Contacts of the strand formed by residues 46 - 53 (chain B) in PDB entry 4WAA
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 LYS 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 4.7 2.3 - - - +
40B ARG* 6.0 2.1 - - - +
43B HIS* 3.1 42.0 + - + +
44B PRO 4.3 3.3 - - - +
45B THR* 1.3 99.2 - - - +
47B ILE* 1.3 69.1 + - - +
48B PRO* 3.9 6.1 - - - +
69B LEU* 4.1 31.0 - - + +
70B VAL 3.4 5.4 - - - +
71B PRO* 3.8 29.6 - - + -
72B ASP* 4.2 0.2 - - - +
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 1.3 77.9 - - - +
48B PRO* 1.3 70.5 - - + +
49B VAL* 3.4 20.2 + - + +
69B LEU* 3.6 3.1 - - - -
70B VAL 2.7 35.2 + - - +
72B ASP* 3.3 23.6 - - - +
111B ILE* 3.9 16.4 - - + +
112B SER* 3.9 25.6 - - - +
115B TYR* 3.5 47.1 - - + -
125B LEU* 4.4 7.4 - - + -
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Residues in contact with PRO 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.6 12.6 - - + -
39B ILE* 4.2 29.6 - - + -
40B ARG* 5.9 4.3 - - + -
46B LYS 3.9 6.5 - - - +
47B ILE* 1.3 88.3 - - + +
49B VAL* 1.3 60.7 - - - +
68B PHE 3.5 7.4 - - - +
69B LEU* 4.0 4.0 - - + -
115B TYR* 4.6 8.5 - - + +
123B GLY 4.0 16.2 - - - +
124B PHE* 3.8 26.8 - - + -
125B LEU* 3.1 22.9 + - - +
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Residues in contact with VAL 49 (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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47B ILE* 3.5 12.1 - - + +
48B PRO* 1.3 78.3 - - - +
50B ILE* 1.3 67.3 + - - +
51B ILE* 3.6 27.8 - - + -
66B THR 3.8 0.3 - - - +
67B LYS* 3.9 0.7 - - - -
68B PHE* 2.9 35.9 + - + +
70B VAL* 3.5 30.7 - - + -
79B LEU* 5.0 0.7 - - + -
111B ILE* 3.9 16.6 - - + -
124B PHE* 4.9 0.2 - - - -
125B LEU* 3.3 14.1 - - + +
127B MET* 3.9 20.9 - - + -
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Residues in contact with ILE 50 (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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23B PHE* 3.5 51.8 - - + -
49B VAL* 1.3 75.8 - - - +
51B ILE* 1.3 66.7 + - - +
52B GLU* 3.8 22.2 - - - +
66B THR* 3.4 16.2 - - + +
67B LYS* 3.9 19.1 - - + -
124B PHE* 4.0 20.0 - - + -
125B LEU 2.9 6.9 + - - +
126B TYR* 3.6 23.3 - - + -
127B MET* 2.9 28.3 + - - +
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Residues in contact with ILE 51 (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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49B VAL* 3.6 22.2 - - + -
50B ILE* 1.3 79.8 - - - +
52B GLU* 1.3 65.9 + - - +
63B LEU* 3.9 23.9 - - + +
65B LYS 4.2 0.2 - - - +
66B THR* 2.9 25.9 + - - +
68B PHE* 3.8 29.8 - - + -
70B VAL* 5.8 0.2 - - + -
79B LEU* 4.7 11.0 - - + -
83B ILE* 4.0 24.9 - - + -
97B LEU* 4.2 15.9 - - + -
127B MET* 3.6 14.6 - - + +
129B TYR* 3.9 15.7 - - + -
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Residues in contact with GLU 52 (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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22B THR* 3.5 23.4 - - + +
23B PHE* 3.0 29.1 + - - +
24B LYS* 5.3 0.3 + - - +
26B ARG* 4.7 2.8 + - - -
50B ILE* 3.8 20.2 - - + +
51B ILE* 1.3 80.6 - - - +
53B ARG* 1.3 64.1 - - - +
66B THR* 3.7 15.3 - - + +
126B TYR* 4.7 7.8 - - - -
127B MET 3.0 11.1 + - - +
128B VAL* 3.1 15.8 - - + +
129B TYR* 2.9 30.7 + - - -
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Residues in contact with ARG 53 (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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52B GLU* 1.3 75.6 - - - +
54B TYR* 1.3 69.8 + - - +
55B LYS* 3.6 8.9 + - - +
57B GLU* 3.2 46.3 + - + +
58B LYS* 4.6 3.8 - - - +
60B LEU 2.7 38.1 + - - -
61B PRO* 3.8 11.0 - - - +
62B VAL* 3.6 32.9 - - + +
128B VAL* 4.1 1.3 - - - +
129B TYR* 3.6 29.4 + - + +
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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