Contacts of the helix formed by residues 38 - 51 (chain A) in PDB entry 3IE7
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 GLY 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A THR* 3.8 15.0 - - - -
8A ASN 3.9 7.0 - - - -
10A ALA* 4.1 2.8 - - - +
37A GLY* 1.3 76.4 - - - -
39A LYS* 1.3 66.6 + - - -
40A GLY 3.3 2.9 - - - -
41A LEU 3.1 12.2 + - - -
42A HIS* 3.2 12.4 + - - -
90A ARG* 4.4 0.4 - - - +
320A MG 3.6 9.2 - - - -
501A GOL 3.0 20.5 + - - -
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Residues in contact with LYS 39 (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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6A THR* 4.6 0.2 - - - +
38A GLY* 1.3 71.4 - - - -
40A GLY* 1.3 63.0 + - - +
42A HIS* 3.1 12.4 + - - +
43A VAL* 3.0 24.8 + - - +
138A ALA* 3.6 17.4 + - + -
139A GLY* 3.3 19.5 - - - +
167A ASP* 2.6 53.8 + - - -
168A ASN* 4.7 1.8 - - - +
190A GLU* 5.3 3.6 + - - -
251A ASP* 3.4 27.7 - - - +
319A MG 4.2 9.2 - - - -
320A MG 3.4 8.9 - - - -
501A GOL 3.4 10.9 + - - +
900A ATP 5.4 1.6 - - - +
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Residues in contact with GLY 40 (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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4A THR* 3.3 25.5 + - - -
5A ILE 4.3 4.7 - - - -
6A THR* 3.0 16.7 + - - -
38A GLY 3.3 1.0 - - - -
39A LYS* 1.3 78.2 - - - +
41A LEU* 1.3 57.5 + - - +
43A VAL* 3.3 4.2 + - - +
44A SER 3.0 21.7 + - - -
136A VAL 5.4 0.2 - - - -
138A ALA* 3.5 20.0 + - - -
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Residues in contact with LEU 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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6A THR* 3.0 15.0 + - - +
9A PRO* 3.9 19.1 - - + -
36A CYS* 4.0 25.4 - - + -
37A GLY 3.2 20.9 - - - +
38A GLY 3.1 8.4 + - - +
40A GLY* 1.3 73.2 - - - +
42A HIS* 1.3 61.4 + - - +
44A SER* 3.2 3.9 + - - -
45A GLY* 2.9 23.6 + - - -
56A ALA* 3.7 20.2 - - + -
68A LEU* 4.5 9.9 - - + -
72A LEU* 4.0 19.3 - - + -
77A ILE* 3.5 11.7 - - + +
81A PHE* 3.6 27.4 - - + -
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Residues in contact with HIS 42 (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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12A ASP* 3.8 2.0 + - - -
35A ASP* 3.6 10.2 + - - -
36A CYS* 2.9 32.5 + - - -
37A GLY* 4.1 0.2 - - - -
38A GLY 3.2 15.3 + - - -
39A LYS* 3.1 8.7 + - - +
41A LEU* 1.3 77.9 - - - +
43A VAL* 1.3 62.0 + - - +
45A GLY* 3.2 2.9 + - - +
46A VAL* 3.0 28.6 + - + +
251A ASP* 3.7 30.5 + - + -
287A SER* 4.6 4.6 + - - -
288A SER* 3.5 28.6 - - - -
501A GOL 3.2 41.6 + - - -
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Residues in contact with VAL 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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4A THR* 3.9 15.9 - - + -
39A LYS 3.0 16.8 + - - +
40A GLY* 3.5 9.4 - - - +
42A HIS* 1.3 77.8 - - - +
44A SER* 1.3 61.8 + - - +
46A VAL* 3.2 9.9 + - - +
47A LEU* 3.0 29.6 + - + +
136A VAL* 4.5 11.4 - - + -
138A ALA* 4.6 10.1 - - + -
251A ASP* 4.0 21.8 - - + +
254A VAL* 4.1 20.4 - - + +
255A GLY* 3.9 17.9 - - - +
258A ILE* 5.5 1.1 - - + -
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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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4A THR* 2.7 33.5 + - - +
40A GLY 3.0 8.6 + - - -
41A LEU* 3.2 11.0 + - - -
43A VAL* 1.3 77.2 - - - +
45A GLY* 1.3 56.8 + - - +
47A LEU* 3.3 4.7 + - - +
48A SER* 2.9 34.4 + - - -
54A ASN* 3.5 18.2 + - - +
55A GLU 4.5 0.2 - - - -
56A ALA* 3.6 8.8 + - - +
77A ILE* 3.7 20.0 - - - -
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Residues in contact with GLY 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 LEU 2.9 11.8 + - - -
42A HIS* 3.2 5.3 + - - -
44A SER* 1.3 77.7 - - - +
46A VAL* 1.3 60.5 + - - +
48A SER* 3.4 4.5 + - - -
49A LYS* 3.1 27.2 + - - +
75A LYS* 4.7 7.1 - - - +
77A ILE* 3.7 20.6 - - - +
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Residues in contact with VAL 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 HIS 3.0 15.3 + - - +
43A VAL 3.2 7.2 + - - +
45A GLY* 1.3 74.9 - - - +
47A LEU* 1.3 64.3 - - - +
49A LYS* 3.0 13.8 + - + +
50A PHE* 3.2 23.0 + - + -
251A ASP* 4.2 4.7 - - + +
252A VAL* 3.9 36.1 - - + +
255A GLY* 3.8 6.7 - - - -
256A ALA* 3.7 26.2 - - + +
288A SER 5.1 3.8 - - - +
290A PHE* 4.0 24.9 - - + -
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Residues in contact with LEU 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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2A ILE* 3.6 47.1 - - + -
4A THR* 4.4 5.8 - - + -
43A VAL* 3.0 31.4 + - + +
44A SER 3.7 3.1 - - - +
46A VAL* 1.3 76.3 - - - +
48A SER* 1.3 63.5 + - - +
50A PHE* 3.1 17.2 + - - +
51A GLY 3.1 8.1 + - - -
52A ILE* 3.3 15.4 + - + +
54A ASN* 3.5 28.0 - - + +
255A GLY 3.4 24.9 - - - +
258A ILE* 4.3 4.5 - - + -
259A ALA* 4.0 15.9 - - + +
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Residues in contact with SER 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 2.9 18.6 + - - -
45A GLY* 3.7 5.6 - - - -
47A LEU* 1.3 73.8 - - - +
49A LYS* 1.3 64.7 + - - +
51A GLY* 3.0 14.9 + - - +
52A ILE 4.6 1.8 - - - -
54A ASN* 3.1 18.3 + - - +
75A LYS 3.9 11.0 - - - -
76A HIS* 3.0 33.9 + - - +
77A ILE* 4.1 2.6 - - - -
78A ASN 5.0 0.2 + - - -
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Residues in contact with LYS 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 GLY 3.1 19.0 + - - +
46A VAL* 3.0 10.3 + - - +
48A SER* 1.3 77.9 - - - +
50A PHE* 1.3 60.6 + - + +
51A GLY 3.5 0.3 + - - -
75A LYS 6.1 0.2 - - - +
288A SER 5.9 0.7 - - - +
289A SER* 5.9 2.0 - - - +
290A PHE* 3.3 67.7 + - + +
292A LEU* 3.3 35.7 - - + +
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Residues in contact with PHE 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 VAL* 3.2 39.2 + - + -
47A LEU* 3.1 10.6 + - - +
49A LYS* 1.3 79.0 - - - +
51A GLY* 1.3 60.0 + - - +
52A ILE* 3.3 21.5 + - + +
256A ALA* 4.0 15.9 - - + -
259A ALA* 4.1 18.2 - - + -
263A MSE 5.0 9.4 - - - -
265A MSE 5.6 4.0 - - + -
273A VAL* 4.0 21.8 - - + -
277A CYS* 3.8 25.8 - - - -
290A PHE* 4.3 6.7 - + - -
292A LEU* 4.7 13.7 - - + -
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Residues in contact with GLY 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 LEU 3.1 0.4 + - - -
48A SER* 3.0 17.0 + - - -
49A LYS 3.2 0.4 - - - -
50A PHE* 1.3 80.1 - - - +
52A ILE* 1.3 64.2 + - - +
53A LYS* 3.7 1.6 + - - -
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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