Contacts of the helix formed by residues 129 - 141 (chain E) in PDB entry 2J3W
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 ASN 129 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ASN* 2.8 34.0 + - - +
42E LYS* 4.9 0.2 - - - +
44E LEU* 4.0 14.1 - - + -
45E ASP* 3.8 17.5 + - - +
126E ILE* 2.8 50.4 + - + +
127E TYR 3.3 1.8 + - - -
128E SER* 1.3 70.5 - - - +
130E LEU* 1.3 63.6 + - - +
131E LEU 3.1 1.5 + - - -
132E CYS* 3.1 20.8 + - - +
133E GLY 3.6 5.9 + - - -
149E LYS* 5.7 0.2 - - - -
150E PHE* 3.9 13.8 + - - -
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Residues in contact with LEU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.5 8.5 - - + -
19E PHE* 5.5 2.7 - - + -
23E TYR* 3.4 41.6 + - + +
26E LEU* 4.6 7.9 - - + -
44E LEU* 3.5 32.4 - - + +
47E MET* 3.9 14.1 - - + -
48E GLY* 3.4 17.1 - - - +
51E ILE* 4.1 20.6 - - + -
112E LEU* 5.5 3.8 - - + -
128E SER 3.0 1.6 + - - +
129E ASN* 1.3 77.4 - - - +
131E LEU* 1.3 62.5 + - + +
133E GLY 3.1 2.8 + - - -
134E VAL* 3.0 36.1 + - + +
1068E PLM 4.8 9.9 - - + -
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Residues in contact with LEU 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E PHE* 4.6 4.9 - - + -
87E LEU* 4.2 19.1 - - + -
107E LEU* 4.1 24.9 - - + -
110E ASN* 4.2 5.6 - - - +
112E LEU* 4.0 20.6 - - + -
128E SER* 3.2 28.7 + - - +
129E ASN 3.1 0.6 - - - -
130E LEU* 1.3 81.4 - - + +
132E CYS* 1.3 61.2 + - - +
134E VAL* 3.2 4.9 + - + +
135E LEU* 3.0 30.9 + - + +
150E PHE* 4.3 0.7 - - + -
163E ILE* 4.1 16.8 - - + -
1068E PLM 4.6 31.1 - - + +
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Residues in contact with CYS 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ASP* 3.9 10.1 - - - +
129E ASN* 3.1 16.4 + - - +
131E LEU* 1.3 78.0 - - - +
133E GLY* 1.3 60.8 + - - +
135E LEU* 3.6 2.8 + - - -
136E ARG* 3.2 23.0 + - - +
148E ALA* 3.3 43.5 - - - +
149E LYS* 3.5 14.6 - - - -
150E PHE* 3.4 35.0 - - - -
163E ILE* 4.7 6.3 - - - -
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Residues in contact with GLY 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ASP* 3.2 33.2 + - - -
48E GLY 3.3 6.7 - - - -
49E TYR* 3.3 8.4 - - - -
129E ASN 3.6 3.8 + - - -
130E LEU 3.1 7.1 + - - -
132E CYS* 1.3 77.5 - - - +
134E VAL* 1.3 64.3 + - - +
136E ARG* 3.3 7.2 + - - +
137E GLY 2.9 19.9 + - - -
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Residues in contact with VAL 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E GLY* 3.1 21.5 + - - +
51E ILE* 4.2 8.1 - - + -
52E GLY* 3.5 12.5 - - - +
55E LEU* 4.1 10.5 - - + -
130E LEU* 3.0 22.0 + - + +
131E LEU* 3.6 8.7 - - - +
133E GLY* 1.3 75.8 - - - +
135E LEU* 1.3 63.2 + - - +
138E ALA* 3.0 24.4 + - - +
1068E PLM 3.9 57.0 - - + -
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Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ILE* 4.0 26.0 - - + -
83E PHE* 4.4 6.7 - - + -
105E LEU* 4.4 6.7 - - + -
131E LEU* 3.0 21.7 + - + +
132E CYS* 3.7 4.7 - - - +
133E GLY 3.2 0.2 - - - -
134E VAL* 1.3 77.5 - - - +
136E ARG* 1.3 63.3 + - - +
138E ALA* 4.2 1.8 - - - +
139E LEU* 3.1 32.8 + - + +
146E VAL* 4.9 0.7 - - - -
148E ALA* 4.2 8.1 - - + -
163E ILE* 4.1 27.6 - - + -
165E MET* 3.5 32.1 - - + -
1068E PLM 3.8 30.5 - - + -
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Residues in contact with ARG 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ASP* 2.6 43.7 + - - -
46E ARG* 5.0 3.0 - - - +
49E TYR* 3.9 31.7 - - + +
132E CYS 3.2 13.6 + - - +
133E GLY* 3.3 1.6 + - - +
135E LEU* 1.3 77.1 - - - +
137E GLY* 1.3 58.3 + - - +
139E LEU* 3.8 0.5 - - - +
140E GLU* 2.8 45.2 + - + +
144E MET 5.0 0.3 - - - +
145E ALA* 6.2 0.4 - - - -
146E VAL* 3.7 38.0 + - + +
147E GLU* 5.5 1.6 - - - +
148E ALA* 4.9 7.7 + - + +
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Residues in contact with GLY 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E TYR* 3.6 36.5 - - - -
52E GLY 3.8 6.3 - - - -
53E VAL* 3.9 1.5 + - - +
133E GLY 2.9 14.5 + - - -
134E VAL 3.8 0.4 - - - -
136E ARG* 1.3 78.3 - - - +
138E ALA* 1.3 61.9 + - - +
140E GLU* 3.3 3.0 + - - +
141E MET* 3.2 26.3 + - - +
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Residues in contact with ALA 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E GLY* 3.4 22.0 + - - +
55E LEU* 4.6 1.1 - - + -
56E ILE* 3.8 24.6 - - + +
134E VAL 3.0 16.8 + - - +
135E LEU 4.2 0.9 - - - +
137E GLY* 1.3 73.3 - - - +
139E LEU* 1.3 63.5 + - - +
141E MET* 3.2 16.5 + - - +
142E VAL* 3.6 8.2 + - - +
1068E PLM 4.1 31.4 - - + -
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E PHE* 4.8 1.8 - - + -
74E THR* 3.9 22.9 - - + -
78E ILE* 4.4 10.1 - - + -
135E LEU* 3.1 18.8 + - + +
136E ARG 4.0 1.8 - - - +
138E ALA* 1.3 74.0 - - - +
140E GLU* 1.3 66.3 + - - +
142E VAL* 2.8 34.1 + - + +
144E MET* 3.0 34.5 + - + +
146E VAL* 3.7 20.2 - - + -
165E MET* 3.6 31.4 - - + -
1068E PLM 4.4 21.8 - - + -
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Residues in contact with GLU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E TYR* 2.9 35.2 + - - -
136E ARG* 2.8 32.2 + - + +
137E GLY* 3.3 6.0 + - - +
139E LEU* 1.3 73.3 - - - +
141E MET* 1.3 76.8 + - + +
143E GLN* 3.1 14.7 + - - +
144E MET 3.7 4.9 + - - +
145E ALA* 5.7 2.2 - - + -
171E ILE* 3.4 29.9 - - + +
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Residues in contact with MET 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E TYR* 4.6 1.3 - - - +
53E VAL* 3.9 35.0 - - + +
56E ILE* 3.7 28.3 - - + -
57E GLU* 5.9 1.1 - - - +
137E GLY 3.2 13.3 + - - +
138E ALA 3.5 9.4 - - - +
139E LEU 3.1 0.8 - - - -
140E GLU* 1.3 106.2 - - + +
142E VAL* 1.3 59.5 + - - +
143E GLN* 3.3 12.8 - - - +
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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