Contacts of the strand formed by residues 106 - 111 (chain B) in PDB entry 5NNZ
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 CYS 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B LEU* 3.7 1.9 - - - +
101B ASN* 2.8 43.8 + - - +
104B GLY 4.2 1.9 - - - +
105B SER* 1.3 94.7 - - - +
107B PHE* 1.3 63.1 + - - +
118B LEU* 4.0 16.6 - - + -
119B TRP 3.1 13.2 - - - +
120B ASP* 4.3 2.5 - - - -
127B LEU* 4.0 19.3 - - - -
142B PHE* 4.1 6.5 - - + -
164B VAL* 5.3 9.2 - - + -
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Residues in contact with PHE 107 (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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88B LEU* 3.5 27.6 - - + -
98B VAL* 4.3 10.3 - - + -
99B ALA 3.4 11.2 - - - +
100B LEU* 3.5 24.5 - - + -
106B CYS* 1.3 75.8 - - - +
108B ILE* 1.3 62.5 + - - +
109B THR* 4.0 12.6 - - + -
118B LEU* 4.4 0.7 - - - -
119B TRP* 3.1 68.5 + + + -
120B ASP 4.3 1.1 - - - -
121B THR* 3.9 22.4 - - + -
142B PHE* 4.4 0.7 - - - -
403B ILE* 4.2 18.8 - - + -
411B CYS* 4.4 3.4 - - + -
413B ILE* 4.0 22.4 - - + -
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Residues in contact with ILE 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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98B VAL* 3.6 1.2 - - - +
99B ALA* 2.9 39.5 + - + +
107B PHE* 1.3 72.5 - - - +
109B THR* 1.3 65.4 + - - +
116B CYS* 3.8 12.6 - - - -
117B LYS 3.2 6.3 - - - +
118B LEU* 3.5 26.0 - - + -
130B LEU* 5.2 0.2 - - + -
140B ILE* 3.3 29.3 - - + +
141B ALA* 3.6 28.3 - - - +
142B PHE* 3.7 21.1 - - + -
150B ILE* 3.7 24.0 - - + -
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Residues in contact with THR 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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90B ALA* 4.7 0.9 - - + -
91B HIS* 3.1 15.7 + - - -
95B LEU* 3.8 15.7 - - - -
97B ASN 3.6 4.5 - - - -
98B VAL* 4.3 8.7 - - + -
107B PHE* 4.0 12.3 - - + -
108B ILE* 1.3 81.7 - - - +
110B GLY* 1.3 60.4 + - - +
116B CYS* 3.1 4.7 - - - -
117B LYS* 2.9 29.0 + - - +
119B TRP* 2.8 34.2 + - + +
140B ILE* 4.0 2.0 - - - -
411B CYS* 4.1 21.5 - - - -
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Residues in contact with GLY 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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95B LEU* 3.1 12.6 - - - +
96B THR* 2.8 31.4 + - - -
97B ASN 3.4 9.3 + - - -
109B THR* 1.3 73.5 - - - +
111B SER* 1.3 60.8 + - - -
115B THR 3.4 9.4 - - - -
116B CYS* 4.3 1.1 - - - -
137B VAL* 3.7 15.9 - - - -
140B ILE* 3.7 7.9 - - - +
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Residues in contact with SER 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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91B HIS* 3.4 21.7 - - - +
93B LEU 2.7 20.7 + - - -
94B PRO 3.2 11.4 - - - -
95B LEU* 4.3 0.2 - - - -
96B THR* 3.9 4.0 - - - +
110B GLY* 1.3 77.0 - - - -
112B TYR* 1.3 71.5 + - - +
113B ASP* 3.0 26.4 + - - -
114B ARG* 3.4 5.4 + - - -
115B THR 3.3 6.3 + - - -
136B VAL* 4.1 5.8 - - - -
137B VAL 3.3 24.5 + - - -
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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