Contacts of the strand formed by residues 116 - 120 (chain A) in PDB entry 3NT7
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LYS* 3.4 16.8 - - - +
62A VAL* 3.4 7.2 - - + +
64A VAL* 3.9 25.4 - - + -
110A LEU* 3.6 28.7 - - + +
111A ASN* 5.1 2.9 - - - +
113A ILE* 3.2 22.3 + - + +
115A GLY* 1.3 79.8 - - - +
117A ILE* 1.3 67.3 + - - +
118A PRO* 3.6 7.1 - - + +
210A ILE* 3.7 35.0 - - + -
212A TRP* 4.0 12.1 - - + -
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Residues in contact with ILE 117 (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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19A TRP* 4.0 17.7 - - + -
52A GLN* 4.2 9.0 - - - +
55A GLN* 4.2 20.4 - - + -
56A PRO 4.9 0.7 - - - +
57A LEU* 3.8 21.8 - - + -
60A LYS* 3.5 25.5 - - + +
62A VAL 2.9 16.9 + - - +
63A CYS* 3.3 16.3 - - + -
64A VAL 3.2 19.6 + - - -
116A VAL* 1.3 74.2 - - - +
118A PRO* 1.3 73.1 - - + +
119A TRP* 4.3 14.6 - - + -
148A ILE* 4.3 9.0 - - + -
152A VAL* 4.3 6.1 - - + -
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Residues in contact with PRO 118 (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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52A GLN* 3.4 13.4 - - - +
64A VAL* 3.3 9.6 - - + +
78A PRO* 3.4 33.4 - - + +
79A PHE* 4.1 6.5 - - + -
110A LEU* 3.7 34.5 - - + +
111A ASN* 3.6 32.3 - - + +
116A VAL* 3.6 10.1 - - + +
117A ILE* 1.3 89.4 - - - +
119A TRP* 1.3 63.0 + - - +
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Residues in contact with TRP 119 (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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19A TRP* 3.7 25.6 - + - -
52A GLN* 3.6 29.4 - - + -
53A LEU* 3.9 15.3 - - + -
63A CYS* 3.6 21.8 - - - -
64A VAL 2.8 9.1 + - - +
65A CYS* 3.2 16.9 - - - -
66A GLY 2.8 31.2 + - - -
78A PRO* 3.5 11.6 - - + +
79A PHE* 4.1 0.7 - - - -
117A ILE* 4.3 7.6 - - + +
118A PRO* 1.3 81.9 - - - +
120A ASN* 1.3 81.5 + - - +
121A TYR* 4.0 6.7 + - - +
123A LEU* 4.3 15.9 - - + -
141A SER* 5.3 1.2 + - - +
144A LEU* 3.7 29.8 - - + +
145A LEU* 4.2 17.4 - - + +
148A ILE* 3.4 24.0 - - + +
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Residues in contact with ASN 120 (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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66A GLY* 3.2 9.9 - - - +
68A ASP* 3.4 15.3 - - - +
69A PRO* 3.7 31.5 - - + +
76A GLY* 5.3 3.2 + - - -
77A VAL 4.8 1.0 - - - -
78A PRO* 3.5 36.5 - - + +
79A PHE* 4.8 6.2 + - - +
119A TRP* 1.3 86.0 + - - +
121A TYR* 1.3 68.2 + - - +
122A TYR 3.3 15.3 - - - +
123A LEU* 3.1 21.7 - - + +
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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