Contacts of the helix formed by residues 51 - 66 (chain A) in PDB entry 4E3C
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LEU* 1.3 84.0 - - - +
52A PRO* 1.3 76.6 - - - +
53A ARG* 4.1 6.1 + - - +
54A ASN* 2.8 31.7 + - - +
55A ARG* 3.2 17.0 + - - +
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Residues in contact with PRO 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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51A SER* 1.3 88.4 - - - +
53A ARG* 1.3 62.8 + - + +
55A ARG* 3.5 17.5 + - + +
56A GLU* 2.9 30.8 + - - +
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Residues in contact with ARG 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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51A SER* 3.3 6.9 - - - +
52A PRO* 1.3 83.8 - - + +
54A ASN* 1.3 82.3 + - - +
56A GLU* 3.2 14.3 + - - +
57A ARG* 2.7 95.9 + - - +
178A LEU 3.9 12.7 + - - -
179A CYS* 4.7 4.4 - - - +
180A THR* 5.0 14.1 + - - +
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Residues in contact with ASN 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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26A PHE* 3.4 24.7 - - + -
50A LEU* 3.8 30.9 - - + +
51A SER* 2.8 27.7 + - - +
53A ARG* 1.3 108.5 + - - +
55A ARG* 1.3 56.4 + - + +
57A ARG* 3.1 7.3 - - - +
58A TRP* 2.8 28.1 + - - +
179A CYS* 5.2 2.1 - - - -
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Residues in contact with ARG 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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49A GLU* 4.3 13.0 + - - -
50A LEU 3.4 20.7 + - - +
51A SER 3.2 16.1 + - - +
52A PRO* 3.8 13.3 - - - +
54A ASN* 1.3 70.8 - - - +
56A GLU* 1.3 65.9 + - - +
57A ARG 3.0 1.8 - - - -
58A TRP* 3.1 5.0 + - - +
59A CYS* 2.9 27.5 + - - +
90A ASP* 3.3 33.6 + - - -
91A LEU* 3.1 51.6 - - + +
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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 PRO 2.9 19.4 + - - +
53A ARG* 3.5 14.8 - - - +
55A ARG* 1.3 77.0 - - - +
57A ARG* 1.3 80.0 + - - +
59A CYS* 3.7 9.7 + - - +
60A LEU* 3.7 14.0 + - - +
175A GLN* 4.5 16.1 - - - +
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Residues in contact with ARG 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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26A PHE* 4.3 1.8 - - + -
53A ARG* 2.7 71.3 + - - +
54A ASN* 3.1 11.9 - - - +
55A ARG 3.0 0.2 - - - -
56A GLU* 1.3 89.5 + - - +
58A TRP* 1.3 60.4 + - - +
60A LEU* 2.8 36.3 + - - +
61A GLU* 3.3 5.2 + - - +
175A GLN 4.9 2.2 + - - -
176A GLY* 4.8 6.8 - - - -
177A GLU* 3.0 44.9 + - - +
178A LEU* 3.8 18.5 - - - +
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Residues in contact with TRP 58 (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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26A PHE* 4.1 27.3 - + + -
27A GLY 5.3 0.8 - - - +
44A LYS* 3.5 29.8 + - - +
46A CYS* 3.4 32.1 - - + +
54A ASN 2.8 16.1 + - - +
55A ARG* 3.5 10.3 - - - +
57A ARG* 1.3 67.2 - - - +
59A CYS* 1.3 66.9 + - - +
60A LEU 2.9 6.4 + - - -
61A GLU* 3.0 37.4 + - - +
62A ILE* 3.1 23.8 + - + +
91A LEU* 4.1 13.7 - - + -
92A PRO* 3.0 54.3 - - + -
93A LEU* 3.7 8.1 - - + -
94A LEU* 3.7 15.7 - - + -
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Residues in contact with CYS 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 ARG* 2.9 12.9 + - - +
56A GLU* 3.8 10.1 - - - +
57A ARG 3.2 0.2 - - - -
58A TRP* 1.3 77.6 - - - +
60A LEU* 1.3 58.6 + - - +
62A ILE* 3.0 23.8 - - - +
63A GLN* 3.2 12.5 - - - +
91A LEU* 3.8 25.8 - - - -
92A PRO* 4.4 17.0 - - - -
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Residues in contact with LEU 60 (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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56A GLU* 3.7 7.7 + - - +
57A ARG* 2.8 22.9 + - - +
59A CYS* 1.3 78.1 - - - +
61A GLU* 1.3 54.2 + - - +
63A GLN* 2.9 13.0 + - - +
64A ILE* 2.8 61.1 + - + +
172A GLU* 4.6 7.9 - - + +
175A GLN* 3.1 70.2 - - + +
176A GLY 4.7 0.2 - - - +
177A GLU 4.3 10.8 - - - +
178A LEU* 5.4 7.0 - - + -
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Residues in contact with GLU 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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26A PHE* 3.9 4.2 - - - +
44A LYS* 2.7 36.9 + - - +
57A ARG 3.3 2.0 + - - -
58A TRP* 3.0 25.6 + - - +
60A LEU* 1.3 80.2 - - - +
62A ILE* 1.3 61.8 + - - +
64A ILE* 3.1 19.3 + - - +
65A MET* 3.1 38.0 + - + +
94A LEU* 3.8 6.1 - - + +
168A GLY* 2.8 30.4 - - - -
178A LEU* 3.1 31.9 - - + +
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Residues in contact with ILE 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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58A TRP* 3.1 16.5 + - + +
59A CYS* 3.0 33.7 - - + +
61A GLU* 1.3 78.9 - - - +
63A GLN* 1.3 61.0 + - - +
65A MET* 3.7 2.3 + - - +
66A ARG* 3.3 35.5 + - + +
92A PRO* 4.0 19.1 - - + -
93A LEU 3.4 31.2 - - - +
94A LEU* 3.5 30.7 - - + +
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Residues in contact with GLN 63 (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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59A CYS 3.2 13.2 - - - +
60A LEU* 2.9 15.8 + - - +
62A ILE* 1.3 81.0 - - - +
64A ILE* 1.3 70.1 + - - +
66A ARG* 3.5 15.4 - - + +
67A ARG* 3.5 35.1 - - - +
175A GLN* 3.7 23.5 + - - +
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Residues in contact with ILE 64 (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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60A LEU* 2.8 41.0 + - + +
61A GLU* 3.4 10.3 - - - +
63A GLN* 1.3 78.7 - - - +
65A MET* 1.3 75.7 + - + +
67A ARG* 2.8 53.1 + - - +
141A ILE* 4.9 15.0 - - + -
167A LEU* 5.7 6.3 - - + -
172A GLU* 3.0 30.5 - - + +
178A LEU* 6.2 2.2 - - + -
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Residues in contact with MET 65 (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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44A LYS* 5.7 0.2 - - - +
61A GLU* 3.2 37.2 - - + +
62A ILE 4.0 0.7 - - - +
64A ILE* 1.3 80.9 - - + +
66A ARG* 1.3 58.8 + - - +
67A ARG 2.9 6.5 + - - -
69A THR* 3.4 19.9 - - - +
74A VAL 5.9 2.9 - - - +
76A ALA* 3.2 28.5 - - + +
94A LEU* 3.7 32.1 - - + -
96A MET* 5.9 6.7 - - + +
166A ASP* 5.9 0.7 - - - -
167A LEU* 3.5 46.0 - - + +
178A LEU* 5.7 1.1 - - + -
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Residues in contact with ARG 66 (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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62A ILE* 3.3 23.7 + - + +
63A GLN* 3.5 13.0 - - - +
64A ILE 3.1 0.4 + - - -
65A MET* 1.3 77.6 - - - +
67A ARG* 1.3 58.2 + - + +
69A THR* 5.4 0.8 - - - +
76A ALA* 3.6 23.8 - - - +
77A ARG 3.5 25.6 + - - -
78A ASP* 4.2 14.1 + - - +
79A VAL* 3.9 26.9 - - - +
93A LEU 4.0 9.3 + - - -
94A LEU* 3.7 18.8 - - - +
95A ALA 3.7 3.4 + - - +
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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