Contacts of the helix formed by residues 129 - 141 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D ASN* 2.8 37.5 + - - +
44D LEU* 4.1 9.4 - - + -
45D ASP* 3.7 19.4 + - - +
126D ILE* 2.7 51.6 + - + +
127D TYR 3.3 1.6 + - - -
128D SER* 1.3 69.2 - - - +
130D LEU* 1.3 62.2 - - - +
131D LEU 3.1 0.4 - - - -
132D CYS* 3.0 32.9 + - - +
133D GLY 3.6 2.9 + - - -
149D LYS* 5.7 0.2 - - - -
150D PHE* 3.9 7.3 + - - -
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Residues in contact with LEU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D PHE* 5.8 1.3 - - + -
23D TYR* 3.5 41.0 + - + +
26D LEU* 5.0 5.2 - - + -
44D LEU* 3.4 23.6 + - + +
47D MET* 3.8 13.5 - - + -
48D GLY* 3.3 30.2 - - - +
51D ILE* 4.2 20.2 - - + -
112D LEU* 5.0 10.3 - - + -
128D SER 2.7 6.0 + - - +
129D ASN* 1.3 74.4 - - - +
131D LEU* 1.3 62.2 + - + +
133D GLY 3.2 3.3 + - - -
134D VAL* 3.0 31.3 + - + +
1068D PLM 5.1 9.2 - - + -
32F LEU* 4.7 9.2 - - + -
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 4.6 13.0 - - + -
87D LEU* 3.9 12.1 - - + -
107D LEU* 4.3 21.3 - - + -
110D ASN* 4.2 12.1 - - - +
112D LEU* 3.8 23.8 - - + -
128D SER* 2.9 16.3 + - - +
130D LEU* 1.3 76.6 - - + +
132D CYS* 1.3 65.2 + - - +
134D VAL* 3.1 6.7 + - + +
135D LEU* 2.9 33.0 + - + +
150D PHE* 4.3 12.6 - - + -
163D ILE* 4.4 8.1 - - + -
1068D PLM 3.7 35.2 - - + -
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Residues in contact with CYS 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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45D ASP* 3.9 12.6 - - - +
129D ASN* 3.0 18.6 + - - +
131D LEU* 1.3 78.4 - - - +
133D GLY* 1.3 57.0 + - - +
135D LEU* 3.7 1.3 + - - -
136D ARG* 3.2 27.2 + - - +
148D ALA* 3.3 42.6 - - - +
149D LYS* 3.5 11.7 - - - -
150D PHE* 3.2 37.5 - - - -
163D ILE* 4.8 4.3 - - - -
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Residues in contact with GLY 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ASP* 3.5 34.8 + - - -
48D GLY 3.4 6.5 - - - -
49D TYR* 3.2 11.2 - - - -
129D ASN 3.6 3.4 + - - -
130D LEU 3.2 5.2 + - - -
131D LEU 3.2 0.4 - - - -
132D CYS* 1.3 77.0 - - - +
134D VAL* 1.3 59.6 + - - +
136D ARG* 3.4 4.7 + - - +
137D GLY 2.8 25.8 + - - -
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D GLY* 3.2 21.9 + - - +
51D ILE* 4.2 12.6 - - + -
52D GLY* 3.5 12.4 - - - +
55D LEU* 4.3 14.1 - - + -
130D LEU* 3.0 28.1 + - + +
131D LEU* 3.1 10.5 + - + +
133D GLY* 1.3 76.7 - - - +
135D LEU* 1.3 58.0 + - - +
138D ALA* 2.9 30.5 + - - +
1068D PLM 4.0 40.8 - - + -
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Residues in contact with LEU 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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78D ILE* 3.8 22.7 - - + -
83D PHE* 4.2 11.2 - - + -
105D LEU* 4.7 6.5 - - + -
131D LEU* 2.9 22.2 + - + +
132D CYS 3.8 3.8 - - - +
134D VAL* 1.3 76.0 - - - +
136D ARG* 1.3 63.3 + - - +
138D ALA* 3.9 3.3 - - - +
139D LEU* 3.0 32.6 + - - +
146D VAL* 4.9 0.2 - - - -
148D ALA* 3.9 10.3 - - + -
163D ILE* 4.1 15.0 - - + -
165D MET* 3.5 40.8 - - + -
1068D PLM 3.8 30.7 - - + -
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Residues in contact with ARG 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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45D ASP* 2.9 29.7 + - - -
46D ARG* 5.7 0.4 - - - +
49D TYR* 3.5 42.3 - - + +
132D CYS 3.2 16.0 + - - +
133D GLY* 3.7 3.8 - - - +
135D LEU* 1.3 79.6 - - - +
137D GLY* 1.3 61.3 + - - +
139D LEU* 3.5 1.6 + - - +
140D GLU* 3.0 31.7 + - + +
144D MET 4.9 1.2 - - - +
146D VAL* 3.8 33.5 + - + +
147D GLU* 5.6 2.7 - - - +
148D ALA* 5.1 4.9 - - - +
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Residues in contact with GLY 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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49D TYR* 3.6 36.3 - - - -
52D GLY 3.8 6.5 - - - -
53D VAL* 4.0 3.7 - - - +
133D GLY 2.8 17.6 + - - -
134D VAL 3.9 0.9 - - - -
136D ARG* 1.3 73.8 - - - +
138D ALA* 1.3 62.3 + - - +
140D GLU* 3.4 9.6 + - - +
141D MET* 3.4 18.0 + - - +
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Residues in contact with ALA 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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52D GLY* 3.5 18.9 - - - +
55D LEU* 4.6 4.7 - - + -
56D ILE* 3.6 24.9 - - + +
134D VAL 2.9 18.1 + - - +
135D LEU 3.9 2.2 - - - +
137D GLY* 1.3 76.8 - - - +
139D LEU* 1.3 62.4 + - - +
141D MET* 3.2 19.1 + - - +
142D VAL* 3.8 2.9 - - - +
1068D PLM 4.0 28.7 - - + -
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Residues in contact with LEU 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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71D PHE* 5.4 2.9 - - + -
74D THR* 3.7 28.7 - - + -
78D ILE* 4.2 10.3 - - + -
135D LEU* 3.0 19.8 + - + +
136D ARG 4.1 0.2 - - - +
138D ALA* 1.3 75.4 - - - +
140D GLU* 1.3 57.7 + - - +
142D VAL* 2.9 27.2 - - + +
144D MET* 2.9 42.9 + - + +
146D VAL* 3.5 32.1 - - + -
165D MET* 3.7 20.9 - - + -
1068D PLM 4.0 19.5 - - + -
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D TYR* 2.6 36.4 + - - -
136D ARG* 3.0 26.7 + - + +
137D GLY* 3.6 7.0 - - - +
138D ALA 3.1 0.6 - - - -
139D LEU* 1.3 74.3 - - - +
141D MET* 1.3 75.3 + - + +
142D VAL 3.0 6.6 + - - -
143D GLN* 3.1 16.5 + - - -
144D MET 3.7 9.4 + - - +
145D ALA* 5.8 1.6 - - - -
171D ILE* 4.1 18.8 - - + +
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Residues in contact with MET 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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49D TYR* 4.6 1.1 - - - +
53D VAL* 3.9 34.1 - - + +
56D ILE* 3.4 35.2 - - + -
137D GLY 3.4 9.2 + - - +
138D ALA 3.2 10.2 + - - +
140D GLU* 1.3 100.8 - - + +
142D VAL* 1.3 59.3 + - - +
143D GLN* 3.5 15.0 + - - +
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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