Contacts of the strand formed by residues 22 - 28 (chain D) in PDB entry 1D1T
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 SER 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D VAL* 2.7 39.8 + - - +
15D TRP* 3.6 29.0 + - - -
20D PRO 5.0 1.8 - - - -
21D PHE* 1.3 74.7 - - - +
23D ILE* 1.3 57.4 + - - +
24D GLU* 3.0 25.7 + - - -
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Residues in contact with ILE 23 (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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10D LYS* 4.2 32.1 - - + -
11D ALA 3.5 7.2 - - - +
12D ALA* 4.2 15.5 - - + -
21D PHE* 4.0 3.3 + - + +
22D SER* 1.3 70.4 + - - +
24D GLU* 1.3 62.4 + - - +
352D PHE* 4.2 16.6 - - + +
353D LYS* 3.8 39.0 - - + +
355D ILE* 4.6 8.1 - - + -
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Residues in contact with GLU 24 (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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10D LYS* 3.2 10.6 - - - +
11D ALA 3.1 28.6 + - - -
13D VAL* 3.6 17.3 - - + -
15D TRP* 2.9 37.0 + - + +
22D SER* 3.0 25.7 + - - +
23D ILE* 1.3 76.1 - - - +
25D GLU* 1.3 62.3 + - - +
26D ILE* 3.9 1.6 - - + -
132D CYS* 3.4 16.6 - - - -
133D LYS* 3.4 23.9 + - - -
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Residues in contact with GLU 25 (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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8D LYS* 4.5 12.6 - - + +
9D CYS* 3.3 27.6 + - - +
10D LYS* 4.1 23.3 - - - +
24D GLU* 1.3 75.2 + - - +
26D ILE* 1.3 59.8 + - - +
27D GLU* 4.4 8.3 - - - +
132D CYS* 3.3 19.6 - - - +
133D LYS* 4.9 2.4 + - - +
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Residues in contact with ILE 26 (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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7D ILE 3.6 0.5 - - - +
8D LYS* 3.3 5.2 - - - +
9D CYS* 2.7 43.9 + - - +
11D ALA* 3.6 33.0 - - + -
13D VAL* 4.1 12.6 - - + -
24D GLU* 4.3 2.7 - - + -
25D GLU* 1.3 79.9 - - - +
27D GLU* 1.3 66.5 + - - +
28D VAL* 4.0 7.6 - - + -
64D ILE* 3.7 8.1 - - + -
130D PHE* 3.5 34.3 - - + -
131D THR 3.2 11.4 - - - +
132D CYS* 3.6 20.2 - - + -
137D VAL* 5.1 2.0 - - + -
147D THR* 3.9 7.6 - - - +
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Residues in contact with GLU 27 (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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6D VAL* 3.7 22.0 - - + -
7D ILE 3.2 3.6 - - - -
8D LYS* 4.2 21.0 - - + +
25D GLU* 4.4 7.6 - - - +
26D ILE* 1.3 82.6 + - - +
28D VAL* 1.3 62.5 + - - +
29D ALA 3.8 0.2 - - - -
129D ARG 3.2 7.3 - - - +
130D PHE* 3.3 2.9 - - - +
131D THR* 2.8 64.4 + - - +
132D CYS* 4.0 3.2 + - - -
133D LYS 4.8 3.0 + - - -
134D GLY 5.1 1.2 + - - -
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Residues in contact with VAL 28 (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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6D VAL* 4.2 1.1 - - - -
7D ILE* 2.7 30.6 + - + +
9D CYS* 3.9 23.3 - - - -
26D ILE* 4.0 11.9 - - + -
27D GLU* 1.3 74.5 - - - +
29D ALA* 1.3 57.6 + - - +
37D ARG* 2.7 37.2 + - - -
129D ARG* 3.4 5.2 - - + +
130D PHE* 4.1 10.3 - - + -
149D TYR* 3.7 29.8 - - + +
150D THR* 4.4 3.1 - - - -
151D VAL* 3.6 29.2 - - + -
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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