Contacts of the helix formed by residues 16 - 34 (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 SER 16 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B THR* 2.9 35.8 + - - +
24B VAL* 3.0 33.1 - - - +
14E MET 3.8 1.0 + - - -
15E SER* 1.3 72.7 + - - +
17E GLU* 1.3 57.3 + - - +
18E LEU 3.5 0.2 - - - -
19E PHE* 3.1 7.6 + - - +
20E THR* 2.8 31.7 + - - +
87E LEU 4.4 1.6 + - - -
111E PRO* 4.3 18.1 - - - +
114E ASP* 5.9 0.2 - - - -
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Residues in contact with GLU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A MET* 5.4 4.5 - - - +
21B LYS* 6.3 2.0 - - + -
65B LEU* 4.2 18.4 - - + +
68B VAL* 3.7 17.9 - - - +
72B ARG* 2.7 42.1 + - - -
15E SER* 3.1 19.1 + - - +
16E SER* 1.3 76.6 - - - +
18E LEU* 1.3 63.1 + - - +
20E THR* 2.7 27.7 - - + +
21E LEU* 2.9 21.1 + - + +
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Residues in contact with LEU 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 3.8 23.3 - - + -
61B VAL* 4.0 24.5 - - + -
65B LEU* 4.8 7.5 - - + +
96B ALA 4.8 3.4 - - - +
97B LEU* 4.3 30.7 - - + +
127B TYR* 3.7 23.1 - - - +
142B PHE* 5.0 0.9 - - + -
146B ILE* 4.6 7.6 - - + -
14E MET* 3.8 27.6 - - + -
15E SER 3.8 2.6 + - - +
16E SER 3.5 0.4 - - - -
17E GLU* 1.3 78.2 - - - +
19E PHE* 1.3 55.9 + - - +
21E LEU* 4.8 2.9 - - - -
22E THR* 2.7 41.4 + - - +
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Residues in contact with PHE 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 4.6 10.3 - - + -
28B ALA* 3.0 37.2 - - + -
29B PHE* 3.4 27.9 - + + -
32B LEU* 3.7 26.6 - - + +
14E MET* 5.3 1.7 - - + +
15E SER 4.5 1.7 + - - +
16E SER* 3.1 16.4 + - - +
18E LEU* 1.3 80.5 - - - +
20E THR* 1.3 57.9 + - - +
22E THR* 3.9 3.9 - - - -
23E TYR* 3.0 31.3 + + + +
87E LEU* 4.1 17.7 - - + -
111E PRO* 6.0 2.2 - - + -
112E LEU* 3.4 30.1 - - + -
130E LEU* 5.5 3.1 - - + -
1068E PLM 3.9 22.4 - - + -
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Residues in contact with THR 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E SER* 2.8 22.3 + - - +
17E GLU* 2.7 34.8 - - + +
19E PHE* 1.3 77.3 - - - +
21E LEU* 1.3 67.1 + - + +
23E TYR* 3.6 6.4 + - - +
24E GLY* 3.2 17.5 + - - -
111E PRO* 3.2 28.8 + - + -
112E LEU* 4.1 14.3 + - - +
114E ASP* 4.1 16.4 + - + +
116E VAL* 5.8 0.3 - - - +
127E TYR* 4.8 0.7 + - - -
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A MET* 4.2 26.5 - - + +
113A PRO* 6.2 1.3 - - + -
61B VAL* 3.9 28.5 - - + +
64B SER* 3.8 34.3 - - - +
65B LEU* 3.9 27.1 - - + +
17E GLU* 2.9 25.8 + - + +
18E LEU* 4.1 2.2 - - - +
20E THR* 1.3 82.2 - - + +
22E THR* 1.3 61.5 + - - +
24E GLY* 3.1 3.4 + - - -
25E ALA* 2.9 26.2 + - - +
114E ASP 6.1 0.7 - - - +
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Residues in contact with THR 22 (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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29B PHE* 3.5 25.4 - - + -
32B LEU* 4.0 8.1 - - + -
33B PHE* 5.1 2.7 - - + -
36B MET* 3.4 34.3 - - + +
61B VAL* 4.2 8.3 - - - +
142B PHE* 3.8 22.5 - - + -
18E LEU* 2.7 27.5 + - - +
19E PHE 3.9 2.5 - - - -
21E LEU* 1.3 74.0 - - - +
23E TYR* 1.3 66.1 + - - +
25E ALA* 3.2 3.7 + - - +
26E LEU 3.0 17.3 + - - -
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Residues in contact with TYR 23 (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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32B LEU* 4.2 15.2 - - + +
19E PHE 3.0 18.2 + - - +
20E THR 3.8 4.3 - - - +
21E LEU 3.2 0.2 - - - -
22E THR* 1.3 77.1 - - - +
24E GLY* 1.3 57.4 + - - +
26E LEU* 3.1 13.4 + - + +
27E VAL* 2.9 46.5 + - + +
44E LEU* 3.5 18.9 - - + +
112E LEU* 3.9 36.1 - - + -
127E TYR* 2.7 52.2 + + - -
128E SER* 3.7 3.0 - - - -
130E LEU* 3.4 50.4 + - + +
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Residues in contact with GLY 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 3.8 18.7 - - - +
20E THR 3.2 8.3 + - - -
21E LEU* 3.1 8.8 + - - -
23E TYR* 1.3 80.4 - - - +
25E ALA* 1.3 61.4 + - - +
27E VAL* 3.4 1.2 + - - +
28E THR* 2.9 27.6 + - - -
127E TYR* 3.2 21.9 + - - -
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Residues in contact with ALA 25 (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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36B MET* 4.9 1.6 - - + -
57B MET* 3.5 45.3 - - + +
60B GLY* 5.9 1.8 - - - -
61B VAL* 4.1 8.7 - - + +
142B PHE* 5.2 0.7 - - + -
21E LEU 2.9 11.6 + - - +
22E THR* 3.2 9.8 + - - +
24E GLY* 1.3 77.3 - - - +
26E LEU* 1.3 55.9 + - - +
28E THR* 3.5 8.3 + - - +
29E GLN* 3.0 25.5 + - - +
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Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.0 16.2 - - + -
36B MET* 3.8 28.7 - - + -
39B TYR* 4.8 6.7 - - + -
57B MET* 3.4 14.9 - - + +
22E THR 3.0 12.8 + - - +
23E TYR* 3.1 23.3 + - + +
25E ALA* 1.3 73.0 - - - +
27E VAL* 1.3 68.2 + - - +
29E GLN* 3.1 3.0 + - + +
30E LEU* 2.9 42.9 + - + +
44E LEU* 4.4 6.1 - - + -
47E MET* 3.8 33.2 - - + -
130E LEU* 4.6 2.9 - - + -
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Residues in contact with VAL 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 4.3 4.9 - - + -
23E TYR* 2.9 58.4 + - + +
24E GLY 3.9 1.8 - - - +
26E LEU* 1.3 72.8 - - - +
28E THR* 1.3 57.3 + - - +
30E LEU* 3.3 9.0 + - - +
31E CYS* 3.0 31.3 + - - -
40E VAL* 4.8 0.9 - - + -
44E LEU* 4.3 13.2 - - + -
125E LEU* 4.1 18.6 - - + -
127E TYR* 3.6 40.2 - - + +
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Residues in contact with THR 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 3.3 28.3 + - - +
114A PHE* 4.8 12.7 - - - -
24E GLY 2.9 18.5 + - - -
25E ALA* 3.7 7.9 - - - +
27E VAL* 1.3 78.2 - - - +
29E GLN* 1.3 63.6 + - + +
31E CYS* 3.6 8.1 + - - +
32E LYS* 3.3 37.8 + - + +
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Residues in contact with GLN 29 (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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39B TYR* 5.7 3.1 - - + -
53B ARG* 3.3 22.3 + - + +
56B ASP* 5.1 10.1 + - - +
57B MET* 3.7 36.3 - - + -
25E ALA 3.0 14.9 + - - +
26E LEU* 3.6 4.3 - - + +
28E THR* 1.3 74.7 - - + +
30E LEU* 1.3 57.1 + - + +
32E LYS* 2.8 40.2 + - - +
33E ASP* 2.7 67.7 + - - +
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Residues in contact with LEU 30 (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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39B TYR* 3.3 39.5 - - + +
26E LEU* 2.9 28.7 + - + +
27E VAL* 3.5 9.2 - - - +
29E GLN* 1.3 76.6 - - - +
31E CYS* 1.3 57.1 + - - +
33E ASP* 2.9 3.1 + - - -
34E TYR* 2.8 44.9 + - + -
40E VAL* 3.8 19.9 - - + +
43E GLN* 3.8 18.6 - - + -
44E LEU* 3.6 38.6 - - + -
47E MET* 4.3 2.5 - - - -
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Residues in contact with CYS 31 (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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114A PHE* 4.3 10.1 - - + -
27E VAL 3.0 20.3 + - - +
28E THR* 3.7 7.9 - - - +
29E GLN 3.3 0.2 - - - -
30E LEU* 1.3 76.2 - - - +
32E LYS* 1.3 57.1 - - + +
34E TYR 2.5 19.9 - - - +
35E GLU* 4.6 1.6 - - - -
37E ASP* 4.8 1.6 - - - -
40E VAL* 3.8 18.6 - - - +
122E HIS* 3.7 34.8 - - + +
125E LEU* 4.2 21.5 - - - -
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Residues in contact with LYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP* 4.8 9.3 + - - -
28E THR* 3.3 25.9 + - + +
29E GLN* 2.8 43.5 + - - +
31E CYS* 1.3 78.5 - - + +
33E ASP* 1.3 65.2 + - - +
34E TYR 3.4 1.8 + - - +
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Residues in contact with ASP 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 2.7 34.7 + - - +
43B ARG* 3.4 27.4 + - - +
53B ARG* 2.9 29.9 + - - -
29E GLN* 2.7 34.1 + - - +
30E LEU 2.9 4.5 + - - +
32E LYS* 1.3 79.2 - - - +
34E TYR* 1.3 65.1 + - + +
35E GLU 4.4 0.2 + - - -
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Residues in contact with TYR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 3.4 27.4 - - - -
43B ARG* 4.0 14.3 + - - -
30E LEU* 2.8 32.1 + - + +
31E CYS* 2.5 29.9 - - - +
32E LYS 4.7 1.6 - - - -
33E ASP* 1.3 82.1 - - + +
35E GLU* 1.3 56.4 + - - +
36E ASN 3.1 12.6 + - - +
39E ASP* 3.5 39.0 - - + +
40E VAL* 4.3 8.8 - - + +
43E GLN* 3.5 34.2 + - + -
46E ARG* 4.4 5.7 + - - -
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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
------------------------------------------------------------
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