Contacts of the strand formed by residues 11 - 16 (chain B) in PDB entry 4D2T
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 TYR 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B LEU* 2.8 35.1 + - + +
8B LEU* 3.6 26.9 - - - +
9B LYS 4.0 0.2 - - - -
10B TYR* 1.3 85.4 - + + +
12B GLU* 1.3 61.1 + - - +
13B LEU* 3.7 5.1 + - + +
28B ALA* 4.2 4.7 - - + -
29B CYS 3.4 2.9 - - - +
30B HIS* 3.4 35.4 - + + -
31B ILE* 4.2 4.0 - - - -
37B VAL* 3.7 22.9 - - + -
39B ILE* 4.0 17.7 - - + -
74B HIS* 3.0 42.8 + + - +
76B LEU* 4.6 0.4 - - + -
85B VAL* 3.6 28.9 - - + +
312B HIS* 4.6 0.2 + - - -
315B ALA* 3.4 14.7 - - - +
319B LEU* 5.1 0.3 - - - +
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Residues in contact with GLU 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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8B LEU* 5.6 3.4 - - - -
11B TYR* 1.3 68.8 - - - +
13B LEU* 1.3 66.9 + - - +
14B HIS* 3.2 30.0 + - + +
28B ALA* 4.4 0.4 - - - -
29B CYS* 2.8 42.6 + - + +
31B ILE* 3.7 26.8 - - + +
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Residues in contact with LEU 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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4B TYR* 3.9 18.2 - - + -
7B LEU* 3.8 23.3 - - + -
8B LEU* 4.4 19.8 - - + +
11B TYR* 3.7 6.8 + - + +
12B GLU* 1.3 74.7 - - - +
14B HIS* 1.3 69.1 + - - +
26B LYS* 3.6 39.9 - - + +
27B LEU 3.9 2.0 - - - -
28B ALA* 3.8 7.0 - - + -
39B ILE* 3.6 30.5 - - + -
41B ILE* 5.4 1.6 - - + -
99C ILE* 4.7 7.4 - - + +
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Residues in contact with HIS 14 (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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12B GLU* 3.2 43.2 + - + -
13B LEU* 1.3 81.3 + - - +
15B GLU* 1.4 71.9 + - + +
26B LYS* 2.8 29.3 + - - -
27B LEU* 2.7 21.4 + - + +
28B ALA 3.9 4.4 + - - -
29B CYS* 3.5 28.6 + - + -
36B MET* 4.6 10.4 - - + -
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Residues in contact with GLU 15 (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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14B HIS* 1.4 79.5 - - + +
16B THR* 1.3 63.0 + - - +
17B ILE* 3.9 5.0 + - - +
27B LEU* 2.8 67.0 + - + +
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Residues in contact with THR 16 (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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14B HIS 3.7 0.6 + - - -
15B GLU* 1.3 78.1 - - - +
17B ILE* 1.4 61.7 + - - +
18B GLY 4.0 6.1 - - - +
19B THR* 3.9 15.0 - - - +
24B LYS* 3.7 24.0 - - + -
25B VAL 3.7 13.0 - - - +
26B LYS* 3.3 19.3 + - + +
17C ILE* 5.1 5.0 - - - +
93C GLU* 5.4 0.7 - - - +
96C ASP* 3.0 25.7 + - - +
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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