Contacts of the strand formed by residues 103 - 107 (chain A) in PDB entry 2NPQ
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 TYR 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE 3.7 1.2 + - - -
18A TRP* 3.6 17.3 - + - -
19A GLU* 3.1 35.9 + - - +
20A VAL* 4.1 5.2 - - + -
52A VAL* 4.1 16.8 - - + -
53A LYS 3.2 4.5 - - - +
54A LYS* 3.4 50.0 - - + -
89A VAL* 3.3 9.5 - - - +
90A PHE* 3.0 72.2 + + + +
92A PRO* 3.8 18.8 - - + +
101A ASP* 4.2 11.9 - - + +
102A VAL* 1.3 78.3 - - - +
104A LEU* 1.3 62.4 + - - +
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Residues in contact with LEU 104 (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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51A ALA 3.5 1.4 - - - +
52A VAL* 3.4 2.4 - - - -
53A LYS* 2.8 48.7 + - + +
55A LEU* 4.1 13.9 - - + -
71A GLU* 3.4 37.2 - - + +
72A LEU* 4.0 19.5 - - + +
75A LEU* 3.8 15.5 - - + -
86A LEU* 4.1 15.3 - - + -
88A ASP 3.8 1.1 - - - -
89A VAL* 3.9 17.5 - - + -
102A VAL* 4.1 11.7 - - + -
103A TYR* 1.3 79.6 - - - +
105A VAL* 1.3 62.5 + - - +
106A THR* 4.2 3.7 + - + +
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Residues in contact with VAL 105 (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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24A TYR* 3.9 17.0 - - + +
50A VAL* 3.7 35.7 - - + -
51A ALA 3.2 4.7 - - - +
52A VAL* 4.3 9.4 - - + -
86A LEU* 3.7 1.6 - - - +
87A LEU* 2.8 33.0 + - + -
88A ASP* 2.9 32.9 + - + +
90A PHE* 3.7 29.8 - - + -
104A LEU* 1.3 76.8 - - - +
106A THR* 1.3 69.2 + - - +
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Residues in contact with THR 106 (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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50A VAL* 3.2 8.0 - - - +
51A ALA* 2.8 38.6 + - - +
75A LEU* 5.0 10.5 - - + -
84A ILE* 4.1 18.0 - - + +
85A GLY 3.4 20.6 - - - +
86A LEU* 4.4 11.2 - - + -
87A LEU* 3.5 11.7 - - - -
104A LEU* 4.2 3.8 - - + -
105A VAL* 1.3 81.0 - - - +
107A HIS* 1.3 68.5 + - - +
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Residues in contact with HIS 107 (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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48A LEU* 3.7 38.2 - - + +
49A ARG 4.1 6.1 + - - -
51A ALA* 4.2 3.5 + - - +
84A ILE* 4.5 6.1 - - + +
85A GLY 4.9 5.5 + - - -
87A LEU* 3.4 27.5 - - + +
106A THR* 1.3 84.8 + - - +
108A LEU* 1.3 62.5 + - - +
109A MET* 3.5 32.0 + - + +
165A LYS* 4.4 20.3 + - - -
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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