Contacts of the strand formed by residues 39 - 46 (chain B) in PDB entry 1PH7
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 LEU 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA* 4.7 15.3 - - + -
14B PHE* 4.8 14.4 - - + -
17B LEU* 4.2 17.9 - - + -
35B LEU 4.7 3.4 - - - +
37B LYS* 3.8 13.0 - - + +
38B PRO* 1.3 73.4 - - - +
40B LYS* 1.3 61.5 + - - +
41B CYS* 3.6 17.7 + - - -
89B VAL* 3.7 2.8 - - - -
90B ILE* 2.9 38.1 + - + +
93B TRP* 3.3 49.1 - - + +
116B LEU* 4.5 12.3 - - + -
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Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PRO 4.1 1.6 + - - -
39B LEU* 1.3 71.9 - - - +
41B CYS* 1.3 62.6 + - - +
54B ASP* 5.3 3.5 - - - +
87B VAL* 4.0 14.1 - - + -
88B ILE 3.7 3.8 - - - -
89B VAL* 4.1 18.8 - - + +
124B ASN* 4.4 7.2 - - - +
127B GLU* 2.8 34.1 + - - +
129B LEU* 4.5 20.1 - - + +
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Residues in contact with CYS 41 (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 PHE* 4.0 22.7 - - + -
39B LEU* 3.7 17.7 - - - -
40B LYS* 1.3 77.7 - - - +
42B TYR* 1.3 65.7 + - - +
52B VAL* 4.1 16.6 - - - -
53B THR 3.1 25.8 - - - +
54B ASP* 4.4 2.5 - - - +
87B VAL* 3.0 15.9 - - - +
88B ILE* 3.1 24.2 + - - +
90B ILE* 4.6 11.9 - - - -
129B LEU* 5.0 2.0 - - - -
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Residues in contact with TYR 42 (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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41B CYS* 1.3 73.9 - - - +
43B VAL* 1.3 83.1 + - - +
44B LYS* 3.6 14.1 + - + -
52B VAL* 3.2 6.1 - - - +
53B THR* 2.9 48.5 + - + +
84B THR* 5.7 0.2 - - - +
85B ASP* 2.8 54.6 + - - +
86B LYS 4.9 2.9 - - - -
87B VAL* 3.7 11.2 - - + +
128B ARG* 4.1 11.2 + - - -
129B LEU* 3.4 34.3 - - + +
135B PRO* 6.2 0.2 - - + -
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B CYS 4.3 0.2 - - - +
42B TYR* 1.3 85.5 - - - +
44B LYS* 1.3 60.2 + - - +
45B GLU 3.1 27.6 - - - +
50B PHE* 4.2 15.3 - - + -
51B LEU 3.7 4.7 - - - +
52B VAL* 3.9 14.1 - - + -
83B LEU* 3.7 16.4 - - + +
84B THR* 3.9 4.3 - - - +
85B ASP 2.9 24.1 + - - -
86B LYS 2.9 26.2 + - - +
88B ILE* 3.9 25.8 - - + -
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Residues in contact with LYS 44 (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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42B TYR* 3.6 17.0 + - + -
43B VAL* 1.3 73.4 - - - +
45B GLU* 1.3 92.3 + - + +
51B LEU* 3.0 14.6 + - + +
53B THR* 4.2 13.0 - - + +
58B PHE* 4.3 17.4 - - + -
84B THR* 3.3 17.2 - - - +
85B ASP 4.6 0.2 + - - -
134B TYR* 3.4 34.4 + - - -
135B PRO* 3.4 34.8 - - + -
6D T 5.1 2.8 + - - -
7D T 4.7 9.5 + - - +
9D G 4.5 3.8 - - - +
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Residues in contact with GLU 45 (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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43B VAL* 3.1 16.0 - - - +
44B LYS* 1.3 110.5 + - + +
46B SER* 1.3 61.8 + - - +
47B TYR 4.6 5.8 - - - +
49B HIS* 3.3 15.2 + - - +
50B PHE* 3.6 0.5 - - - -
51B LEU* 3.0 30.7 + - + +
84B THR* 3.7 8.1 - - - -
7D T 3.8 8.6 - - - +
9D G 2.5 53.2 + - - +
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Residues in contact with SER 46 (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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45B GLU* 1.3 76.3 - - - +
47B TYR* 1.3 66.6 + - - +
49B HIS 3.5 7.9 - - - -
50B PHE* 3.6 23.3 + - - -
80B ILE 3.9 10.8 - - - -
81B VAL* 2.9 25.0 + - - +
82B ASP* 3.6 1.9 + - - -
84B THR* 2.9 32.1 + - - -
215B ILE* 3.3 23.2 - - - +
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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