Contacts of the helix formed by residues 127 - 143 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PRO* 1.3 73.3 - - - +
128B LYS* 1.3 62.6 + - - +
129B LEU* 4.5 2.0 - - + +
130B THR* 2.4 50.9 + - + +
131B ILE* 3.2 8.3 + - - +
3F T 3.5 40.5 - - - +
4F T 5.4 1.8 - - - +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 5.5 8.1 - - + -
105B MET* 5.8 3.1 - - + +
106B THR* 3.2 26.3 - - - +
109B ILE* 3.9 37.4 - - + +
126B PRO 3.4 3.8 + - - +
127B ASP* 1.3 69.1 - - - +
129B LEU* 1.3 60.9 + - - +
131B ILE* 2.6 28.1 + - + +
132B LEU* 2.9 17.2 + - + +
3F T 4.4 4.4 + - - -
4F T 3.4 37.5 + - - +
5F G 2.2 34.6 + - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 5.3 3.4 - - + +
42A ARG* 3.9 34.3 - - + +
43A LEU* 4.9 18.6 - - + +
46A GLU* 2.9 36.0 - - - +
127B ASP* 4.5 2.7 - - + +
128B LYS* 1.3 77.1 - - - +
130B THR* 1.3 68.2 + - + +
132B LEU* 2.9 18.2 + - - +
133B ARG* 2.9 37.0 + - - +
3F T 3.0 35.5 - - - +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PRO* 4.4 2.8 - - - +
127B ASP* 2.4 53.2 + - + +
129B LEU* 1.3 80.7 - - + +
131B ILE* 1.3 58.5 + - - +
133B ARG* 3.3 10.7 + - - +
134B MET* 2.9 39.1 + - - +
3F T 6.2 0.2 - - - +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 3.8 31.0 - - + +
110B THR* 5.8 0.4 - - - -
112B LEU* 4.0 16.8 - - + +
113B SER* 3.8 35.2 - - - -
116B VAL* 5.4 4.5 - - + +
118B THR* 6.0 0.9 - - - +
126B PRO* 3.9 29.8 - - + +
127B ASP 3.3 15.7 - - - +
128B LYS* 2.6 15.9 + - + +
130B THR* 1.3 79.8 + - - +
132B LEU* 1.3 54.9 + - + -
134B MET* 3.8 6.9 - - - +
135B ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 4.2 22.9 - - + +
46A GLU* 3.3 24.0 - - + +
47A LEU* 3.5 26.7 - - + -
50A LEU* 5.1 5.0 - - + +
70A LEU* 3.7 21.1 - - + -
109B ILE* 3.5 31.6 - - + -
112B LEU* 4.1 9.6 - - + -
128B LYS* 2.9 16.9 + - + +
129B LEU* 2.9 5.6 + - - +
131B ILE* 1.3 76.5 - - + +
133B ARG* 1.3 60.4 + - - +
135B ALA* 3.2 3.9 + - - +
136B VAL* 2.9 33.9 + - - +
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 4.2 27.7 - - - +
46A GLU* 2.6 33.2 + - + +
129B LEU* 2.9 32.0 + - - +
130B THR* 3.8 13.1 - - - +
132B LEU* 1.3 75.4 - - - +
134B MET* 1.3 60.1 + - + +
136B VAL* 3.3 10.0 + - - +
137B SER* 2.9 26.5 + - - -
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 5.3 11.8 - - + +
117B PRO* 4.1 26.9 - - + +
118B THR* 5.7 3.8 - - + -
130B THR* 2.9 24.4 + - - +
131B ILE* 3.8 7.2 - - + +
133B ARG* 1.3 77.9 - - + +
135B ALA* 1.3 58.4 + - - +
137B SER* 3.2 14.8 + - - +
138B HIS* 2.9 28.1 + - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.8 8.7 - - + -
73A SER* 5.9 0.2 - - - +
77A LEU* 5.5 2.1 - - + +
112B LEU* 3.8 38.6 - - + +
116B VAL* 4.8 6.0 - - + +
131B ILE 2.9 19.8 + - - +
132B LEU* 3.2 6.9 + - - +
134B MET* 1.3 73.4 - - - +
136B VAL* 1.3 66.1 + - - +
138B HIS* 3.2 8.7 + - - +
139B MET* 2.9 28.7 + - + +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 3.8 30.1 - - + +
49A ARG* 4.6 20.6 - - + +
50A LEU* 4.0 15.7 - - + +
53A LEU* 4.1 13.2 - - + +
132B LEU* 2.9 21.8 + - + +
133B ARG* 3.5 9.6 - - - +
135B ALA* 1.3 73.7 - - - +
137B SER* 1.3 64.5 + - - +
139B MET* 3.2 8.4 + - - +
140B LYS* 2.9 29.7 + - + +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ARG 2.9 14.2 + - - -
134B MET* 3.2 23.2 + - - +
136B VAL* 1.3 74.8 - - - +
138B HIS* 1.3 62.3 + - - +
140B LYS* 2.8 41.2 - - - +
141B SER* 2.9 10.8 + - - -
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Residues in contact with HIS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.6 14.5 - - + +
115B MET 3.1 28.1 + - - -
116B VAL* 4.0 16.6 - - + -
117B PRO* 4.4 9.2 - - + +
134B MET 2.9 13.7 + - - +
135B ALA* 3.4 11.7 - - - +
137B SER* 1.3 75.2 + - - +
139B MET* 1.3 63.3 + - - +
141B SER* 2.6 30.5 + - - -
142B LEU* 2.9 38.1 - - + +
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Residues in contact with MET 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.2 35.7 - - + +
53A LEU* 3.6 32.0 - - + +
54A LEU* 4.3 12.8 - - + -
73A SER* 4.1 8.1 - - - +
76A TYR* 3.1 43.7 - - + +
77A LEU* 4.7 11.6 - - + +
135B ALA* 2.9 18.3 + - + +
136B VAL* 3.5 8.5 - - - +
138B HIS* 1.3 75.7 - - - +
140B LYS* 1.3 63.7 + - - +
142B LEU* 3.0 18.9 + - + +
143B ARG* 3.1 10.7 + - - +
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.5 15.4 - - + +
136B VAL* 2.9 20.0 + - + +
137B SER* 2.8 41.5 - - - +
139B MET* 1.3 76.7 - - - +
141B SER* 1.3 59.8 + - - +
143B ARG 2.7 27.4 - - - +
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B SER* 2.9 12.8 + - - -
138B HIS* 2.6 27.6 + - - -
140B LYS* 1.3 77.4 - - - +
142B LEU* 1.3 71.0 + - - +
143B ARG* 3.1 1.6 + - - -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TYR* 4.3 26.5 + - + +
77A LEU* 5.1 7.2 - - + -
80A LYS* 4.6 22.9 - - + -
84A ASP* 5.9 2.7 - - - +
138B HIS* 2.9 58.5 + - + +
139B MET* 3.0 10.7 + - - +
141B SER* 1.3 83.0 + - - +
143B ARG* 1.3 64.7 + - + +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 6.0 2.5 - - - -
76A TYR* 5.3 5.8 - - - +
139B MET 3.1 8.4 + - - +
140B LYS* 2.7 25.7 - - - +
141B SER 3.1 4.3 - - - -
142B LEU* 1.3 83.7 - - + +
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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
------------------------------------------------------------
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