Contacts of the strand formed by residues 114 - 121 (chain B) in PDB entry 5WY8
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 GLY 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS* 4.9 0.9 - - - -
79B SER 3.5 10.3 - - - -
80B SER 4.0 13.2 - - - -
112B ASP 3.7 0.8 + - - -
113B SER* 1.3 76.1 - - - +
115B LEU* 1.3 64.0 + - - +
116B TYR* 4.0 6.0 - - - -
131B ILE 3.9 0.3 - - - +
132B SER* 3.8 2.1 + - - -
133B LEU* 2.9 34.2 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 4.1 28.7 - - + -
77B TYR 3.8 0.2 - - - +
78B LYS* 3.2 5.2 - - - -
79B SER* 2.9 48.1 + - - +
81B GLY* 3.9 10.3 - - - +
82B PRO* 3.6 35.4 - - + +
86B GLU* 5.8 0.2 - - - +
114B GLY* 1.3 73.6 - - - +
116B TYR* 1.3 62.3 + - - +
117B ALA 3.9 1.5 + - - +
130B SER* 4.4 16.4 - - - +
131B ILE 3.5 4.3 - - - +
132B SER* 3.6 32.8 - - - +
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Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.0 13.7 - - + -
76B TRP* 3.6 20.6 - - + -
77B TYR 3.2 4.9 - - - -
78B LYS* 3.5 32.3 + - + +
89B ILE* 3.8 25.6 - - + -
96B MET* 4.6 7.8 - - + -
103B ILE* 4.2 11.0 - - + -
105B PHE* 3.6 28.6 - + - -
112B ASP* 2.6 34.5 + - - -
114B GLY 4.0 10.5 - - - -
115B LEU* 1.3 74.1 - - - +
117B ALA* 1.3 63.3 + - - +
118B CYS 3.5 2.1 + - - -
130B SER* 4.4 0.4 - - - -
131B ILE* 2.9 37.3 + - + +
133B LEU* 4.0 22.0 - - + -
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Residues in contact with ALA 117 (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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75B MET 3.6 1.0 - - - +
76B TRP* 3.3 10.5 - - - -
77B TYR* 2.9 47.0 + - + -
86B GLU* 4.0 22.4 - - + +
115B LEU 3.9 2.2 + - - +
116B TYR* 1.3 69.8 - - - +
118B CYS* 1.3 60.7 + - - +
119B VAL* 3.7 9.4 + - + +
128B LYS* 4.4 9.2 - - + +
129B VAL 3.3 9.6 - - - +
130B SER* 4.2 10.1 - - - +
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Residues in contact with CYS 118 (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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53B CYS* 2.0 52.7 - - + -
55B LEU* 3.9 2.8 - - - +
74B LEU* 3.4 22.9 - - - -
75B MET 4.0 1.1 - - - -
76B TRP* 3.7 22.4 - - + -
116B TYR 3.5 2.6 + - - -
117B ALA* 1.3 71.8 - - - +
119B VAL* 1.3 58.5 + - - +
120B ILE 4.3 0.2 - - - -
128B LYS* 3.0 5.7 - - - +
129B VAL* 2.9 39.2 + - + +
131B ILE* 4.1 6.5 - - + -
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Residues in contact with VAL 119 (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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307A THR* 4.9 7.4 - - - -
31B CYS* 4.2 0.9 - - - -
73B SER 3.6 0.7 - - - +
74B LEU* 3.3 5.9 - - - +
75B MET* 2.9 62.1 + - + +
77B TYR* 3.8 26.9 - - + -
117B ALA* 4.1 5.8 - - + +
118B CYS* 1.3 78.7 - - - +
120B ILE* 1.3 64.7 + - - +
126B CYS* 4.0 20.2 - - - -
127B MET 3.4 10.3 - - - +
128B LYS* 3.5 26.5 - - + -
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Residues in contact with ILE 120 (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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55B LEU* 3.8 17.5 - - + +
56B PHE* 3.8 21.5 - - + -
60B ILE* 3.5 31.6 - - + -
67B ALA* 5.4 4.5 - - + -
72B LEU* 4.4 23.6 - - + -
73B SER 3.1 9.4 - - - +
74B LEU* 3.5 28.5 - - + -
119B VAL* 1.3 72.0 - - - +
121B ARG* 1.3 63.0 + - - +
125B TYR* 4.6 4.3 - - + -
126B CYS* 3.4 0.9 - - - -
127B MET* 2.9 49.8 + - + +
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Residues in contact with ARG 121 (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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305A MET* 4.4 18.6 - - + +
306A SER 3.3 22.5 + - - -
307A THR 3.5 16.2 + - - -
308A LEU 4.5 1.0 + - - -
309A GLY* 4.1 12.3 - - - +
310A VAL* 4.2 13.3 - - - +
27B SER 4.2 8.7 + - - -
28B ALA* 4.0 17.2 + - - +
31B CYS* 5.5 0.6 - - - +
71B GLY 4.5 0.2 - - - +
72B LEU* 3.6 7.7 - - - +
73B SER* 2.9 34.4 + - - +
75B MET* 3.5 23.6 - - + -
120B ILE* 1.3 77.1 - - - +
122B ASN* 1.3 76.5 + - - +
123B SER 4.1 10.3 + - - -
125B TYR 3.1 14.1 + - - +
126B CYS* 2.9 35.7 - - - +
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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