Contacts of the strand formed by residues 107 - 112 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LYS 3.6 1.9 - - - +
60A LYS* 3.6 3.0 - - - +
61A VAL* 3.0 33.6 + - + +
64A MET* 3.6 21.8 - - + -
74A ILE* 3.9 10.5 - - + -
78A ILE* 4.6 4.5 - - + -
95A LEU* 4.6 9.4 - - + -
96A ILE 4.3 9.6 - - - +
98A PRO* 5.2 2.2 - - + -
104A PHE* 5.0 5.6 - - + -
106A GLU* 1.3 80.6 - - - +
108A TYR* 1.3 74.1 + - - +
109A ILE* 3.9 16.8 + - + +
405A PHE* 3.5 34.3 - - + -
409A ILE* 4.0 27.4 - - + -
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Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN 3.1 8.7 + - - -
24A VAL* 3.6 19.5 - - + -
25A LYS* 3.2 25.8 + - + +
26A VAL* 3.5 16.2 - - + -
58A ILE* 4.0 16.4 - - + -
59A LYS 3.5 2.5 - - - -
60A LYS* 3.1 52.6 + - + -
95A LEU* 3.8 5.5 - - - +
96A ILE* 3.2 52.8 + - + +
106A GLU* 4.1 18.7 + - + -
107A LEU* 1.3 81.0 - - - +
109A ILE* 1.3 62.4 + - - +
110A VAL 3.8 0.4 + - - -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA 3.7 0.7 - - - +
58A ILE* 3.3 1.6 - - - -
59A LYS* 2.6 68.2 + - + +
61A VAL* 4.3 7.9 - - + -
74A ILE* 4.1 15.5 - - + -
77A GLU* 4.4 11.7 - - - +
78A ILE* 3.3 42.4 - - + -
81A LEU* 5.6 0.7 - - + -
92A LEU* 3.8 15.5 - - + -
94A ASP 4.1 2.0 - - - -
95A LEU* 4.2 5.8 - - + -
107A LEU* 4.3 10.3 - - + +
108A TYR* 1.3 74.3 - - - +
110A VAL* 1.3 62.4 + - - +
111A LEU* 3.9 17.5 + - + +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.8 17.7 - - + +
56A VAL* 3.8 31.2 - - + -
57A ALA 3.3 4.9 - - - +
58A ILE* 4.2 13.0 - - + -
92A LEU* 3.7 7.1 - - - +
93A HIS* 3.0 30.2 + - + -
94A ASP* 2.9 30.9 + - + +
96A ILE* 3.8 34.5 - - + -
108A TYR 4.3 0.2 - - - +
109A ILE* 1.3 76.3 - - - +
111A LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 6.1 0.4 - - + -
56A VAL* 3.4 9.2 - - - +
57A ALA* 2.6 39.1 + - + +
59A LYS* 5.0 18.8 - - + +
77A GLU* 5.4 1.8 - - - +
81A LEU* 3.9 20.4 - - + -
90A ILE* 4.4 12.8 - - + -
91A ARG 3.3 14.1 - - - +
92A LEU* 3.9 9.6 - - + -
93A HIS* 4.1 6.5 - - - +
109A ILE* 3.9 24.7 - - + +
110A VAL* 1.3 81.2 - - - +
112A GLU* 1.3 67.1 + - - +
173A CYS* 5.4 3.8 - - + -
430A ANP 3.8 29.2 - - - +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASN 5.5 0.2 - - - -
56A VAL* 5.2 2.9 - - - +
89A ILE 4.1 1.0 - - - +
90A ILE* 3.3 25.1 - - + +
91A ARG* 3.0 51.4 + - + +
93A HIS* 4.3 6.0 - - - +
111A LEU* 1.3 70.4 - - - +
113A ILE* 1.3 64.0 + - + +
165A ASN* 5.1 1.0 + - - -
171A LYS* 2.8 36.0 + - - +
430A ANP 2.7 32.1 + - - -
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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