Contacts of the helix formed by residues 101 - 105 (chain B) in PDB entry 1NSX
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 SER 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASN* 4.7 0.4 - - - +
66B GLY 2.7 20.7 + - - -
67B PRO* 4.1 4.3 - - - +
96B HIS 3.7 12.6 - - - -
97B GLY 3.6 11.1 + - - -
98B GLY 3.4 18.4 - - - -
99B GLU 3.8 1.8 - - - -
100B GLU* 1.3 77.5 - - - +
102B ILE* 1.3 66.5 + - - +
103B HIS* 3.1 18.1 - - - -
104B THR* 2.6 31.8 + - - -
105B LYS* 3.6 6.8 - - - +
131B ASN* 4.4 3.4 + - - +
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY* 3.6 0.5 - - - -
64B THR* 3.9 15.0 - - + +
65B VAL 4.0 3.8 - - - -
66B GLY* 3.6 39.7 - - - +
67B PRO* 4.5 8.1 - - + -
101B SER* 1.3 79.6 + - - +
103B HIS* 1.3 62.5 + - - +
104B THR 3.0 6.1 + - - -
105B LYS* 3.3 15.2 + - + +
107B TRP* 2.9 49.8 + - + -
124B LEU* 4.1 6.7 - - + -
126B SER* 5.4 4.5 - - - +
139B MET* 3.9 33.9 - - + -
165B PHE* 6.1 0.2 - - + -
167B PRO* 5.4 3.4 - - + -
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Residues in contact with HIS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.1 1.6 - - - +
31B GLY* 3.4 13.0 + - - -
33B ARG* 3.0 26.2 + - - -
55B LEU* 5.6 0.3 - - - +
59B ALA* 3.5 29.3 - - + +
60B TYR* 3.5 37.1 + + - -
63B ALA* 3.6 16.2 - - + -
64B THR 3.4 19.7 - - - +
65B VAL* 4.3 7.5 - - + +
96B HIS 4.8 3.7 + - - -
98B GLY 4.7 4.3 - - - -
100B GLU 4.9 1.8 - - - -
101B SER* 3.7 27.5 - - - -
102B ILE* 1.3 80.4 - - - +
104B THR* 1.3 80.9 + - + +
105B LYS 3.5 0.2 - - - -
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Residues in contact with THR 104 (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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108A THR* 5.6 3.1 - - - +
30B LEU* 3.5 15.4 - - - +
55B LEU* 5.0 13.5 - - + +
59B ALA* 4.6 8.7 - - + -
100B GLU* 3.4 34.5 + - - +
101B SER 2.6 17.9 + - - -
103B HIS* 1.3 113.0 - - + +
105B LYS* 1.3 65.0 + - - +
106B LEU 4.2 0.2 + - - -
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Residues in contact with LYS 105 (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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124A LEU* 5.6 9.5 - - + +
125A VAL* 3.2 28.9 + - - +
127A ASN* 3.0 24.9 + - - +
30B LEU* 3.6 3.7 - - - -
31B GLY 2.8 25.5 + - - -
100B GLU* 3.3 23.1 + - - +
101B SER 3.6 11.0 - - - +
102B ILE* 3.3 16.6 + - + +
104B THR* 1.3 85.9 + - - +
106B LEU* 1.4 63.5 + - - +
107B TRP* 3.2 5.0 - - - -
124B LEU* 4.0 24.0 - - + -
130B THR* 6.1 0.9 - - - -
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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