Contacts of the helix formed by residues 37 - 54 (chain B) in PDB entry 5CVE
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.4 6.5 - - + -
34B TYR* 3.0 22.1 + - + +
36B HIS* 1.3 97.5 - - + +
38B SER* 1.3 65.0 + - - +
39B SER 3.3 2.0 - - - -
40B ILE* 3.2 22.2 + - + +
41B ASP* 3.1 20.0 + - + +
136B TRP* 4.3 12.6 - - + -
210B LEU* 4.1 23.8 - - + -
211B PRO* 4.1 22.9 - - + -
214B ILE* 4.5 4.7 - - + -
2E PRO* 3.8 31.6 - - + -
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.2 6.4 - - - +
31B LEU* 3.7 16.8 - - - +
35B GLY 3.2 16.7 + - - -
36B HIS 3.3 1.2 - - - -
37B ILE* 1.3 78.2 - - - +
39B SER* 1.3 59.2 + - - +
41B ASP* 3.2 4.5 + - - +
42B ILE* 2.9 32.9 + - - +
74B ARG* 3.0 35.1 + - - +
78B ARG* 4.1 13.4 + - - -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS 4.7 3.4 + - - -
37B ILE 3.3 0.6 - - - -
38B SER* 1.3 73.8 - - - +
40B ILE* 1.3 62.6 + - - +
42B ILE* 4.4 0.4 - - - +
43B ASN* 2.9 44.9 + - - -
78B ARG* 2.9 37.2 + - - +
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS 5.1 3.3 + - - +
37B ILE* 3.2 27.9 + - + +
39B SER* 1.3 76.7 - - - +
41B ASP* 1.3 63.4 + - - +
43B ASN* 4.2 4.1 - - - +
44B SER* 3.2 24.8 + - - +
207B GLN* 3.5 18.6 - - - +
208B GLU 3.7 11.2 - - - +
209B ASN* 3.7 31.2 - - + +
210B LEU* 4.6 6.5 - - + -
211B PRO* 6.2 0.2 - - + -
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Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.1 11.5 + - + +
38B SER* 3.4 7.2 - - - +
40B ILE* 1.3 80.6 - - - +
42B ILE* 1.3 67.8 + - - +
44B SER 3.2 1.9 + - - -
45B SER* 3.0 27.9 + - - -
74B ARG* 2.9 36.6 + - - +
135B GLN* 2.8 27.5 + - - +
136B TRP* 4.0 15.7 - - + -
166B LYS* 2.8 27.4 + - - +
207B GLN* 4.1 11.0 - - + +
210B LEU* 6.0 2.0 - - + -
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 2.9 29.1 + - - +
39B SER 3.9 3.1 - - - +
41B ASP* 1.3 78.1 - - - +
43B ASN* 1.3 61.6 + - - +
45B SER* 3.2 6.3 + - - -
46B ARG* 2.9 52.8 + - - +
74B ARG* 3.8 24.7 - - - +
75B ILE* 4.1 28.0 - - + -
78B ARG* 3.8 34.3 - - + +
79B LEU* 4.4 13.1 - - + +
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Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER* 2.9 32.7 + - - +
40B ILE* 4.2 4.1 - - - +
42B ILE* 1.3 77.9 - - - +
44B SER* 1.3 62.4 + - - +
46B ARG* 2.9 30.4 + - - +
47B LYS* 3.3 21.1 + - - +
78B ARG* 4.4 7.5 + - - +
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 3.2 7.5 + - - +
41B ASP 3.2 1.6 + - - -
43B ASN* 1.3 74.8 - - - +
45B SER* 1.3 60.7 + - - +
47B LYS* 3.2 7.5 + - - +
48B PHE* 2.9 29.2 + - - +
166B LYS* 4.1 1.3 - - - -
205B GLU* 4.5 10.9 - - - +
207B GLN* 3.0 42.1 + - - -
208B GLU* 5.1 1.9 + - - +
209B ASN* 6.0 0.2 + - - -
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP* 3.0 12.2 + - - -
42B ILE* 3.6 11.8 - - - +
44B SER* 1.3 75.4 - - - +
46B ARG* 1.3 62.2 + - - +
48B PHE* 3.3 8.2 + - - +
49B LEU* 3.1 23.7 + - - +
79B LEU* 3.9 12.5 - - - +
133B TRP* 3.4 35.6 - - - -
135B GLN* 4.1 1.9 + - - -
166B LYS* 2.9 24.5 + - - +
219B SER* 5.8 0.7 - - - -
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 2.9 26.3 + - - +
43B ASN* 2.9 33.3 + - - +
44B SER 3.2 0.2 - - - -
45B SER* 1.3 77.6 - - - +
47B LYS* 1.3 61.7 + - - +
49B LEU* 3.3 12.7 + - - +
50B GLN* 3.3 11.4 + - - +
78B ARG* 3.0 31.7 + - - +
79B LEU* 3.6 18.6 + - + +
82B PRO* 6.0 2.8 - - - +
83B LEU* 4.8 16.0 - - + +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASN 3.3 9.8 + - - +
44B SER* 3.2 10.8 + - - +
46B ARG* 1.3 78.9 - - - +
48B PHE* 1.3 64.0 + - - +
50B GLN* 2.8 57.4 + - - +
51B ARG* 4.4 3.8 + - - -
54B ARG* 5.3 0.2 - - - +
205B GLU* 6.0 2.5 - - - +
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER 2.9 15.7 + - - +
45B SER* 3.5 8.5 - - - +
47B LYS* 1.3 79.1 - - - +
49B LEU* 1.3 61.7 + - - +
50B GLN 3.3 0.7 + - - -
51B ARG* 4.0 19.2 + - - +
52B PHE* 3.6 20.1 - + - -
133B TRP* 4.7 6.7 - + - -
164B VAL* 4.1 19.7 - - + -
203B ALA* 3.9 22.9 - - + -
205B GLU* 3.8 46.2 + - + +
219B SER* 3.8 28.7 - - - +
221B ALA* 3.7 40.4 - - + -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER 3.1 13.5 + - - +
46B ARG* 3.7 6.1 - - - +
48B PHE* 1.3 76.4 - - + +
50B GLN* 1.3 65.9 + - - +
51B ARG 3.4 0.2 - - - -
52B PHE* 3.0 20.6 + - + +
53B LEU* 3.6 26.6 + - + +
79B LEU* 4.3 11.4 - - + -
80B LEU* 4.8 1.3 - - + -
83B LEU* 4.0 22.7 - - + -
84B PHE* 4.2 18.6 - - + -
131B VAL* 4.4 10.3 - - + -
133B TRP* 3.9 31.2 - - + -
162B ILE* 3.9 27.4 - - + -
164B VAL* 4.4 3.8 - - + -
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Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ARG 3.3 8.4 + - - +
47B LYS* 2.8 52.2 + - - +
48B PHE 3.2 1.0 - - - -
49B LEU* 1.3 75.8 - - - +
51B ARG* 1.3 63.2 + - - +
52B PHE 3.1 0.9 + - - -
53B LEU* 3.2 17.4 + - - +
54B ARG* 3.2 45.0 + - + +
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS 4.4 3.6 + - - -
48B PHE* 4.0 20.4 + - - +
50B GLN* 1.3 79.0 - - - +
52B PHE* 1.3 95.1 + - + +
53B LEU 3.6 0.2 + - - -
54B ARG* 3.6 34.6 + - - +
203B ALA* 4.0 20.8 - - - +
205B GLU* 3.9 20.2 + - - +
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.6 30.3 - + - -
49B LEU* 3.0 11.8 + - + +
51B ARG* 1.3 103.4 - - + +
53B LEU* 1.3 62.3 + - + +
54B ARG 3.4 0.6 + - - -
58B ASN 4.4 1.6 - - - +
59B LYS* 3.8 4.2 - - - -
60B THR* 2.9 39.8 + - - +
162B ILE* 3.8 29.6 - - + -
202B LEU* 4.0 25.6 - - + -
203B ALA* 4.0 11.2 - - + -
221B ALA* 3.3 30.5 - - + -
223B ARG* 5.0 4.0 - - - -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.6 26.9 - - + +
50B GLN* 3.2 10.1 + - - +
52B PHE* 1.3 80.3 - - + +
54B ARG* 1.3 65.6 + - - +
55B GLU* 3.8 1.2 + - - +
59B LYS* 3.8 16.2 - - - +
60B THR* 3.6 31.1 - - + +
61B GLY 4.1 3.8 - - - +
62B THR* 4.0 23.6 - - + -
83B LEU* 4.3 34.8 - - + -
84B PHE* 4.7 8.3 - - + -
131B VAL* 5.2 0.7 - - + -
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Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS* 5.3 0.2 - - - +
50B GLN* 3.2 51.5 + - + +
51B ARG* 3.6 33.3 + - - +
52B PHE 3.4 2.5 - - - +
53B LEU* 1.3 80.0 - - - +
55B GLU* 1.3 71.0 + - - +
56B GLY* 4.4 0.5 - - - -
59B LYS* 3.2 21.1 - - - +
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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