Contacts of the strand formed by residues 107 - 115 (chain B) in PDB entry 3OUY
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 VAL 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B LYS* 3.6 40.2 - - + +
24B GLY* 4.4 2.9 - - - +
27B ALA* 3.4 22.7 - - + -
58B LEU* 4.7 13.5 - - + -
60B ILE* 3.4 25.8 - - + -
103B VAL* 3.4 7.7 - - - +
104B VAL 3.1 24.8 + - - +
105B LYS 3.2 14.3 + - - +
106B GLY* 1.3 81.2 - - - +
108B GLU* 1.3 64.4 + - - +
109B VAL* 3.4 3.0 - - + +
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Residues in contact with GLU 108 (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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57B SER* 6.2 0.3 - - - -
58B LEU 3.2 24.7 + - - +
59B GLU* 3.7 20.5 - - + +
60B ILE* 3.2 18.4 + - - +
101B HIS* 3.4 25.5 + - + -
102B GLY 3.7 3.9 - - - +
103B VAL* 5.2 6.5 - - - +
107B VAL* 1.3 78.9 - - - +
109B VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.7 27.4 - - + -
59B GLU* 4.3 2.4 + - - -
60B ILE* 3.4 24.7 - - + +
62B VAL* 4.4 4.5 - - + -
87B LEU* 4.7 11.0 - - + -
100B VAL 4.9 0.2 - - - -
101B HIS* 3.5 3.5 + - - -
102B GLY 2.8 40.5 + - - +
104B VAL* 4.0 25.8 - - + -
107B VAL* 3.4 18.4 - - + +
108B GLU* 1.3 80.8 - - - +
110B ASP* 1.3 77.7 + - - +
111B VAL* 5.5 0.9 - - + -
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Residues in contact with ASP 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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59B GLU* 3.0 19.5 - - - +
60B ILE 2.8 8.4 + - - +
61B ASP* 3.6 20.3 - - - +
62B VAL* 2.7 35.5 + - - +
99B TYR* 3.5 15.9 - - + -
100B VAL 3.8 1.3 - - - -
101B HIS* 2.9 32.3 + - - +
109B VAL* 1.3 73.4 - - - +
111B VAL* 1.3 58.0 + - - +
112B VAL* 4.2 11.3 - - + +
34D C 3.6 27.1 + - - +
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Residues in contact with VAL 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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35B LEU* 6.2 0.9 - - + -
62B VAL* 3.2 15.3 - - + +
64B LEU* 3.5 35.7 - - + -
79B GLY 4.4 0.4 - - - +
82B ILE* 5.0 0.9 - - + -
83B GLY* 3.8 33.7 - - - -
86B VAL* 5.7 1.6 - - + -
87B LEU* 4.0 23.8 - - + -
99B TYR* 3.2 5.0 - - - +
100B VAL* 3.1 45.5 + - + +
109B VAL* 5.5 1.6 - - + -
110B ASP* 1.3 74.5 - - - +
112B VAL* 1.3 62.4 + - - +
113B PRO* 3.9 1.4 - - - +
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Residues in contact with VAL 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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62B VAL 2.9 8.8 + - - +
63B PHE* 3.5 36.3 - - + -
64B LEU* 2.9 25.2 + - - -
97B HIS* 3.5 32.1 - - + +
99B TYR* 3.7 16.4 - - + -
110B ASP* 4.5 4.9 - - + -
111B VAL* 1.3 84.9 - - - +
113B PRO* 1.3 65.7 - - + +
114B CYS 3.6 0.7 + - - -
127B VAL* 3.9 16.4 - - + -
34D C 3.8 20.0 - - - +
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Residues in contact with PRO 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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64B LEU* 3.8 17.9 - - + +
66B PHE* 4.2 2.9 - - + -
75B LEU* 3.9 39.3 - - + +
79B GLY* 4.0 23.6 - - - +
80B LEU* 5.0 4.5 - - + -
97B HIS* 2.8 29.5 + - - -
98B PRO* 3.3 26.5 - - + +
99B TYR* 4.2 3.1 - - - -
111B VAL 3.9 5.6 - - - +
112B VAL* 1.3 86.4 - - - +
114B CYS* 1.3 60.1 + - - +
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Residues in contact with CYS 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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63B PHE* 3.5 28.3 - - + -
64B LEU 3.0 25.4 + - - +
65B LEU* 4.3 8.7 - - - -
66B PHE* 3.1 19.2 + - - +
75B LEU* 4.4 5.5 - - - +
113B PRO* 1.3 75.7 - - - +
115B TYR* 1.3 72.6 + - - +
125B SER* 4.2 4.3 - - - -
127B VAL* 3.7 14.8 - - + -
128B ASP* 3.1 15.7 - - - +
131B PRO* 4.2 15.5 - - - -
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Residues in contact with TYR 115 (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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65B LEU* 4.7 0.7 - - - +
66B PHE* 3.7 3.6 - - + -
67B PRO 3.6 12.6 - - - -
68B GLU* 3.6 33.2 - - + -
70B PHE* 2.6 30.5 + - + -
71B SER 3.6 13.5 - - - -
72B LYS* 3.8 4.2 + - - +
75B LEU* 3.7 24.3 - - + +
114B CYS* 1.3 85.6 - - - +
116B LYS* 1.3 59.9 + - - +
117B LEU* 3.1 18.8 + - + +
124B LYS* 3.6 33.7 - - + -
125B SER* 3.7 17.9 - - - -
128B ASP* 3.0 40.6 + - - +
131B PRO* 5.0 2.8 - - - +
132B PHE* 5.5 0.3 - - - -
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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