Contacts of the strand formed by residues 97 - 101 (chain B) in PDB entry 2NTT
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 ILE 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE 3.5 16.2 - - - +
96B PRO* 1.3 75.4 - - - +
98B ASN* 1.3 75.8 + - - +
99B ILE* 3.9 9.1 + - + -
107B THR* 3.3 7.3 - - - -
108B ILE* 2.9 60.6 + - + +
110B THR* 4.7 8.7 - - + -
113B VAL* 4.3 20.4 - - + -
129B LEU* 4.0 20.0 - - + -
132B TYR* 5.1 4.0 - - + -
133B LEU* 6.3 0.2 - - + -
209B LEU* 3.4 18.4 - - + +
211B VAL* 3.9 19.1 - - + -
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Residues in contact with ASN 98 (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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97B ILE* 1.3 72.7 + - - +
99B ILE* 1.3 54.5 + - - +
100B TRP* 3.5 18.4 - - + -
105B HIS* 3.1 23.2 - - + -
106B LYS 3.7 2.7 - - - -
107B THR* 3.3 16.2 - - - +
208B HIS* 3.6 16.2 + - - -
209B LEU 2.8 7.1 + - - +
210B ASP* 3.1 24.2 - - - +
211B VAL* 2.7 32.6 + - - +
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 3.9 9.6 - - + -
98B ASN* 1.3 74.4 - - - +
100B TRP* 1.3 67.6 + - - +
101B ILE* 3.4 30.7 - - + +
104B ASN 3.4 1.9 - - - +
105B HIS* 3.2 3.6 + - - -
106B LYS* 2.8 73.6 + - + +
108B ILE* 4.4 17.5 - - + -
132B TYR* 6.2 0.2 - - + -
133B LEU* 3.7 30.3 - - + -
137B TYR* 3.8 9.2 - - + +
211B VAL* 3.3 19.3 - - + +
213B ILE* 4.7 1.3 - - + -
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Residues in contact with TRP 100 (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 ASN* 3.5 36.6 - - + -
99B ILE* 1.3 78.5 - - - +
101B ILE* 1.3 61.0 + - - +
102B ASN 4.0 0.4 - - - -
103B GLY* 3.8 26.5 - - - -
104B ASN 3.3 4.0 - - - +
105B HIS* 3.5 33.3 - + + +
210B ASP* 3.9 23.6 - - + -
211B VAL 2.8 20.3 + - - +
212B ASP* 3.5 26.3 - - + +
213B ILE* 3.0 30.5 + - - +
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Residues in contact with ILE 101 (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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99B ILE* 3.4 25.6 - - + -
100B TRP* 1.3 72.4 - - - +
102B ASN* 1.3 75.1 + - - +
104B ASN* 2.9 30.1 + - + +
106B LYS* 4.7 9.6 - - - -
137B TYR* 3.5 24.0 - - + +
151B TYR* 3.7 34.1 - - + +
161B PHE* 3.7 15.9 - - + -
213B ILE* 3.1 33.4 - - + -
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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