Contacts of the helix formed by residues 114 - 124 (chain A) in PDB entry 3NSB
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ALA 3.0 19.9 + - - +
111A LEU 3.9 2.7 - - - +
113A GLY* 1.3 75.7 - - - +
115A ASP* 1.3 57.6 + - - +
117A ILE* 3.3 12.0 + - - +
118A MET* 2.9 28.1 + - - +
144A ALA* 3.7 11.3 - - + +
147A TYR* 3.7 27.6 - - + -
148A ILE* 3.9 13.0 - - + -
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 5.4 0.2 - - - -
90A THR* 2.5 40.3 + - - -
91A PRO* 3.3 17.2 - - + +
94A LEU* 3.3 23.1 - - + +
111A LEU 2.8 20.3 + - - +
112A VAL* 3.5 7.9 - - - +
114A ALA* 1.3 75.1 - - - +
116A GLY* 1.3 65.4 + - - +
118A MET* 3.1 10.1 + - - +
119A ILE* 2.9 24.8 + - - +
148A ILE* 3.6 9.5 - - + +
182A TRP* 3.6 10.2 - - - -
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.8 17.3 - - - +
91A PRO* 5.3 2.9 - - - +
112A VAL 2.9 15.1 + - - -
113A GLY 3.2 4.9 + - - -
115A ASP* 1.3 77.5 + - - +
117A ILE* 1.3 58.0 + - - +
119A ILE* 4.1 1.2 - - - +
120A GLY* 2.8 28.2 + - - -
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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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113A GLY 3.0 20.1 + - - +
114A ALA* 3.5 11.7 - - - +
116A GLY* 1.3 76.4 - - - +
118A MET* 1.3 56.1 + - - +
120A GLY* 5.0 0.4 - - - -
121A THR* 2.7 51.3 + - + +
140A ILE* 4.8 9.2 - - + -
144A ALA* 4.2 12.8 - - + -
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Residues in contact with MET 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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90A THR* 4.6 0.9 - - - +
114A ALA 2.9 13.4 + - - +
115A ASP* 3.1 32.7 + - - +
117A ILE* 1.3 76.7 - - - +
119A ILE* 1.3 78.1 + - + +
121A THR* 3.9 1.6 - - - -
122A GLY* 3.1 11.4 + - - -
141A SER* 2.6 40.0 + - - +
144A ALA* 3.9 12.3 - - + -
145A MET* 3.5 36.6 - - - -
148A ILE* 4.0 5.4 - - + -
182A TRP* 3.9 10.1 - - + -
300A RET 3.6 35.5 - - + +
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Residues in contact with ILE 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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83A TYR* 3.6 38.7 - - + +
86A TRP* 3.6 34.1 - - + +
87A LEU* 3.7 19.5 - - + +
90A THR* 3.7 9.0 - - + +
115A ASP* 2.9 27.3 + - - +
116A GLY* 4.1 2.2 - - - +
118A MET* 1.3 94.6 - - + +
120A GLY* 1.3 61.1 + - - +
122A GLY* 3.2 2.1 + - - -
123A LEU* 2.9 28.2 + - + +
300A RET 4.6 8.1 - - + -
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Residues in contact with GLY 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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87A LEU* 5.3 3.5 - - - +
116A GLY 2.8 22.3 + - - -
117A ILE* 3.9 0.7 - - - -
119A ILE* 1.3 74.9 - - - +
121A THR* 1.3 56.8 + - - +
123A LEU* 3.3 11.5 + - - +
124A VAL* 3.0 32.4 + - - +
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Residues in contact with THR 121 (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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117A ILE* 2.7 33.5 + - + +
120A GLY* 1.3 73.8 - - - +
122A GLY* 1.3 60.2 + - - +
124A VAL* 3.4 7.6 + - + +
125A GLY* 2.9 23.0 + - - -
137A TRP* 3.5 44.4 - - + +
140A ILE* 4.0 16.3 - - + +
141A SER* 3.2 25.8 - - - -
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Residues in contact with GLY 122 (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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83A TYR* 3.7 9.8 + - - -
118A MET 3.1 16.2 + - - -
119A ILE 3.2 4.2 + - - -
121A THR* 1.3 78.3 + - - +
123A LEU* 1.3 54.9 + - - +
125A GLY* 3.3 2.2 + - - -
126A ALA* 2.9 28.2 + - - +
137A TRP 5.2 0.9 - - - -
141A SER* 4.1 6.7 + - - -
189A TRP* 4.2 5.1 - - - -
300A RET 4.0 22.7 - - - -
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Residues in contact with LEU 123 (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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80A TRP* 4.5 7.4 - - + -
83A TYR* 3.7 39.8 - - + -
119A ILE* 2.9 13.7 + - + +
120A GLY* 3.5 12.1 - - - +
122A GLY* 1.3 74.8 - - - +
124A VAL* 1.3 68.9 + - + +
126A ALA* 3.1 3.0 + - - +
127A LEU* 3.1 48.0 + - + +
1002A LI1 3.8 33.9 - - + -
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Residues in contact with VAL 124 (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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120A GLY 3.0 17.3 + - - +
121A THR* 3.7 9.4 - - + +
123A LEU* 1.3 77.8 - - + +
125A GLY* 1.3 58.0 + - - +
127A LEU* 3.2 6.3 + - - +
128A THR* 2.6 35.4 + - - +
137A TRP* 3.4 44.2 - - + +
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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