Contacts of the helix formed by residues 114 - 124 (chain A) in PDB entry 3NIA
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 VAL 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A VAL* 3.5 30.5 - - + -
78A ILE* 4.5 2.5 - - + -
83A GLU* 4.0 20.0 - - + +
84A ARG 3.5 26.2 - - - +
85A GLY* 3.7 5.8 - - - +
87A ARG* 2.9 24.7 + - + +
89A LEU* 3.9 26.6 - - + +
112A MET 3.9 0.2 + - - -
113A THR* 1.3 72.4 - - - +
115A LEU* 1.3 59.0 + - - +
117A ALA* 3.3 1.7 + - - +
118A ALA* 2.9 28.1 + - - +
133A LEU* 3.9 7.5 - - + +
136A GLU* 4.7 2.5 - - + -
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Residues in contact with LEU 115 (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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74A VAL* 6.0 0.4 - - + -
75A PHE* 3.9 33.4 - - + -
78A ILE* 4.3 10.3 - - + -
85A GLY* 3.1 34.9 + - - +
86A ASP* 5.4 0.4 - - + -
113A THR* 3.2 3.8 - - - +
114A VAL* 1.3 74.8 - - + +
116A GLU* 1.3 60.9 + - - +
118A ALA* 4.5 2.5 - - + +
119A GLN* 2.9 31.3 + - - +
201A THR* 5.7 0.9 - - + -
205A TRP* 3.9 14.9 - - + -
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Residues in contact with GLU 116 (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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106A PHE* 4.2 27.1 - - + -
111A HIS* 4.6 2.9 - - - +
112A MET* 3.4 23.1 - - + +
113A THR* 2.9 47.1 + - - +
115A LEU* 1.3 76.7 - - + +
117A ALA* 1.3 59.1 + - - +
119A GLN* 3.4 5.5 + - - +
120A ALA* 3.0 30.3 + - - +
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Residues in contact with ALA 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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89A LEU* 4.7 1.1 - - + -
112A MET* 3.8 11.8 - - + +
113A THR 2.9 17.4 + - - +
114A VAL* 3.7 4.0 - - - +
116A GLU* 1.3 76.2 - - - +
118A ALA* 1.3 58.1 + - - +
120A ALA 3.3 0.3 + - - -
121A ALA* 2.9 30.7 + - - +
129A ALA* 3.6 18.1 - - + +
132A LEU* 4.3 18.2 - - + -
133A LEU* 3.8 22.2 - - + +
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Residues in contact with ALA 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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71A ALA* 4.8 11.4 - - + -
74A VAL* 4.9 12.3 - - + -
75A PHE* 5.1 2.0 - - + -
114A VAL 2.9 17.4 + - - +
115A LEU* 3.9 2.9 - - + +
117A ALA* 1.3 76.7 - - - +
119A GLN* 1.3 63.1 + - - +
121A ALA* 3.3 1.9 + - - +
122A VAL* 3.0 29.9 + - - +
133A LEU* 3.5 19.2 - - + +
205A TRP* 3.7 21.5 - - + -
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Residues in contact with GLN 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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115A LEU 2.9 18.3 + - - +
116A GLU* 3.9 5.4 - - - +
118A ALA* 1.3 78.1 - - - +
120A ALA* 1.3 57.0 + - - +
123A GLN* 2.8 59.2 + - - +
205A TRP* 3.4 42.7 + - + +
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Residues in contact with ALA 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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102A ALA* 3.8 30.1 - - + -
112A MET* 4.1 2.9 - - + -
116A GLU 3.0 17.2 + - - +
117A ALA 3.7 3.8 - - - +
119A GLN* 1.3 73.6 - - - +
121A ALA* 1.3 66.8 + - - +
123A GLN* 5.3 0.2 - - - -
124A LEU* 3.0 28.7 + - + +
125A SER 3.1 5.9 + - - -
126A ASP* 3.2 17.2 + - + -
129A ALA* 4.1 6.1 - - + -
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Residues in contact with ALA 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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67A LYS* 3.4 20.5 - - + +
70A LEU* 5.4 2.5 - - + -
117A ALA 2.9 17.7 + - - +
118A ALA* 3.6 5.4 - - - +
120A ALA* 1.3 78.4 - - - +
122A VAL* 1.3 60.4 + - + +
125A SER* 3.1 22.7 - - - -
126A ASP 4.0 12.8 - - - +
129A ALA* 4.3 0.6 - - - +
130A THR* 3.6 23.1 - - + +
133A LEU* 4.3 13.0 - - + -
229A LYS* 3.5 2.3 - - - -
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Residues in contact with VAL 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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67A LYS* 4.0 13.0 - - - +
68A PHE* 4.8 2.7 - - - -
71A ALA* 3.7 28.3 - - + -
118A ALA 3.0 16.3 + - - +
119A GLN 4.1 1.8 - - - +
121A ALA* 1.3 79.8 - - + +
123A GLN* 1.3 60.4 + - + +
124A LEU 3.6 0.4 + - - -
125A SER 4.2 0.5 + - - -
202A ILE* 5.3 3.1 - - + +
205A TRP* 4.1 32.8 - - + +
206A LEU* 3.9 28.7 - - + -
209A ASN* 3.3 13.5 - - + +
229A LYS* 3.4 22.7 - - + +
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Residues in contact with GLN 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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119A GLN* 2.8 52.2 + - + +
122A VAL* 1.3 75.9 - - - +
124A LEU* 1.3 62.6 + - + +
204A ARG 4.2 1.0 + - - -
205A TRP* 3.0 48.9 + - + +
208A GLY* 3.4 22.1 + - - -
209A ASN* 3.1 13.7 - - - +
210A GLN* 2.9 45.1 + - + +
211A THR* 3.6 2.4 - - - +
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Residues in contact with LEU 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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99A TRP* 2.7 37.6 + - + -
101A PRO* 4.0 24.9 - - + -
102A ALA* 4.1 22.2 - - + -
105A ARG* 4.4 11.9 - - - +
120A ALA* 3.0 17.4 + - + +
123A GLN* 1.3 78.1 - - + +
125A SER* 1.3 58.2 + - - +
126A ASP* 4.2 3.6 - - + +
210A GLN* 3.5 42.0 - - + +
211A THR* 3.8 12.2 - - + +
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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