Contacts of the helix formed by residues 104 - 125 (chain D) in PDB entry 2J3T
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 THR 104 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ARG 3.4 3.7 + - - -
103D LEU* 1.3 75.0 - - - +
105D SER* 1.3 78.9 + - - +
106D ASN* 3.2 24.7 - - + +
107D GLU* 2.5 26.9 + - + -
108D LYS* 2.9 22.4 + - - +
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Residues in contact with SER 105 (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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103D LEU 4.0 0.6 + - - -
104D THR* 1.3 78.4 - - - +
106D ASN* 1.3 68.0 + - - -
108D LYS* 3.1 15.7 + - - +
109D LEU* 3.0 26.0 + - - +
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Residues in contact with ASN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D THR* 3.2 12.0 - - + +
105D SER* 1.3 82.4 - - - +
107D GLU* 1.3 66.3 + - + +
109D LEU* 2.9 28.5 + - + +
110D MET* 2.9 22.5 + - - +
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LYS* 5.4 9.2 + - + +
44D ASP* 5.4 9.4 - - - +
46D ARG* 6.1 1.4 - - - -
102D ARG 3.7 4.5 - - - +
103D LEU* 3.2 26.0 - - + +
104D THR* 2.5 44.2 + - - +
106D ASN* 1.3 76.5 - - + +
108D LYS* 1.3 57.5 + - - +
110D MET* 3.3 16.5 + - + +
111D LEU* 2.9 37.9 + - + +
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Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D TYR* 3.9 20.1 - - + +
15D LEU* 3.9 16.0 - - + +
18D GLN* 2.5 49.8 - - + +
20D ASP* 2.8 20.4 + - - -
103D LEU* 3.9 33.6 + - + -
104D THR 2.9 15.8 + - - +
105D SER* 3.2 13.9 - - - +
107D GLU* 1.3 78.4 - - - +
109D LEU* 1.3 61.9 + - - +
111D LEU* 3.5 7.3 + - - +
112D ALA* 3.0 25.1 + - - +
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Residues in contact with LEU 109 (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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13D GLY 4.6 0.7 - - - +
15D LEU* 3.8 35.9 - - + +
105D SER* 3.0 18.2 + - - +
106D ASN* 2.9 30.8 + - - +
108D LYS* 1.3 77.2 - - - +
110D MET* 1.3 62.6 + - - +
112D ALA* 3.3 4.7 + - - +
113D SER* 3.0 27.2 + - - -
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Residues in contact with MET 110 (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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51C LYS* 3.8 28.3 - - + +
106D ASN 2.9 11.4 + - - +
107D GLU* 3.5 19.1 - - + +
109D LEU* 1.3 77.1 - - - +
111D LEU* 1.3 82.7 + - + +
113D SER* 2.9 9.1 + - - -
114D MET* 2.7 53.6 + - + +
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Residues in contact with LEU 111 (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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47C SER 5.6 0.2 - - - -
48C PHE* 3.2 47.2 - - + +
51C LYS* 4.2 19.3 - - + -
52C MET* 3.8 29.8 - - + -
7D TYR* 5.3 1.3 - - + -
103D LEU* 3.9 26.0 - - + -
107D GLU* 2.9 23.3 + - + +
108D LYS* 3.9 4.9 - - - +
110D MET* 1.3 96.2 - - + +
112D ALA* 1.3 56.5 + - - +
114D MET* 3.5 8.4 - - - +
115D PHE* 2.9 24.4 + - - +
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Residues in contact with ALA 112 (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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7D TYR* 4.6 9.1 - - + -
9D VAL* 4.1 22.6 - - + +
13D GLY 4.0 8.6 - - - +
15D LEU* 3.8 26.2 - - + -
108D LYS 3.0 18.1 + - - +
109D LEU 3.6 5.2 - - - +
111D LEU* 1.3 76.9 - - - +
113D SER* 1.3 61.9 + - - +
115D PHE* 3.5 7.0 + - - +
116D HIS* 3.2 20.1 + - - +
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Residues in contact with SER 113 (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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13D GLY* 3.1 22.3 + - - -
109D LEU* 3.0 13.3 + - - +
110D MET* 2.9 10.8 + - - -
112D ALA* 1.3 73.5 - - - +
114D MET* 1.3 67.6 + - - +
116D HIS* 3.1 23.0 + - - +
117D SER* 3.3 8.0 + - - -
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Residues in contact with MET 114 (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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44C SER* 3.3 43.3 - - - +
47C SER* 4.5 8.7 - - - -
48C PHE* 3.7 23.8 - - + +
51C LYS* 6.3 0.2 - - - -
110D MET* 2.7 52.0 + - + +
111D LEU* 3.5 10.3 - - - +
113D SER* 1.3 73.4 - - - +
115D PHE* 1.3 59.1 + - - +
117D SER* 3.0 22.5 + - - -
118D LEU* 3.1 18.3 + - + +
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Residues in contact with PHE 115 (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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48C PHE* 3.9 24.9 - + + -
9D VAL* 5.3 4.9 - - + -
111D LEU 2.9 16.7 + - - +
112D ALA* 3.7 8.1 - - - +
114D MET* 1.3 74.7 - - - +
116D HIS* 1.3 58.1 + - - +
118D LEU* 3.4 14.2 - - + +
119D PHE* 2.8 44.6 + + + +
134D ILE* 4.3 22.0 - - + -
137D LEU* 5.4 4.0 - - + -
144D LEU* 3.9 30.7 - - + -
146D CYS* 3.7 30.1 - - + -
154D LYS* 3.8 18.8 - - + -
156D VAL* 3.8 16.8 - - + -
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Residues in contact with HIS 116 (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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9D VAL* 5.1 1.6 - - + -
10D ASN 4.6 2.4 + - - -
11D LYS 3.3 26.8 + - - -
12D ALA* 4.4 6.5 + - - -
13D GLY* 3.8 25.6 + - - -
112D ALA 3.2 11.4 + - - +
113D SER* 3.1 12.5 + - - +
115D PHE* 1.3 81.8 - - - +
117D SER* 1.3 68.4 + - - +
119D PHE* 3.3 4.5 - - - +
120D ALA* 3.3 21.9 + - + +
154D LYS* 4.1 25.0 + - - +
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Residues in contact with SER 117 (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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113D SER 3.3 4.8 + - - -
114D MET* 3.0 18.4 + - - -
116D HIS* 1.3 83.6 - - - +
118D LEU* 1.3 69.1 + - - +
120D ALA* 3.2 7.4 + - - +
121D ILE* 2.9 38.1 + - - +
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Residues in contact with LEU 118 (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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41C MET* 3.2 27.2 - - + +
44C SER* 3.4 28.3 - - - +
45C ILE* 4.1 26.2 - - + +
48C PHE* 4.3 27.8 - - + -
114D MET* 3.1 21.6 + - + +
115D PHE* 3.4 18.8 - - + +
117D SER* 1.3 85.4 + - - +
119D PHE* 1.3 63.7 + - - +
121D ILE* 3.4 5.6 + - + -
122D GLY* 3.0 20.1 + - - -
134D ILE* 3.9 9.9 - - + +
137D LEU* 5.7 2.9 - - + -
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Residues in contact with PHE 119 (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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115D PHE* 2.8 27.1 + + + +
116D HIS 3.3 6.3 - - - +
118D LEU* 1.3 78.4 - - - +
120D ALA* 1.3 66.9 + - + +
122D GLY* 3.4 1.6 + - - -
123D SER* 3.3 14.5 + - - -
132D SER* 5.2 2.7 - - - -
133D GLY* 3.3 36.6 - - - -
134D ILE* 3.1 49.1 - - - +
135D GLU* 5.6 2.2 - - + -
146D CYS* 3.9 12.1 - - - -
148D GLN* 3.6 43.3 - - + -
154D LYS* 3.4 26.7 - - + -
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Residues in contact with ALA 120 (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 HIS* 3.3 13.1 + - + +
117D SER* 3.2 11.1 + - - +
119D PHE* 1.3 82.1 - - + +
121D ILE* 1.3 62.6 + - + +
123D SER* 2.8 23.7 + - - -
124D GLN* 2.8 17.3 + - - +
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Residues in contact with ILE 121 (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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37C LEU* 3.7 31.2 - - + +
41C MET* 3.6 35.2 - - + +
117D SER* 2.9 32.9 + - - +
118D LEU* 3.8 7.0 - - + +
120D ALA* 1.3 73.1 - - + +
122D GLY* 1.3 56.7 + - - +
124D GLN* 2.9 12.1 + - - +
125D LEU* 2.7 63.3 + - + +
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Residues in contact with GLY 122 (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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41C MET* 3.3 21.9 - - - +
64C PHE* 4.4 4.3 - - - -
66C THR* 4.3 7.1 - - - +
69C TYR* 2.5 38.5 + - - -
118D LEU 3.0 11.1 + - - -
119D PHE 3.8 4.5 - - - -
120D ALA 3.2 0.4 - - - -
121D ILE* 1.3 77.6 - - - +
123D SER* 1.3 58.3 + - - +
125D LEU* 5.1 1.3 - - - -
126D SER 3.6 2.6 + - - -
134D ILE* 4.7 5.2 - - - -
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Residues in contact with SER 123 (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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25C LYS* 3.4 14.8 + - - -
119D PHE* 3.3 10.4 + - - -
120D ALA* 2.8 13.1 + - - -
122D GLY* 1.3 77.1 - - - +
124D GLN* 1.3 63.9 + - - +
126D SER* 3.1 20.0 - - - -
131D SER* 3.1 22.2 + - - -
132D SER* 3.7 17.1 + - - -
133D GLY* 3.9 5.2 - - - -
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Residues in contact with GLN 124 (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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25C LYS* 3.8 20.4 - - - +
27C ALA* 4.5 16.8 + - + +
28C GLY 5.6 2.3 - - - +
29C ILE* 4.5 19.8 - - - +
37C LEU* 3.8 28.2 - - + +
120D ALA* 2.8 12.1 + - - +
121D ILE* 3.5 15.2 + - - +
123D SER* 1.3 78.7 - - - +
125D LEU* 1.3 62.1 + - + +
126D SER 3.3 4.2 + - - +
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Residues in contact with LEU 125 (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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5C ASN* 5.6 0.9 + - - -
7C TYR* 4.9 5.7 + - - +
23C ARG* 4.1 12.1 + - - +
27C ALA* 4.3 10.5 - - + -
34C GLU* 3.6 32.8 - - + -
37C LEU* 4.0 17.3 - - + -
38C MET* 3.6 49.4 - - + +
41C MET* 4.8 1.3 - - - -
69C TYR* 4.2 7.3 + - - +
85C ASN* 4.6 5.7 + - - -
121D ILE* 2.7 43.2 + - + +
122D GLY* 4.9 1.8 - - - +
124D GLN* 1.3 74.6 - - + +
126D SER* 1.3 62.3 + - - +
127D PRO* 3.5 7.1 - - - +
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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
------------------------------------------------------------
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