Contacts of the helix formed by residues 127 - 143 (chain D) in PDB entry 5NJ8
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 ASP 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C HIS* 6.0 0.3 + - - -
126D PRO* 1.3 75.1 - - - +
128D LYS* 1.3 75.8 + - - +
129D LEU* 2.9 19.8 + - - +
130D THR* 2.9 25.1 + - - +
131D ILE* 2.5 37.8 + - - +
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS* 5.6 8.5 - - + +
43C LEU* 4.4 21.8 - - + -
105D MET* 5.7 3.4 - - - -
106D THR* 3.5 38.5 + - - +
109D ILE* 3.5 34.1 - - + +
110D THR* 5.7 0.2 + - - -
126D PRO 3.9 2.4 + - - -
127D ASP* 1.3 74.5 + - - +
129D LEU* 1.3 66.0 + - - +
131D ILE* 2.9 25.9 + - - +
132D LEU* 3.0 10.7 + - - +
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS* 5.1 9.4 + - + +
42C ARG* 4.5 30.1 - - + +
43C LEU* 3.8 30.4 - - + +
46C GLU* 4.7 13.0 - - + +
127D ASP* 2.9 12.3 + - - +
128D LYS* 1.3 76.4 - - - +
130D THR* 1.3 66.1 + - - +
132D LEU* 3.1 4.9 + - + +
133D ARG* 2.9 66.7 + - + +
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Residues in contact with THR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 4.8 6.1 - - + -
127D ASP* 2.9 32.9 + - - +
129D LEU* 1.3 79.1 - - - +
131D ILE* 1.3 65.4 + - - +
133D ARG* 3.0 9.9 + - - +
134D MET* 2.9 49.7 + - + +
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ILE* 3.4 27.1 - - + +
110D THR* 5.0 3.8 - - - +
112D LEU* 3.4 27.3 - - + +
113D SER* 3.6 28.5 - - - +
116D VAL* 5.4 1.0 - - + +
119D CYS* 4.7 9.9 - - - -
126D PRO* 3.8 26.7 - - + +
127D ASP 2.5 27.6 + - - +
128D LYS* 3.2 13.2 - - - +
130D THR* 1.3 72.8 - - - +
132D LEU* 1.3 64.7 + - - +
134D MET* 3.4 1.4 + - - +
135D ALA* 2.9 24.9 + - - +
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 4.1 42.8 - - + +
46C GLU* 4.2 11.7 - - + +
47C LEU* 4.6 19.5 - - + -
50C LEU* 3.5 31.6 - - + -
70C LEU* 4.1 17.0 - - + -
109D ILE* 3.6 24.5 - - + -
112D LEU* 5.3 2.9 - - + -
128D LYS 3.0 6.6 + - - +
129D LEU* 3.1 7.8 + - - +
131D ILE* 1.3 76.4 - - - +
133D ARG* 1.3 63.0 + - - +
135D ALA* 3.2 5.4 + - - +
136D VAL* 2.9 28.3 + - - +
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Residues in contact with ARG 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ARG* 4.3 16.4 - - - +
46C GLU* 3.6 35.6 + - + +
129D LEU* 2.9 52.1 + - + +
130D THR* 3.6 9.9 - - - +
132D LEU* 1.3 77.0 - - - +
134D MET* 1.3 59.7 + - + +
136D VAL* 3.1 6.1 + - - +
137D SER* 2.9 26.2 + - - -
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Residues in contact with MET 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL* 4.1 4.3 - - - +
118D THR* 3.3 42.7 + - + +
119D CYS* 3.3 26.7 - - - -
122D LEU* 5.5 8.3 - - + -
126D PRO* 5.8 0.4 - - - -
130D THR* 2.9 39.4 + - + +
131D ILE 4.1 0.7 - - - +
133D ARG* 1.3 78.2 - - + +
135D ALA* 1.3 57.5 + - - +
137D SER* 3.3 10.8 + - - -
138D HIS* 2.9 27.7 + - - +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 4.6 13.9 - - + -
77C LEU* 5.2 5.5 - - + +
112D LEU* 3.6 26.7 - - + -
116D VAL* 3.8 17.4 - - + +
131D ILE 2.9 19.0 + - - +
132D LEU* 3.4 6.7 - - - +
134D MET* 1.3 73.8 - - - +
136D VAL* 1.3 63.6 - - - +
138D HIS* 2.9 13.0 + - - +
139D MET* 2.9 17.7 + - - +
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Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 3.6 40.6 - - + +
49C ARG* 4.1 21.3 - - + -
50C LEU* 3.8 25.3 - - + +
53C LEU* 4.2 12.6 - - + +
132D LEU* 2.9 19.1 + - + +
133D ARG 3.1 8.0 + - - +
135D ALA* 1.3 74.4 - - - +
137D SER* 1.3 65.0 + - - +
139D MET* 3.2 2.8 + - - +
140D LYS* 2.9 25.5 + - + +
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Residues in contact with SER 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D THR* 6.1 2.0 - - - +
133D ARG 2.9 12.8 + - - -
134D MET* 3.4 14.4 - - - -
135D ALA 3.2 0.2 - - - -
136D VAL* 1.3 77.6 - - - +
138D HIS* 1.3 58.9 + - - +
140D LYS* 3.5 6.5 + - - +
141D SER* 2.9 29.9 + - - -
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Residues in contact with HIS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU* 3.3 32.4 - - + +
115D MET 5.6 0.4 - - - -
116D VAL* 3.7 14.1 - - + +
117D PRO* 3.1 44.0 - - + +
118D THR* 5.5 6.3 - - + -
134D MET 2.9 12.2 + - - +
135D ALA* 2.9 8.9 + - - +
137D SER* 1.3 76.8 - - - +
139D MET* 1.3 58.4 + - - +
141D SER* 3.4 9.1 + - - -
142D LEU* 2.9 44.9 + - + +
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Residues in contact with MET 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 3.5 27.8 - - - +
53C LEU* 3.5 38.6 - - + +
54C LEU* 4.3 16.6 - - + -
73C SER* 3.9 17.9 - - - +
76C TYR* 3.9 28.3 - - + -
77C LEU* 4.4 22.2 - - + -
135D ALA 2.9 15.6 + - - +
136D VAL* 3.9 4.0 - - - +
138D HIS* 1.3 74.8 - - - +
140D LYS* 1.3 65.6 + - - +
142D LEU* 2.9 15.7 + - + -
143D ARG* 2.9 22.2 + - + +
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LEU* 3.9 18.4 - - + +
136D VAL* 2.9 20.2 + - + +
137D SER* 3.7 6.3 - - - +
139D MET* 1.3 76.2 - - - +
141D SER* 1.3 60.8 + - - +
143D ARG 3.2 20.5 - - - +
144D GLY* 4.3 3.3 + - - -
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Residues in contact with SER 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D SER* 2.9 19.6 + - - -
138D HIS* 3.6 12.6 - - - -
139D MET 3.1 0.2 - - - -
140D LYS* 1.3 77.0 - - - +
142D LEU* 1.3 60.5 + - - +
143D ARG 5.0 0.4 - - - -
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C TYR* 3.6 33.5 + - + +
77C LEU* 4.4 18.4 - - + -
80C LYS* 4.0 23.8 - - + -
138D HIS* 2.9 31.1 + - + +
139D MET* 2.9 7.9 + - - +
141D SER* 1.3 79.2 - - - +
143D ARG* 1.3 60.2 + - + +
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Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B ASP 5.9 0.6 + - - -
52C SER 5.0 1.0 + - - -
53C LEU* 2.8 50.1 + - + +
54C LEU 3.4 14.6 + - - -
55C PRO* 4.1 15.0 - - - +
76C TYR* 3.4 36.8 + - + +
139D MET* 2.9 18.5 + - - +
140D LYS* 3.2 16.7 - - - +
141D SER 3.5 0.6 - - - -
142D LEU* 1.3 80.0 - - - +
144D GLY* 1.3 57.4 - - - +
156D PRO* 4.9 10.3 - - - +
157D SER 5.3 2.6 + - - +
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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