 18.2 - - + +
56L THR* 3.9 24.7 - - + -
101L ILE* 5.5 7.0 - - + -
103L CYS 4.2 1.6 - - - +
104L CYS* 3.7 18.8 - - + -
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Residues in contact with GLU 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L VAL* 1.3 76.8 - - - +
23L GLU* 1.3 61.2 + - - +
24L THR* 2.6 40.8 + - - -
29L ALA* 3.9 3.7 - - - -
30L LEU 3.4 20.4 + - - +
31L TRP* 4.1 16.8 - - + +
101L ILE* 3.7 6.6 - - - +
102L ASP* 3.5 29.2 + - - +
103L CYS* 3.0 40.3 + - - +
104L CYS* 4.6 0.4 - - - +
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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