Contacts of the helix formed by residues 139 - 149 (chain A) in PDB entry 2NPJ
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A TRP* 2.8 43.3 + - - -
137A THR 3.6 0.2 - - - -
138A LEU* 1.3 75.1 - - - +
140A TYR* 1.3 65.6 + - - +
141A ILE 3.4 0.4 - - - -
142A PRO* 3.4 0.7 - - - +
143A ILE* 3.1 32.9 + - - +
170A ASN* 3.0 22.3 + - - -
365A TRP* 3.9 3.1 - - - +
366A SER* 3.4 11.3 - - - -
369A VAL* 3.7 11.4 - - - -
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Residues in contact with TYR 140 (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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59A TRP* 4.1 15.7 - + - -
68A PHE* 6.1 0.2 - + - -
104A GLN* 4.2 2.9 + - - -
107A PHE* 3.3 26.5 - - - +
108A ALA* 3.5 26.9 + - + -
111A THR* 3.4 35.4 - - + -
135A TRP* 3.1 14.5 + + + -
136A LEU* 3.6 28.3 - - + +
139A SER* 1.3 77.6 - - - +
141A ILE* 1.3 62.5 + - - +
143A ILE* 3.8 0.7 - - - +
144A ALA* 2.9 39.7 + - + +
148A TRP* 3.8 6.8 - - - -
166A VAL* 3.5 38.6 - - + +
167A VAL* 4.6 1.0 - - + +
170A ASN* 3.7 6.9 - - - +
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Residues in contact with ILE 141 (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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59A TRP* 4.3 13.7 - - + -
62A TYR* 4.0 14.6 - - + -
63A GLY* 3.6 31.9 - - - +
66A LEU* 3.6 39.5 - - + +
67A ALA* 3.7 5.6 - - - +
75A PHE* 5.5 3.1 - - + -
136A LEU* 3.0 29.8 + - + +
137A THR* 3.6 19.7 - - + +
140A TYR* 1.3 78.2 - - + +
142A PRO* 1.4 68.6 - - + +
144A ALA* 3.3 2.1 + - - +
145A HIS* 2.9 26.7 + - - +
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Residues in contact with PRO 142 (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 PHE* 3.2 21.4 - - + +
75A PHE* 5.3 4.9 - - + -
137A THR 3.4 17.7 - - - +
138A LEU* 3.3 25.6 - - + +
139A SER 3.4 9.0 - - - +
141A ILE* 1.4 91.2 - - + +
143A ILE* 1.3 56.6 + - - +
145A HIS* 3.3 0.9 + - + -
146A MET* 2.8 35.5 + - - +
365A TRP* 3.5 28.9 - - + -
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Residues in contact with ILE 143 (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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139A SER* 3.1 25.0 + - - +
140A TYR 4.0 1.3 - - - +
142A PRO* 1.3 72.4 - - - +
144A ALA* 1.3 60.8 + - - +
146A MET* 3.2 22.5 + - + +
147A VAL* 2.9 37.0 + - + +
153A LEU* 5.7 0.4 - - + -
166A VAL* 3.8 31.2 - - + +
170A ASN* 3.3 30.1 - - - +
362A THR* 4.1 27.6 - - + +
365A TRP* 4.0 22.4 - - + -
366A SER 4.4 0.2 - - - +
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Residues in contact with ALA 144 (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 ALA* 4.3 13.5 - - + -
68A PHE* 4.7 7.5 - - + -
140A TYR* 2.9 38.7 + - + +
141A ILE 3.6 4.3 - - - +
143A ILE* 1.3 77.0 - - - +
145A HIS* 1.3 58.6 + - - +
148A TRP* 2.8 38.1 + - + +
149A GLY 3.2 4.3 + - - -
166A VAL* 3.8 17.4 - - + +
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Residues in contact with HIS 145 (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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66A LEU 4.2 2.0 - - - +
67A ALA* 2.8 31.5 + - - +
69A GLY 3.4 21.1 - - - -
70A GLU* 5.0 0.9 - - - -
71A GLY 4.4 4.3 - - - -
72A ASN 2.7 25.4 + - - -
73A ASN 3.8 5.4 - - - -
74A PHE 3.4 29.4 - - - +
75A PHE* 3.4 7.2 + - - -
76A GLY* 3.7 11.6 + - - -
141A ILE 2.9 16.7 + - - +
142A PRO 3.5 4.5 - - - +
143A ILE 3.2 0.2 - - - -
144A ALA* 1.3 77.6 - - - +
146A MET* 1.3 56.6 + - - +
149A GLY 3.0 36.7 + - - +
150A GLY 4.9 0.4 - - - -
151A GLY* 2.9 23.8 + - - -
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Residues in contact with MET 146 (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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73A ASN 3.2 19.3 - - - +
74A PHE* 3.8 27.4 - - - -
142A PRO 2.8 16.9 + - - +
143A ILE* 3.2 33.0 + - + +
145A HIS* 1.3 76.8 - - - +
147A VAL* 1.3 59.9 + - - +
151A GLY* 3.4 11.5 - - - -
152A LEU* 4.1 15.5 - - - +
153A LEU* 3.1 22.4 + - + +
154A ALA* 2.9 24.6 + - - +
361A ILE* 4.3 16.2 - - + -
365A TRP* 3.7 28.9 - - + -
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Residues in contact with VAL 147 (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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143A ILE* 2.9 19.7 + - + +
146A MET* 1.3 77.8 - - - +
148A TRP* 1.3 78.7 + - + +
149A GLY 3.7 0.2 - - - -
153A LEU* 3.7 28.3 - - + -
154A ALA* 3.4 21.9 - - - +
158A ALA* 5.7 5.2 - - + +
160A ASP* 4.0 17.0 - - + +
165A THR* 3.6 17.7 - - - +
166A VAL* 3.6 15.7 - - + -
601A ACT 3.5 20.5 - - - +
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Residues in contact with TRP 148 (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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68A PHE* 3.6 24.7 - + + -
104A GLN* 3.9 6.7 - - - +
107A PHE* 3.9 7.9 - + - -
140A TYR* 3.8 12.8 - - - -
144A ALA* 2.8 17.2 + - + +
147A VAL* 1.3 84.4 - - + +
149A GLY* 1.3 57.8 + - - +
150A GLY 3.4 3.7 + - - -
154A ALA* 5.5 0.2 - - - -
160A ASP* 3.2 18.6 + - - -
161A PHE 4.0 0.6 + - - -
162A ALA 3.5 7.9 - - - -
163A GLY* 3.3 33.7 - - - -
166A VAL* 3.5 43.5 - - + -
167A VAL* 4.5 1.1 - - + -
601A ACT 4.0 17.0 - - + -
701A IMD 3.2 50.0 + + - +
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Residues in contact with GLY 149 (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 ALA 4.0 9.2 - - - -
68A PHE* 4.1 11.9 - - - +
69A GLY 4.8 1.7 - - - +
70A GLU* 6.0 0.2 - - - -
144A ALA 3.2 4.2 + - - -
145A HIS* 3.0 42.7 + - - -
148A TRP* 1.3 78.5 - - - +
150A GLY* 1.3 58.2 + - - +
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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