Contacts of the strand formed by residues 29 - 32 (chain D) 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 ALA 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLU* 3.2 30.1 - - + +
23D GLU 3.8 9.2 - - - -
24D THR* 4.2 4.8 + - - +
27D GLY 4.3 0.2 + - - -
28D LYS* 1.3 82.1 - - + +
30D LEU* 1.3 60.0 + - - +
102D ASP* 4.3 9.9 - - - +
117D ASN* 3.3 24.7 + - - +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL 3.5 0.9 - - - +
22D GLU* 3.4 5.7 - - - -
23D GLU* 3.1 40.4 + - + +
25D ILE* 3.9 23.6 - - + -
26D ASN 4.8 3.4 - - - +
28D LYS* 3.2 42.0 - - + +
29D ALA* 1.3 78.3 - - - +
31D TRP* 1.3 64.7 + - - +
116D SER 5.3 0.4 - - - +
117D ASN* 2.9 27.4 - - + +
118D LEU 4.7 3.8 - - - +
119D ARG* 3.9 26.9 - - + -
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Residues in contact with TRP 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 3.4 19.7 - - + +
21D VAL 3.4 4.9 - - - -
22D GLU* 3.2 43.2 - - + +
30D LEU* 1.3 77.3 - - - +
32D ASN* 1.3 61.3 + - - +
105D ARG* 4.6 10.3 - - - +
107D VAL* 3.7 29.8 - - + -
111D GLU* 3.7 31.2 - - + -
112D ILE* 4.6 6.7 - - + -
115D ALA* 4.4 13.9 - - + -
117D ASN* 2.6 38.9 + - - +
118D LEU* 3.8 24.4 - - + -
119D ARG* 2.6 35.1 + - - +
123D VAL* 3.9 5.0 - - + +
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Residues in contact with ASN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 3.3 9.2 - - - -
21D VAL* 3.0 31.2 + - + -
23D GLU* 4.2 7.4 - - - +
31D TRP* 1.3 77.2 - - - +
33D GLN* 1.3 87.5 + - - +
35D ALA* 3.6 2.6 - - - +
81D ARG* 3.1 17.9 + - - -
119D ARG* 3.4 31.3 - - + +
123D VAL* 3.3 21.0 - - - +
157D SO4 3.6 5.3 + - - -
158D SO4 3.2 30.0 + - - -
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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