Contacts of the helix formed by residues 43 - 57 (chain A) in PDB entry 3EJW
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LYS 4.8 0.4 + - - -
39A PRO* 4.9 0.3 - - - +
41A GLU* 2.8 21.4 + - - +
42A PRO* 1.3 73.9 - - - +
44A VAL* 1.3 65.0 + - - +
45A SER* 4.0 6.4 - - - -
46A GLY* 2.9 25.4 + - - -
47A GLN* 3.0 22.9 + - - +
67A VAL* 3.7 3.8 - - - -
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Residues in contact with VAL 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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43A SER* 1.3 71.1 - - - +
45A SER* 1.3 66.6 + - - +
47A GLN* 3.2 2.6 + - - +
48A VAL* 2.9 35.1 + - + +
67A VAL* 3.7 12.6 - - + +
68A SER* 3.7 30.5 - - - +
71A GLY* 3.6 30.7 - - - +
72A LEU* 4.3 4.0 - - + -
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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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43A SER* 3.2 7.7 - - - -
44A VAL* 1.3 81.6 - - - +
46A GLY* 1.3 62.0 + - - +
48A VAL* 3.3 6.8 + - - +
49A GLN* 3.0 41.5 + - - +
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Residues in contact with GLY 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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39A PRO* 4.1 14.4 - - - -
43A SER* 2.9 21.2 + - - -
45A SER* 1.3 76.6 - - - +
47A GLN* 1.3 61.5 + - - +
49A GLN* 3.3 14.3 + - - +
50A PHE* 3.1 32.9 + - - -
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Residues in contact with GLN 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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7A ILE* 4.3 3.6 - - + +
8A PRO 3.0 20.0 + - - -
9A LYS* 3.5 6.1 - - - +
39A PRO* 4.0 17.2 - - + +
43A SER 3.0 18.7 + - - +
46A GLY* 1.3 75.5 - - - +
48A VAL* 1.3 57.9 + - - +
50A PHE* 3.3 6.6 + - - +
51A ILE* 2.9 37.5 + - + +
64A VAL* 3.7 13.1 - - + +
65A SER 2.8 25.6 + - - -
66A SER* 3.6 4.0 - - - -
67A VAL* 2.9 37.6 + - + +
72A LEU* 3.6 20.2 - - + +
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Residues in contact with VAL 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 VAL* 2.9 31.7 + - + +
45A SER* 3.6 6.7 - - - +
47A GLN* 1.3 74.8 - - - +
49A GLN* 1.3 59.6 + - + +
51A ILE* 3.6 7.4 - - - +
52A ASN* 2.8 46.6 + - - +
71A GLY 4.1 8.7 - - - +
72A LEU* 3.8 17.0 - - + -
75A ALA* 4.0 18.8 - - + -
78A ARG* 4.6 2.5 - - - +
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Residues in contact with GLN 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 34.0 + - - +
46A GLY* 3.7 12.9 - - - +
47A GLN 3.2 0.2 - - - -
48A VAL* 1.3 81.3 - - + +
50A PHE* 1.3 60.2 + - + +
52A ASN* 3.4 7.9 + - - +
53A ASN* 3.0 28.8 + - - +
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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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7A ILE* 4.6 12.1 - - + -
37A ASP* 3.4 35.4 - - - -
38A GLY* 3.4 19.5 - - - -
39A PRO* 3.3 31.9 - - + -
46A GLY* 3.1 25.2 + - - -
47A GLN* 3.7 7.2 - - - +
49A GLN* 1.3 78.0 - - + +
51A ILE* 1.3 65.7 + - - +
53A ASN* 3.2 11.4 + - + +
54A PHE* 3.1 42.7 + + + -
78B ARG* 3.8 17.5 - - - -
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Residues in contact with ILE 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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7A ILE* 4.2 19.3 - - + -
47A GLN* 2.9 26.5 + - + +
48A VAL* 3.6 7.0 - - - +
50A PHE* 1.3 75.9 - - - +
52A ASN* 1.3 65.0 + - - +
54A PHE* 3.3 2.4 + - - +
55A VAL* 3.0 32.3 + - + +
62A LEU* 4.2 15.2 - - + +
64A VAL* 4.9 5.6 - - + -
72A LEU* 4.0 28.5 - - + -
75A ALA* 3.9 31.0 - - + +
76A LEU* 3.7 32.5 - - + -
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Residues in contact with ASN 52 (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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48A VAL* 2.8 36.1 + - - +
49A GLN* 3.8 8.3 - - - +
50A PHE 3.3 0.2 - - - -
51A ILE* 1.3 74.7 - - - +
53A ASN* 1.3 57.3 + - - +
55A VAL* 3.7 5.1 - - - +
56A ASN* 2.8 45.5 + - - +
75A ALA* 3.8 9.4 - - - +
78A ARG* 2.7 33.9 + - - +
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Residues in contact with ASN 53 (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 ASP* 5.8 1.4 + - - -
49A GLN 3.0 17.7 + - - +
50A PHE* 3.2 15.6 + - + +
52A ASN* 1.3 76.9 - - - +
54A PHE* 1.3 63.4 + - + +
56A ASN* 3.3 7.6 + - - +
57A GLN* 3.0 60.7 + - - +
78B ARG* 5.5 8.1 - - - +
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ALA* 3.6 23.3 - - + -
7A ILE* 4.1 18.4 - - + -
35A THR* 3.7 24.2 - - + -
37A ASP* 3.8 22.4 - - + -
50A PHE* 3.1 38.6 + + - +
51A ILE* 4.0 3.4 - - - +
53A ASN* 1.3 78.0 - - + +
55A VAL* 1.3 65.3 + - - +
57A GLN* 3.2 16.0 + - - -
59A TYR* 3.0 79.2 + + + +
62A LEU* 5.2 7.2 - - + -
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Residues in contact with VAL 55 (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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51A ILE* 3.0 25.4 + - + +
52A ASN* 3.7 7.4 - - - +
54A PHE* 1.3 77.2 - - - +
56A ASN* 1.3 62.8 + - - +
58A GLY* 2.8 21.5 + - - -
59A TYR 4.8 0.4 - - - +
62A LEU* 4.2 10.5 - - + -
75A ALA 5.1 1.1 - - - +
78A ARG* 5.3 1.6 - - + -
79A ALA* 3.6 34.8 - - + +
82A ARG* 3.5 43.6 + - - +
84A VAL* 4.4 16.1 - - + +
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Residues in contact with ASN 56 (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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52A ASN* 2.8 34.5 + - - +
53A ASN* 3.7 8.4 + - - +
55A VAL* 1.3 81.6 - - - +
57A GLN* 1.3 59.6 + - + +
58A GLY 3.2 1.2 + - - -
82A ARG* 4.1 24.4 + - - +
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Residues in contact with GLN 57 (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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3A GLN* 4.7 6.8 + - - +
53A ASN* 3.0 54.3 + - - +
54A PHE* 3.7 13.2 - - - +
55A VAL 3.1 0.6 - - - -
56A ASN* 1.3 77.5 - - + +
58A GLY* 1.3 61.8 + - - +
59A TYR* 3.3 29.5 + - + -
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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