Contacts of the strand formed by residues 108 - 114 (chain B) in PDB entry 2P5V
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 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ILE* 3.8 19.3 - - + -
72B ILE 3.4 1.9 - - - +
74B VAL* 2.8 38.4 + - + +
76B ILE* 4.0 30.5 - - + -
83B ARG* 3.1 41.7 + - - +
86B PHE* 4.0 20.2 - + + -
87B ALA* 5.7 0.6 - - + +
99B CYS* 3.8 15.0 - - - -
100B PHE 3.2 4.0 - - - +
101B ALA* 3.7 28.9 - - + -
106B THR* 3.1 9.5 - - - +
107B ASP* 1.3 84.6 - - + +
109B LEU* 1.3 59.4 + - - +
110B LEU* 3.8 16.6 - - + -
1015B CL 2.9 20.0 - - + +
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Residues in contact with LEU 109 (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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71A PHE* 3.5 45.1 - - + -
109A LEU* 4.5 5.8 - - + -
71B PHE* 4.2 31.4 - - + -
72B ILE 3.5 13.5 - - - +
73B ARG* 4.0 21.3 - - + +
98B SER* 3.9 0.5 + - - +
99B CYS* 3.2 4.0 + - - -
100B PHE* 2.8 39.4 + - + +
102B LEU* 3.7 23.7 - - + +
106B THR* 4.1 2.4 - - + +
108B TYR* 1.3 71.3 - - - +
110B LEU* 1.3 63.8 + - - +
111B GLN* 5.2 2.4 - - + +
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Residues in contact with LEU 110 (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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70B ALA 3.6 0.2 - - - +
71B PHE* 3.2 6.8 - - - +
72B ILE* 2.8 61.9 + - + +
74B VAL* 3.9 16.2 - - + -
86B PHE* 4.1 19.3 - - + -
90B VAL* 4.3 5.6 - - + -
93B TRP* 4.8 1.6 - - + -
96B VAL* 4.1 30.3 - - + -
98B SER 3.3 4.3 - - - +
99B CYS* 3.7 25.4 - - - -
108B TYR* 3.8 15.0 - - + -
109B LEU* 1.3 81.7 - - - +
111B GLN* 1.3 64.0 + - - +
112B ALA 4.1 0.2 - - - -
123B PHE* 5.4 0.4 - - + -
128B LEU* 4.7 9.0 - - + -
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Residues in contact with GLN 111 (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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71A PHE* 4.0 7.4 - - - -
98A SER* 5.8 1.0 + - - -
100A PHE* 4.6 6.1 - - - -
111A GLN* 3.2 24.6 + - - +
69B GLN* 4.1 14.5 - - - +
70B ALA 3.4 4.9 - - - +
71B PHE* 3.3 47.3 - - + -
96B VAL* 3.7 2.4 - - - -
97B LEU* 2.9 28.6 + - + +
98B SER* 3.0 32.5 + - - +
100B PHE* 4.2 5.6 - - + -
109B LEU* 5.2 3.4 - - + +
110B LEU* 1.3 71.8 - - - +
112B ALA* 1.3 60.4 + - - +
113B PHE* 5.2 4.9 - - + -
148B HIS* 6.0 3.2 - - - -
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Residues in contact with ALA 112 (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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68B LEU 3.9 0.2 - - - +
69B GLN* 3.4 4.7 - - - +
70B ALA* 2.8 38.5 + - - +
72B ILE* 4.4 12.6 - - + -
95B GLU 3.0 20.6 - - - +
96B VAL* 3.9 12.6 - - + -
110B LEU 4.1 0.2 - - - -
111B GLN* 1.3 74.4 - - - +
113B PHE* 1.3 66.2 + - - +
114B PHE* 3.4 25.9 - - + -
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Residues in contact with PHE 113 (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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152A LEU* 3.8 15.9 - - + -
153A PRO* 4.3 4.6 - - + +
61B PRO* 3.6 37.2 - - + -
66B LEU* 4.1 31.5 - - + +
68B LEU 3.4 3.8 - - - -
69B GLN* 3.4 51.1 - - + -
95B GLU* 3.0 26.2 + - - +
97B LEU* 3.9 30.7 - - + -
111B GLN* 5.3 4.3 - - + -
112B ALA* 1.3 79.2 - - - +
114B PHE* 1.3 67.8 + - - +
148B HIS* 6.2 1.8 - - - -
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Residues in contact with PHE 114 (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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66B LEU* 3.3 9.6 - - - -
67B GLY 3.2 5.9 + - - -
68B LEU* 2.8 39.7 + - + +
70B ALA* 4.1 4.5 - - + -
95B GLU* 3.8 19.3 - - + -
112B ALA* 3.4 37.5 - - + -
113B PHE* 1.3 77.2 - - - +
115B THR* 1.3 61.8 + - - +
116B ASP 3.8 16.6 - - - +
119B ALA* 4.0 8.5 - - + -
120B PHE* 3.4 42.6 - + + +
123B PHE* 3.6 44.6 - + + -
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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