Contacts of the strand formed by residues 107 - 112 (chain B) in PDB entry 3NIE
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B LYS 3.6 1.4 - - - +
60B LYS* 3.5 3.5 - - - +
61B VAL* 2.9 39.2 + - + +
64B MET* 3.4 17.1 - - + +
74B ILE* 4.3 7.0 - - + -
78B ILE* 3.9 17.5 - - + -
95B LEU* 4.7 4.0 - - + -
96B ILE 4.2 12.1 - - - +
98B PRO* 4.9 2.9 - - + -
104B PHE* 4.9 3.6 - - + -
106B GLU* 1.3 76.5 - - - +
108B TYR* 1.3 70.5 + - - +
109B ILE* 4.0 20.9 - - + -
405B PHE* 3.8 31.2 - - + -
409B ILE* 4.0 26.2 - - + -
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Residues in contact with TYR 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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23B ASN 3.3 0.7 + - - -
24B VAL* 3.7 15.9 - - + -
25B LYS* 2.9 38.0 + - + +
26B VAL* 3.4 24.0 - - + -
58B ILE* 4.0 15.7 - - + -
59B LYS 3.4 4.0 - - - -
60B LYS* 3.0 48.0 + - + -
95B LEU* 4.0 1.9 - - - -
96B ILE* 3.2 52.0 + - + +
106B GLU* 4.9 13.0 - - + +
107B LEU* 1.3 82.4 - - - +
109B ILE* 1.3 62.2 + - - +
110B VAL 4.1 0.2 - - - -
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA 3.7 0.7 - - - +
58B ILE* 3.4 1.7 - - - -
59B LYS* 2.7 59.0 + - + +
61B VAL* 4.5 8.7 - - + -
74B ILE* 4.4 11.4 - - + -
77B GLU* 4.5 14.6 - - - +
78B ILE* 3.4 28.5 - - + -
81B LEU* 5.2 2.0 - - + -
92B LEU* 3.6 26.5 - - + -
94B ASP 4.1 2.2 - - - -
95B LEU* 4.1 9.6 - - + -
107B LEU* 4.1 15.3 - - + -
108B TYR* 1.3 75.3 - - - +
110B VAL* 1.3 62.3 + - - +
111B LEU* 3.8 17.0 + - + +
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Residues in contact with VAL 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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30B TYR* 3.9 14.6 - - + +
56B VAL* 3.5 33.9 - - + -
57B ALA 3.3 4.0 - - - +
58B ILE* 4.1 13.5 - - + +
92B LEU* 3.8 3.1 - - - +
93B HIS* 2.8 44.4 + - + +
94B ASP* 2.9 38.3 + - + +
96B ILE* 4.0 20.6 - - + -
109B ILE* 1.3 73.5 - - - +
111B LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 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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44B VAL* 5.7 0.2 - - + -
56B VAL* 3.3 9.7 - - - +
57B ALA* 2.5 38.6 + - + +
59B LYS* 4.7 23.3 - - + -
77B GLU* 5.0 2.2 - - - +
81B LEU* 3.3 32.8 - - + -
90B ILE* 4.3 12.3 - - + -
91B ARG 3.4 14.1 - - - +
92B LEU* 4.0 14.1 - - + -
93B HIS* 4.2 4.5 - - - -
109B ILE* 4.0 13.2 - - + +
110B VAL* 1.3 74.3 - - - +
112B GLU* 1.3 66.6 + - - +
173B CYS* 5.4 3.8 - - + -
430B ANP 3.9 27.8 - - - +
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Residues in contact with GLU 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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55B ASN 5.3 0.4 - - - -
56B VAL* 5.2 2.2 - - - +
89B ILE 3.9 3.3 - - - +
90B ILE* 3.1 20.2 - - + +
91B ARG* 3.0 59.6 + - + +
93B HIS* 4.3 6.2 - - + +
111B LEU* 1.3 70.2 - - - +
113B ILE* 1.3 64.8 + - + +
165B ASN* 5.2 0.3 + - - -
171B LYS* 3.1 32.3 + - - +
430B ANP 2.7 30.3 + - - -
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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