Contacts of the helix formed by residues 46 - 56 (chain A) in PDB entry 3NJ0
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 PRO 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ALA* 1.3 93.2 - - + +
47A ALA* 1.3 61.2 + - - +
48A SER* 3.8 15.3 - - - +
49A VAL* 2.9 34.9 + - + +
50A VAL* 3.3 9.7 + - - +
132A GLU* 3.4 12.3 - - - +
141A VAL* 3.9 21.5 - - + -
143A THR* 4.1 0.2 - - - +
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Residues in contact with ALA 47 (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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46A PRO* 1.3 71.7 - - - +
48A SER* 1.3 55.3 + - - +
50A VAL* 4.4 1.3 - - - +
51A TRP* 2.9 34.3 + - - +
108A ARG* 3.6 29.8 - - - +
130A VAL* 3.8 17.7 - - + +
132A GLU* 2.7 30.8 + - + +
143A THR* 3.2 16.4 + - - +
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.8 13.9 - - - +
47A ALA* 1.3 78.4 - - - +
49A VAL* 1.3 65.5 + - - +
51A TRP* 5.1 1.1 - - - -
52A PRO* 3.1 23.4 - - - +
108A ARG* 4.2 15.2 - - - +
132A GLU* 4.3 1.4 + - - -
186A MET* 4.2 5.4 - - - +
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Residues in contact with VAL 49 (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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45A ALA* 4.5 0.7 - - + -
46A PRO* 2.9 31.1 + - + +
48A SER* 1.3 86.2 - - - +
50A VAL* 1.3 65.3 + - - +
51A TRP 3.5 0.2 - - - -
52A PRO* 3.4 8.8 - - - +
53A LEU* 3.8 13.4 - - + +
180A ALA 5.5 0.2 - - - +
181A ALA* 3.5 32.8 - - + +
184A ALA 6.0 0.9 - - - +
186A MET* 4.3 35.2 - - + +
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Residues in contact with VAL 50 (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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43A ILE* 4.0 17.9 - - + -
45A ALA* 4.3 2.9 - - + +
46A PRO 3.3 13.2 + - - +
47A ALA 4.0 4.0 - - - +
49A VAL* 1.3 75.6 - - - +
51A TRP* 1.3 66.1 + - - +
53A LEU* 3.1 22.0 + - - +
54A ILE* 3.7 7.6 + - + +
130A VAL* 3.9 12.1 - - + -
143A THR* 4.0 15.3 - - - +
145A VAL* 3.8 27.4 - - + -
177A LEU* 4.0 18.2 - - + +
181A ALA* 3.8 23.1 - - + -
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Residues in contact with TRP 51 (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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47A ALA 2.9 18.4 + - - +
48A SER* 5.1 0.9 - - - -
50A VAL* 1.3 77.4 - - - +
52A PRO* 1.4 65.9 - - + +
54A ILE* 3.0 23.1 + - + +
55A ARG* 2.8 51.0 + - + +
103A VAL* 4.1 2.2 - - + -
105A ASP* 3.2 44.7 + - - +
108A ARG* 3.4 55.0 - - + +
109A VAL 3.6 29.4 - - - -
110A LEU* 4.1 8.3 - - + -
128A THR 5.0 1.1 - - - -
130A VAL* 4.0 15.9 - - + -
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Residues in contact with PRO 52 (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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48A SER 3.1 27.1 - - - +
49A VAL 3.4 11.2 - - - +
51A TRP* 1.4 99.6 - - + +
53A LEU* 1.3 62.6 + - + +
55A ARG* 4.2 7.4 - - + -
56A ARG* 3.1 26.3 + - - +
186A MET* 4.4 14.6 - - + -
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Residues in contact with LEU 53 (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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49A VAL* 3.8 18.2 - - + +
50A VAL 3.1 7.4 + - - +
52A PRO* 1.3 78.6 - - + +
54A ILE* 1.3 61.7 + - - +
56A ARG* 4.1 12.0 + - - +
59A ASN 4.8 5.0 - - - +
60A PRO* 5.6 0.2 - - - +
62A ARG* 3.4 55.0 - - + +
63A TYR* 3.7 18.7 - - + -
177A LEU* 3.6 26.7 - - + -
180A ALA* 4.0 11.7 - - + -
181A ALA* 3.9 30.5 - - + +
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Residues in contact with ILE 54 (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* 3.7 7.8 + - + +
51A TRP* 3.0 22.8 + - + +
53A LEU* 1.3 79.1 - - - +
55A ARG* 1.3 64.1 + - - +
56A ARG 3.2 5.6 + - - +
57A PHE* 4.4 3.3 + - - -
63A TYR* 4.0 31.0 + - + +
83A ARG* 5.7 1.2 + - - -
110A LEU* 3.6 28.3 - - + +
128A THR* 3.9 24.7 - - + -
130A VAL* 3.4 31.2 - - + -
145A VAL* 4.5 0.9 - - + -
174A LEU* 6.4 0.2 - - + -
177A LEU* 3.9 26.9 - - + -
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Residues in contact with ARG 55 (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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51A TRP* 2.8 41.1 + - + +
52A PRO* 3.5 7.6 + - + +
54A ILE* 1.3 80.0 - - - +
56A ARG* 1.3 56.4 + - - +
57A PHE* 2.8 10.7 + - - +
77A GLY 2.9 22.6 + - - -
78A ASP* 2.9 32.3 + - - +
79A VAL 5.1 0.4 - - - +
100A LEU* 4.0 8.5 - - - +
103A VAL* 3.3 29.4 - - - +
105A ASP* 3.3 25.6 + - - +
110A LEU* 4.1 8.9 - - - +
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Residues in contact with ARG 56 (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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52A PRO 3.1 18.2 + - - +
53A LEU* 4.3 7.9 - - - +
54A ILE 3.2 5.1 - - - +
55A ARG* 1.3 71.4 - - - +
57A PHE* 1.3 65.1 + - - +
58A ASP* 2.8 37.4 + - - +
59A ASN* 3.1 30.3 + - + +
60A PRO* 4.4 0.7 - - - +
83A ARG* 5.0 0.5 + - - -
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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