Contacts of the strand formed by residues 125 - 130 (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 LEU 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 4.4 4.9 - - + -
48B PRO 3.1 15.8 + - - +
49B VAL* 3.3 8.3 - - + +
50B ILE 2.9 24.6 + - - -
99B VAL* 3.7 25.8 - - + -
111B ILE* 4.0 22.9 - - + -
114B VAL* 4.5 5.2 - - + -
115B TYR* 4.0 25.6 - - + -
118B GLU* 3.7 31.2 - - + +
119B LYS* 4.0 1.3 - - - +
123B GLY 4.0 0.4 + - - -
124B PHE* 1.3 73.5 - - - +
126B TYR* 1.3 61.4 + - - +
127B MET* 3.8 28.3 - - + -
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Residues in contact with TYR 126 (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* 3.8 16.3 - + + -
24B LYS* 3.7 34.3 - - + +
32B ARG* 3.8 1.9 + - - -
50B ILE* 3.6 32.8 - - + -
52B GLU* 4.7 7.0 - - - -
99B VAL* 3.7 19.4 - - - +
100B ASN* 3.8 17.6 + - - +
118B GLU 5.3 1.2 + - - -
120B ASP* 3.6 41.3 - - + +
122B ASP* 2.8 26.0 + - - -
124B PHE* 3.7 13.4 - - + -
125B LEU* 1.3 75.9 - - - +
127B MET* 1.3 65.6 + - - +
128B VAL* 5.5 3.8 - - + -
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Residues in contact with MET 127 (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* 3.9 18.2 - - + -
50B ILE 2.9 13.5 + - - +
51B ILE* 4.4 7.0 - - + -
52B GLU* 3.0 25.2 + - - +
76B MET* 3.8 27.6 - - + -
79B LEU* 3.9 14.4 - - + -
97B LEU* 3.8 36.8 - - + -
98B LEU 3.1 7.4 - - - +
99B VAL* 4.0 15.3 - - + -
111B ILE* 4.0 4.7 - - + -
114B VAL* 5.6 0.2 - - + -
125B LEU* 3.8 28.3 - - + +
126B TYR* 1.3 80.1 - - - +
128B VAL* 1.3 68.4 + - - +
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Residues in contact with VAL 128 (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* 3.1 15.9 - - + +
53B ARG 4.1 0.7 - - - -
54B TYR* 3.4 43.5 - - + +
97B LEU* 4.4 1.8 - - - -
98B LEU* 2.6 55.0 + - + +
101B GLY 6.2 2.0 - - - +
126B TYR* 5.5 3.1 - - + -
127B MET* 1.3 82.1 - - - +
129B TYR* 1.3 56.6 + - - +
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Residues in contact with TYR 129 (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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51B ILE* 3.9 13.9 - - + -
52B GLU* 2.9 23.1 + - - -
53B ARG* 3.6 32.7 - - + +
54B TYR* 2.9 23.8 + - - +
60B LEU* 3.8 15.0 - - + -
61B PRO 2.6 29.8 + - - -
62B VAL* 3.4 3.1 - - - -
63B LEU* 3.0 40.9 + - + -
83B ILE* 4.8 2.5 - - + -
87B LEU* 3.5 16.2 - - + +
95B PHE* 3.7 31.0 - + + -
96B PHE 3.1 12.8 - - - +
97B LEU* 3.8 6.7 - - + -
128B VAL* 1.3 75.5 - - - +
130B ALA* 1.3 59.2 + - - +
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Residues in contact with ALA 130 (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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54B TYR* 3.9 18.2 - - + -
57B GLU* 3.4 13.0 - - - +
60B LEU* 3.5 9.5 - - - +
95B PHE* 3.6 3.3 - - - -
96B PHE* 2.9 32.6 + - + +
98B LEU* 5.1 9.6 - - + +
128B VAL 4.3 0.2 + - - -
129B TYR* 1.3 75.7 - - - +
131B SER* 1.3 62.1 + - - +
132B GLN* 3.3 24.5 - - - +
134B THR* 5.8 2.0 - - - +
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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