Contacts of the helix formed by residues 51 - 62 (chain A) in PDB entry 5E63
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 ASP 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 5.8 2.4 - - - -
47A VAL* 3.6 28.2 - - + +
48A ASP* 2.9 9.0 + - - +
50A LYS* 1.3 91.3 + - - +
52A LEU* 1.3 61.6 + - - +
53A PHE* 3.3 5.9 - - - -
54A LEU* 3.1 21.8 + - + +
55A LEU 3.3 8.5 + - - -
259A ILE 5.4 0.5 - - - +
260A GLY* 3.6 9.5 - - - -
261A SER* 2.8 39.7 + - - -
262A ALA* 4.9 2.8 + - - +
14B A 4.7 7.0 + - - +
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Residues in contact with LEU 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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47A VAL* 5.0 0.2 - - - -
48A ASP 3.9 1.0 + - - -
49A LYS* 3.2 14.8 + - - +
50A LYS 3.6 1.2 - - - -
51A ASP* 1.3 72.8 - - - +
53A PHE* 1.3 66.0 + - - +
55A LEU* 3.1 10.9 + - + +
56A GLU* 2.9 38.7 + - - +
68A ILE* 4.3 14.8 - - + -
76A PHE* 3.5 47.8 - - + -
404A MXE 4.0 31.0 - - - -
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Residues in contact with PHE 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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50A LYS 3.7 23.3 - - - -
51A ASP* 3.7 12.8 - - - -
52A LEU* 1.3 78.1 - - - +
54A LEU* 1.3 64.5 + - + +
56A GLU* 3.3 13.1 + - - +
57A SER* 2.9 32.6 + - - -
260A GLY* 3.5 32.8 - - - -
261A SER* 3.7 6.3 - - - -
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Residues in contact with LEU 54 (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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8A LEU* 3.9 19.1 - - + -
16A PHE* 3.8 36.1 - - + -
47A VAL* 5.3 2.0 - - + -
51A ASP* 3.1 21.5 + - + +
53A PHE* 1.3 82.7 - - + +
55A LEU* 1.3 64.3 + - + +
57A SER* 3.2 8.4 + - - +
58A LEU* 3.0 37.5 + - + +
259A ILE* 3.7 31.2 - - + +
260A GLY* 4.2 27.4 - - - +
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Residues in contact with LEU 55 (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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45A VAL* 4.0 20.2 - - + +
47A VAL* 3.8 28.3 - - + -
51A ASP 3.3 3.1 + - - +
52A LEU* 3.1 10.8 + - + +
54A LEU* 1.3 78.0 - - + +
56A GLU* 1.3 61.1 + - - +
58A LEU* 3.1 13.1 + - + +
59A LYS* 3.1 18.4 + - - +
68A ILE* 3.7 30.2 - - + +
76A PHE* 3.6 31.9 - - + +
77A SER 3.6 17.7 - - - -
78A TYR* 3.7 19.6 - - + +
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Residues in contact with GLU 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 LEU* 2.9 40.6 + - - +
53A PHE* 3.6 13.6 - - - +
54A LEU 3.2 0.2 - - - -
55A LEU* 1.3 76.3 - - - +
57A SER* 1.3 56.2 + - - +
59A LYS* 3.5 4.4 + - - +
60A THR* 3.1 31.9 + - - -
68A ILE* 4.1 17.7 - - - +
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Residues in contact with SER 57 (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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8A LEU* 3.6 24.5 - - - +
53A PHE* 2.9 20.6 + - - -
54A LEU* 3.2 13.0 + - - +
56A GLU* 1.3 74.2 - - - +
58A LEU* 1.3 55.6 + - - +
60A THR* 3.3 7.0 + - - -
61A PHE* 2.7 35.2 + - - +
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Residues in contact with LEU 58 (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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8A LEU* 3.7 20.6 - - + -
13A VAL* 4.1 27.6 - - + -
16A PHE* 4.6 17.7 - - + -
17A ILE* 5.2 6.1 - - + -
45A VAL* 4.4 13.5 - - + -
54A LEU* 3.0 31.5 + - + +
55A LEU* 3.1 24.9 + - + +
57A SER* 1.3 73.2 - - - +
59A LYS* 1.3 60.1 + - - +
61A PHE* 3.0 5.9 + - + +
62A PHE* 2.7 42.2 + - + -
78A TYR* 4.2 13.9 - - + -
259A ILE* 6.1 0.4 - - + -
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Residues in contact with LYS 59 (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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55A LEU 3.1 11.0 + - - +
56A GLU* 3.7 9.2 - - - +
58A LEU* 1.3 77.4 - - - +
60A THR* 1.3 66.0 + - - +
62A PHE 3.0 8.3 + - - +
64A GLY* 3.0 39.9 + - - -
65A LEU 3.4 13.6 + - - +
66A GLY 3.3 24.8 + - - +
67A SER* 5.2 2.4 - - - +
68A ILE* 4.2 19.6 - - + +
78A TYR* 3.5 23.5 - - + -
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Residues in contact with THR 60 (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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56A GLU* 3.1 16.2 + - - +
57A SER* 3.6 6.7 - - - -
59A LYS* 1.3 81.6 - - - +
61A PHE* 1.3 61.2 + - - +
63A GLY* 3.3 10.6 + - - -
64A GLY* 3.7 9.9 + - - +
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Residues in contact with PHE 61 (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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8A LEU* 3.6 39.7 - - + -
10A PRO* 3.9 22.9 - - + -
13A VAL* 4.1 13.9 - - + -
57A SER 2.7 18.6 + - - +
58A LEU* 3.2 12.1 - - - +
60A THR* 1.3 73.5 - - - +
62A PHE* 1.3 82.3 + + - +
63A GLY 3.3 4.2 + - - -
93A PHE* 3.8 34.8 - + - -
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Residues in contact with PHE 62 (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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13A VAL* 4.3 15.3 - - + -
17A ILE* 5.8 0.7 - - + -
43A PHE* 4.6 13.0 - + - -
58A LEU* 2.7 32.2 + - + -
59A LYS 3.3 0.4 - - - -
61A PHE* 1.3 93.2 - + - +
63A GLY* 1.3 59.6 + - - -
64A GLY 3.2 4.0 + - - -
65A LEU* 3.2 22.3 + - - +
78A TYR* 3.6 28.3 - + - +
80A ILE* 4.6 4.7 - - + -
89A ILE* 3.9 23.2 - - + +
90A ILE* 3.7 30.3 - - + -
93A PHE* 4.0 36.8 - + + -
94A PHE* 4.5 8.1 - + - -
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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
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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