Contacts of the helix formed by residues 37 - 51 (chain A) in PDB entry 2EX4
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 ILE 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.9 11.4 - - + +
34A TYR* 3.0 33.4 + - + +
35A GLY 3.0 0.4 + - - -
36A HIS* 1.3 95.2 - - + +
38A SER* 1.3 66.5 + - - +
39A SER 3.3 1.1 - - - -
40A ILE* 3.1 35.2 - - + +
41A ASP* 3.1 9.0 + - + +
137A TRP* 4.0 28.7 - - + -
211A LEU* 4.7 12.3 - - + -
212A PRO* 4.0 26.2 - - + -
215A ILE* 6.2 4.7 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.1 9.5 - - - +
31A LEU* 4.0 9.6 - - - -
35A GLY 2.9 16.0 + - - -
36A HIS 3.2 1.0 - - - -
37A ILE* 1.3 80.6 - - - +
39A SER* 1.3 57.4 + - - +
41A ASP* 3.3 2.7 + - - +
42A ILE* 2.8 35.1 + - - +
75A ARG* 3.0 38.8 + - - +
79A ARG* 4.0 10.3 + - - -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A HIS 4.4 5.8 + - - -
37A ILE 3.3 0.6 - - - -
38A SER* 1.3 77.0 - - - +
40A ILE* 1.3 58.2 + - - +
42A ILE* 3.9 0.2 - - - -
43A ASN* 2.8 46.0 + - - -
79A ARG* 2.9 36.8 + - - +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A HIS 5.3 2.2 + - - +
37A ILE* 3.1 42.2 - - + +
39A SER* 1.3 73.9 - - - +
41A ASP* 1.3 65.7 + - - +
43A ASN* 4.2 5.4 - - - +
44A SER* 3.1 26.7 + - - -
208A GLN* 3.6 8.7 + - - +
210A ASN* 3.1 39.7 - - + +
211A LEU* 4.3 11.2 - - + -
212A PRO* 5.1 1.6 - - + -
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Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.1 15.4 + - + +
38A SER* 3.4 7.4 - - - +
40A ILE* 1.3 79.3 - - + +
42A ILE* 1.3 59.6 + - - +
44A SER 3.3 0.2 + - - -
45A SER* 2.9 33.6 + - - -
75A ARG* 2.8 34.1 + - - +
136A GLN* 2.8 26.2 + - - +
137A TRP* 3.8 16.1 - - + -
167A LYS* 2.9 26.6 + - - -
208A GLN* 4.1 10.2 - - - +
211A LEU* 6.0 2.7 - - + -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 2.8 29.1 + - - +
39A SER 3.9 3.1 - - - +
41A ASP* 1.3 77.2 - - - +
43A ASN* 1.3 54.4 + - - +
45A SER* 3.2 6.2 + - - -
46A ARG* 2.8 60.0 + - - +
75A ARG* 3.6 21.5 - - + +
76A ILE* 4.0 29.6 - - + -
79A ARG* 3.9 36.6 - - + +
80A LEU* 4.4 14.2 - - + +
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Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER* 2.8 34.3 + - - +
40A ILE* 4.2 5.4 - - - +
42A ILE* 1.3 76.1 - - - +
44A SER* 1.3 60.9 + - - +
46A ARG* 2.7 36.2 + - - +
47A LYS* 3.2 22.5 + - - +
79A ARG* 4.7 8.5 + - - +
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE 3.1 20.0 + - - -
41A ASP 3.7 0.2 - - - -
43A ASN* 1.3 73.1 - - - +
45A SER* 1.3 65.3 + - - +
47A LYS* 3.4 6.5 + - - +
48A PHE* 3.1 23.4 + - - +
167A LYS* 4.2 1.4 + - - -
206A GLU* 4.1 14.2 + - - +
208A GLN* 3.0 34.9 + - - -
209A GLU 5.3 0.5 + - - -
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP* 2.9 16.9 + - - -
42A ILE* 3.5 9.0 - - - -
44A SER* 1.3 77.4 - - - +
46A ARG* 1.3 62.3 + - - +
48A PHE* 3.3 6.5 + - - +
49A LEU* 3.0 25.1 + - - +
80A LEU* 4.1 12.3 - - - -
134A TRP* 3.5 24.5 - - - -
136A GLN* 4.1 2.8 + - - -
167A LYS* 2.6 37.4 + - - +
220A SER* 5.8 0.2 - - - -
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 2.8 35.2 + - - +
43A ASN* 2.7 35.1 + - - +
44A SER 3.3 0.2 - - - -
45A SER* 1.3 73.8 - - - +
47A LYS* 1.3 52.0 + - - +
49A LEU* 3.3 2.0 + - - +
50A GLN* 2.8 63.9 + - + +
79A ARG* 3.1 31.9 + - - +
80A LEU* 3.6 18.9 - - + +
83A PRO* 6.1 1.8 - - - +
84A LEU* 4.6 14.4 - - + +
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASN 3.2 14.8 + - - +
44A SER* 3.8 6.3 - - - +
45A SER 3.3 0.2 - - - -
46A ARG* 1.3 79.5 - - - +
48A PHE* 1.3 62.2 + - - +
50A GLN* 3.6 18.9 + - - +
51A ARG* 3.4 23.4 + - + +
206A GLU* 6.1 0.9 - - - +
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER 3.1 17.1 + - - +
45A SER* 3.6 6.5 - - - +
47A LYS* 1.3 76.7 - - - +
49A LEU* 1.3 64.6 + - - +
51A ARG* 3.5 22.2 - - + +
52A PHE* 3.6 12.9 - + - -
134A TRP* 4.8 4.7 - + - -
165A VAL* 4.1 18.8 - - + -
204A ALA* 3.7 31.6 - - + -
206A GLU* 3.7 49.9 + - + +
220A SER* 3.8 31.6 - - - +
222A ALA* 3.8 31.4 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A SER 3.0 17.2 + - - +
46A ARG* 3.8 4.0 - - - +
48A PHE* 1.3 74.7 - - - +
50A GLN* 1.3 65.6 + - - +
51A ARG 3.1 2.7 - - - -
52A PHE* 3.0 18.5 + - + +
53A LEU* 3.6 16.7 + - + +
80A LEU* 4.2 12.6 - - + -
81A LEU* 4.5 1.8 - - + -
84A LEU* 4.2 14.4 - - + -
85A PHE* 3.9 25.8 - - + -
132A VAL* 3.9 26.9 - - + -
134A TRP* 4.1 24.0 - - + -
163A ILE* 3.9 20.2 - - + -
165A VAL* 4.8 0.2 - - + -
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG* 2.8 49.4 + - + +
47A LYS* 3.8 19.9 - - - +
48A PHE 3.4 0.2 - - - -
49A LEU* 1.3 73.3 - - - +
51A ARG* 1.3 62.0 + - - +
53A LEU* 3.1 26.0 + - + +
54A ARG* 3.3 12.8 + - - +
84A LEU* 5.3 9.4 - - + +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.4 23.0 - - + +
48A PHE* 3.5 15.5 - - + +
49A LEU 3.0 0.2 + - - -
50A GLN* 1.3 76.2 - - - +
52A PHE* 1.3 66.7 + - + +
54A ARG* 3.2 83.6 + - - +
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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