Contacts of the strand formed by residues 7 - 13 (chain B) 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 ILE 7 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B THR* 3.8 26.7 - - + -
5B LYS 3.4 0.8 + - - +
6B VAL* 1.3 77.7 - - - +
8B LYS* 1.3 74.4 + - - +
9B CYS* 4.2 4.7 - - + -
27B GLU* 3.2 5.5 - - - -
28B VAL* 2.9 36.2 + - + +
37B ARG* 3.5 28.9 - - - +
74B GLU* 3.9 11.2 - - - +
149B TYR* 3.4 59.0 - - + -
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Residues in contact with LYS 8 (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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6B VAL* 3.9 10.1 + - - +
7B ILE* 1.3 81.0 - - - +
9B CYS* 1.3 64.4 + - - +
25B GLU* 4.7 12.3 - - + +
26B ILE 3.4 6.7 - - - +
27B GLU* 4.3 22.2 - - + +
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Residues in contact with CYS 9 (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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7B ILE* 4.2 1.6 - - + -
8B LYS* 1.3 76.8 - - - +
10B LYS* 1.3 72.4 + - - +
25B GLU* 3.4 16.0 + - - +
26B ILE* 2.8 45.6 + - - -
28B VAL* 4.1 12.8 - - - -
147B THR* 3.9 3.8 - - - -
148B GLU* 3.8 20.0 - - + +
149B TYR* 3.9 33.2 - - + -
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Residues in contact with LYS 10 (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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9B CYS* 1.3 78.4 - - - +
11B ALA* 1.3 62.8 + - - +
23B ILE* 4.0 20.4 - - + -
24B GLU 3.2 9.0 - - - +
25B GLU* 3.6 30.5 - - - +
147B THR* 3.7 0.2 - - - -
148B GLU* 3.2 43.2 + - + +
352B PHE* 4.9 7.0 - - + -
353B LYS* 6.1 5.8 - - + -
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Residues in contact with ALA 11 (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 LYS* 1.3 76.4 - - - +
12B ALA* 1.3 62.8 + - - +
13B VAL* 3.3 3.9 + - + +
23B ILE* 3.3 4.2 - - - -
24B GLU 2.9 29.8 + - - +
26B ILE* 3.4 33.4 - - + -
64B ILE* 3.7 13.5 - - + -
146B PHE 3.6 5.2 - - - +
147B THR* 3.5 16.2 - - - +
352B PHE* 4.6 2.7 - - - -
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Residues in contact with ALA 12 (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 ALA* 1.3 70.3 - - - +
13B VAL* 1.3 60.1 + - - +
21B PHE* 3.6 32.8 - - + -
22B SER 3.9 4.7 - - - -
23B ILE* 4.1 10.5 - - + +
63B VAL 4.2 0.3 - - - +
64B ILE* 4.0 16.5 - - - +
65B VAL 4.6 0.3 + - - -
146B PHE* 3.0 18.2 + - + +
352B PHE* 3.7 21.4 - - + -
355B ILE* 3.8 14.4 - - + -
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Residues in contact with VAL 13 (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 ALA 3.8 10.3 - - - +
12B ALA* 1.3 75.7 - - - +
14B LEU* 1.3 81.0 + - - +
15B TRP* 3.8 24.0 - - + +
20B PRO 4.2 0.2 - - - +
21B PHE* 3.5 6.6 - - - -
22B SER* 3.0 35.9 + - - +
24B GLU* 4.1 15.7 - - + -
26B ILE* 4.3 11.4 - - + -
62B PRO* 3.9 13.2 - - + -
63B VAL 3.7 7.6 - - - +
64B ILE* 4.1 15.7 - - + -
132B CYS* 4.6 4.3 - - - -
137B VAL* 4.6 6.5 - - + -
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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