Contacts of the helix formed by residues 124 - 139 (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 ARG 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 1.3 73.9 - - - +
125A PHE* 1.3 69.2 + - + +
126A SER* 3.2 24.7 - - - +
127A ALA* 3.1 5.3 + - + +
128A VAL* 3.1 19.4 + - - +
381A VAL* 3.1 26.5 + - - -
382A GLY* 3.2 18.2 + - - +
383A LEU 3.0 17.8 + - - +
384A ARG 4.1 6.7 + - - -
385A VAL* 3.7 11.1 - - - +
386A PRO* 3.7 50.4 - - + +
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 4.9 4.5 - - - -
46A THR* 3.6 25.1 - - + -
47A GLN* 3.7 38.4 - - + +
50A VAL* 3.9 44.2 - - + -
51A THR* 5.7 0.2 - - + -
123A ILE 3.6 2.2 + - - -
124A ARG* 1.3 74.5 - - + +
126A SER* 1.3 62.0 + - - +
128A VAL* 3.1 25.0 - - + +
129A LEU* 3.3 22.2 + - + +
385A VAL* 5.8 0.2 - - - +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 3.2 25.2 - - - +
125A PHE* 1.3 78.0 - - - +
127A ALA* 1.3 60.3 + - - +
129A LEU* 3.4 13.9 + - - +
130A ILE* 3.2 27.4 + - - +
381A VAL* 3.4 22.3 - - - +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.8 16.6 - - + -
124A ARG* 3.1 12.2 + - + +
126A SER* 1.3 78.0 + - - +
128A VAL* 1.3 58.7 + - - +
130A ILE* 3.4 1.1 + - - -
131A PHE* 3.0 27.9 + - - +
377A ALA* 3.6 20.4 - - + +
381A VAL* 3.7 10.3 - - + -
382A GLY 3.6 24.7 - - - +
383A LEU* 4.1 3.6 - - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 3.4 33.9 - - + +
51A THR* 4.1 14.1 - - + -
116A VAL* 3.8 31.0 - - + -
119A LEU* 6.2 1.3 - - + -
123A ILE* 3.8 26.0 - - + +
124A ARG 3.1 7.0 + - - +
125A PHE* 3.1 21.5 - - + +
127A ALA* 1.3 74.3 - - - +
129A LEU* 1.3 62.7 + - + +
131A PHE* 3.3 7.9 + - + +
132A VAL* 2.9 37.7 + - + +
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Residues in contact with LEU 129 (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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50A VAL* 4.0 26.5 - - + +
51A THR* 4.0 18.6 - - + -
54A LEU* 3.8 20.9 - - + +
125A PHE* 3.3 31.3 + - + +
126A SER* 3.7 12.3 - - - +
127A ALA 3.3 0.4 - - - -
128A VAL* 1.3 78.2 - - - +
130A ILE* 1.3 63.3 + - + +
132A VAL* 3.4 3.4 + - - +
133A VAL* 3.2 28.5 + - - +
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Residues in contact with ILE 130 (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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126A SER* 3.2 15.5 + - - +
127A ALA 3.7 6.3 - - - +
129A LEU* 1.3 78.4 - - + +
131A PHE* 1.3 62.3 + - - +
133A VAL* 3.3 7.7 + - - +
134A VAL* 3.1 24.0 + - + +
373A GLY 4.6 0.7 - - - +
376A LEU* 4.3 21.3 - - + -
377A ALA* 3.9 23.1 - - + +
380A THR* 4.2 19.1 - - + -
381A VAL* 3.9 32.8 - - + -
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Residues in contact with PHE 131 (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 ILE* 4.0 24.7 - - + -
116A VAL* 5.9 0.9 - - + -
123A ILE* 5.0 1.8 - - + -
127A ALA 3.0 17.8 + - - +
128A VAL* 3.7 12.6 - - + +
130A ILE* 1.3 77.6 - - - +
132A VAL* 1.3 70.5 + - + +
134A VAL* 3.3 2.5 + - - +
135A TRP* 2.8 60.4 + + + +
174A ALA* 4.2 9.2 - - + -
370A ALA* 3.7 16.2 - - - -
373A GLY* 3.9 14.1 - - - +
374A TYR* 3.4 66.4 - + + -
377A ALA* 5.1 0.9 - - + -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 3.9 18.4 - - + +
54A LEU* 3.9 19.7 - - + -
55A VAL* 3.9 27.8 - - + -
58A LEU* 5.1 1.3 - - + -
112A VAL* 3.9 24.9 - - + -
116A VAL* 4.0 9.6 - - + -
128A VAL* 2.9 22.5 + - + +
129A LEU* 3.8 4.7 - - - +
130A ILE 3.3 0.2 - - - -
131A PHE* 1.3 85.1 - - + +
133A VAL* 1.3 58.9 + - - +
135A TRP* 4.9 0.9 - - - -
136A LEU* 2.8 39.6 + - + +
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.9 20.0 - - + -
58A LEU* 4.0 18.6 - - + -
62A TYR* 4.4 7.6 - - - +
129A LEU 3.2 17.0 + - - +
130A ILE* 3.7 9.4 - - - +
131A PHE 3.3 0.2 - - - -
132A VAL* 1.3 75.2 - - - +
134A VAL* 1.3 63.5 + - + +
136A LEU* 4.3 0.3 - - - +
137A THR* 2.6 38.5 + - - +
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Residues in contact with VAL 134 (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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130A ILE* 3.1 16.5 + - + +
131A PHE 3.7 5.2 - - - +
133A VAL* 1.3 80.4 - - + +
135A TRP* 1.3 58.3 + - - +
137A THR* 4.8 1.6 - - - -
138A LEU* 2.9 49.7 + - + +
369A VAL* 4.3 8.1 - - + +
372A ILE* 4.5 8.7 - - + -
373A GLY* 3.7 30.5 - - - +
376A LEU* 3.7 29.4 - - + -
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Residues in contact with TRP 135 (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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111A THR* 3.5 30.5 - - + -
112A VAL* 4.2 15.5 - - + -
115A ILE* 3.7 22.9 - - + -
131A PHE* 2.8 41.6 + + + +
132A VAL* 4.3 1.8 - - - +
134A VAL* 1.3 71.8 - - + +
136A LEU* 1.3 64.3 + - - +
139A SER* 2.8 43.8 + - - -
140A TYR* 3.1 20.1 + - + -
170A ASN* 3.1 45.8 - - - -
174A ALA* 3.5 11.7 - - + +
366A SER* 3.2 16.8 + - - -
369A VAL* 3.9 5.6 - - + +
370A ALA* 3.8 28.0 - - + -
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Residues in contact with LEU 136 (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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55A VAL* 4.2 24.2 - - + +
58A LEU* 3.9 36.3 - - + -
59A TRP* 4.9 7.4 - - + +
108A ALA* 3.9 24.0 - - + -
112A VAL* 4.2 13.5 - - + -
132A VAL* 2.8 27.8 + - + +
133A VAL 4.3 1.3 - - - +
135A TRP* 1.3 76.9 - - - +
137A THR* 1.3 60.9 + - - +
140A TYR* 3.8 25.1 - - + -
141A ILE* 3.0 44.9 + - + +
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Residues in contact with THR 137 (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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62A TYR* 2.7 37.3 + - + +
66A LEU* 5.1 7.9 - - + +
133A VAL* 2.6 25.4 + - - +
134A VAL* 3.9 2.7 - - - -
136A LEU* 1.3 81.3 - - - +
138A LEU* 1.3 73.7 + - + +
141A ILE* 3.6 16.4 - - + +
142A PRO* 3.4 16.6 - - - +
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Residues in contact with LEU 138 (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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134A VAL* 2.9 34.3 + - + +
137A THR* 1.3 92.0 - - + +
139A SER* 1.3 60.0 + - - +
142A PRO* 3.3 12.8 - - + +
365A TRP* 2.7 23.2 + - - -
369A VAL* 3.5 17.6 - - + +
372A ILE* 5.6 8.1 - - + -
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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