Contacts of the strand formed by residues 106 - 111 (chain B) in PDB entry 1NQ3
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 ALA 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL 2.9 16.3 + - - +
78B LYS* 3.4 14.5 - - + -
79B ALA 3.1 21.3 + - - -
105B PRO* 1.3 79.3 - - - +
107B ARG* 1.3 60.6 + - - +
22C SER 3.7 7.6 - - - +
24C ALA* 4.5 0.2 - - - -
25C VAL* 3.7 9.9 - - + +
32C TYR* 3.3 29.4 - - + +
34C SER* 3.3 16.2 - - - +
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LYS* 4.1 3.1 - - - +
79B ALA 3.3 20.6 - - - +
81B VAL* 3.8 16.5 - - + +
89B PHE* 4.1 10.1 - - - -
92B VAL* 6.2 1.0 - - - +
93B ASN* 3.1 43.2 + - - +
96B TYR* 3.5 50.3 - - - +
105B PRO 3.7 0.6 + - - +
106B ALA* 1.3 76.7 - - - +
108B ALA* 1.3 75.6 + - - +
109B ALA* 4.6 9.2 - - - +
19C GLY* 4.7 1.2 - - - -
20C PRO* 4.1 1.3 - - - +
21C TYR* 3.8 43.9 - - + +
34C SER* 2.8 16.5 + - - +
35C GLY 3.1 22.3 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LYS* 4.6 3.1 - - - +
79B ALA 3.3 3.9 + - - +
80B THR* 3.4 6.1 - - + +
81B VAL 2.8 24.9 + - - -
107B ARG* 1.3 80.0 - - - +
109B ALA* 1.3 62.2 + - - +
110B TYR* 4.3 11.2 - - + -
35C GLY 4.4 3.8 - - - +
122C GLU* 4.1 16.2 - - - +
124C GLU* 3.7 33.2 - - - +
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Residues in contact with ALA 109 (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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81B VAL* 3.3 24.2 - - + +
83B LEU* 5.3 1.8 - - + -
86B ILE* 5.3 0.9 - - - -
89B PHE* 3.7 28.9 - - + -
107B ARG* 4.6 10.8 - - - +
108B ALA* 1.3 76.2 - - - +
110B TYR* 1.3 67.9 + - - +
116C PRO* 3.3 23.3 - - - +
122C GLU* 3.8 6.0 + - - +
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Residues in contact with TYR 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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110A TYR* 3.9 8.2 + + - -
80B THR* 3.9 14.0 - - + +
81B VAL 3.3 6.2 + - - +
82B LEU* 3.6 28.8 - - + +
83B LEU* 3.0 26.7 + - - +
86B ILE* 4.1 11.2 - - - -
108B ALA* 4.3 15.7 - - + -
109B ALA* 1.3 83.1 - - - +
111B GLN* 1.3 64.6 + - - +
112B VAL* 3.9 8.7 + - + -
82C LEU* 3.3 33.2 - - + +
110C TYR* 3.8 15.9 + - - -
112C VAL* 3.8 26.5 - - + -
114C ALA 3.6 11.9 - - - +
115C LEU* 3.6 15.7 - - + -
116C PRO* 4.6 0.2 - - - -
122C GLU* 4.5 2.0 - - - -
124C GLU* 4.4 6.7 + - - -
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Residues in contact with GLN 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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83B LEU* 3.1 16.6 - - - +
84B ALA 3.3 23.0 + - - +
85B ASP* 3.5 4.4 - - - +
86B ILE* 2.7 44.1 + - + +
110B TYR* 1.3 74.3 - - - +
112B VAL* 1.3 65.3 + - - +
113B ALA* 5.5 0.4 - - - +
112C VAL* 3.4 11.3 - - - +
113C ALA* 3.0 41.7 + - - +
114C ALA* 2.9 24.6 + - - +
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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