Contacts of the helix formed by residues 54 - 66 (chain A) in PDB entry 3FIA
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 PRO 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLY 3.8 2.4 - - - +
53A LEU* 1.3 100.8 - - + +
55A GLN* 1.3 65.5 + - - +
56A PRO* 3.7 13.7 - - + -
57A VAL* 3.0 25.7 + - + +
58A LEU* 3.0 18.8 + - - +
88A LYS* 6.1 0.2 - - - -
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Residues in contact with GLN 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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49A PHE* 4.0 35.6 - - + -
53A LEU 3.6 1.8 + - - -
54A PRO* 1.3 69.9 - - - +
56A PRO* 1.4 69.4 - - + +
58A LEU* 3.1 7.4 + - + +
59A ALA* 2.9 33.6 + - + +
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Residues in contact with PRO 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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54A PRO* 3.3 13.5 - - + -
55A GLN* 1.4 99.3 - - + +
57A VAL* 1.3 63.5 + - + +
59A ALA* 3.4 8.8 + - + +
60A GLN* 3.2 21.1 + - - +
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Residues in contact with VAL 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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53A LEU* 4.3 9.2 - - + -
54A PRO* 3.0 33.3 + - + +
56A PRO* 1.3 79.8 - - + +
58A LEU* 1.3 57.3 + - - +
60A GLN* 3.2 10.8 + - - +
61A ILE* 3.0 32.4 + - + +
88A LYS* 3.6 48.0 - - + +
94A LEU* 3.9 10.9 - - + +
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Residues in contact with LEU 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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45A ARG* 5.4 3.3 - - - +
48A PHE* 3.5 40.9 - - + +
49A PHE* 3.7 25.1 - - + +
51A SER* 3.8 15.7 - - - +
53A LEU* 3.6 39.7 - - + +
54A PRO 3.0 13.1 + - - +
55A GLN* 3.7 7.0 - - + +
57A VAL* 1.3 72.5 - - - +
59A ALA* 1.3 60.8 + - - +
61A ILE* 3.7 7.4 - - + +
62A TRP* 2.8 28.9 + - - +
85A ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 59 (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 ARG* 5.8 4.0 - - - +
55A GLN* 2.9 19.4 + - + +
56A PRO* 3.5 13.0 - - + +
58A LEU* 1.3 75.1 - - - +
60A GLN* 1.3 63.9 + - - +
62A TRP* 3.3 9.8 + - - +
63A ALA* 3.1 22.3 + - - +
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Residues in contact with GLN 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 PRO 3.2 9.1 + - - +
57A VAL* 3.2 12.5 + - - +
59A ALA* 1.3 78.4 - - - +
61A ILE* 1.3 57.6 + - - +
63A ALA* 3.2 6.5 + - + +
64A LEU* 3.0 35.2 + - + +
94A LEU* 3.6 30.6 + - + +
95A PRO 3.4 24.0 + - - -
96A SER* 4.9 3.6 - - - +
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Residues in contact with ILE 61 (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 PHE* 5.3 3.4 - - + -
53A LEU* 4.2 6.1 - - + -
57A VAL* 3.0 33.2 + - + +
58A LEU* 3.7 12.6 - - + +
59A ALA 3.3 0.2 - - - -
60A GLN* 1.3 72.9 - - - +
62A TRP* 1.3 66.1 + - - +
64A LEU* 3.2 8.3 + - - +
65A ALA* 2.9 22.3 + - - +
81A ALA* 3.9 32.1 - - + +
84A LEU* 4.0 15.3 - - + +
85A ILE* 3.8 37.5 - - + +
88A LYS* 4.6 0.9 - - + -
94A LEU* 3.7 21.8 - - + -
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Residues in contact with TRP 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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41A GLY* 3.6 16.6 - - - -
44A ALA* 3.7 22.0 - - + -
45A ARG* 3.2 49.7 - - + +
48A PHE* 4.4 9.8 - + + -
58A LEU 2.8 17.3 + - - +
59A ALA* 3.5 7.4 - - - +
60A GLN 3.3 0.2 - - - -
61A ILE* 1.3 78.5 - - - +
63A ALA* 1.3 64.0 + - + +
65A ALA* 3.2 3.5 + - - +
66A ASP* 2.9 60.3 + - + +
71A GLY* 3.6 22.3 - - - -
72A ARG 3.9 13.9 - - - -
73A MSE 3.5 26.5 - - + -
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Residues in contact with ALA 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 ALA 3.1 16.5 + - - +
60A GLN* 3.8 6.7 - - - +
61A ILE 3.2 0.4 - - - -
62A TRP* 1.3 86.2 - - + +
64A LEU* 1.3 63.1 + - + +
66A ASP* 3.9 14.3 + - - +
69A ASN* 4.7 5.7 - - - +
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Residues in contact with LEU 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 GLN* 3.0 34.3 + - + +
61A ILE* 3.6 6.1 - - - +
63A ALA* 1.3 80.0 - - - +
65A ALA* 1.3 60.5 + - - +
67A MSE 4.2 5.0 + - - +
84A LEU* 3.8 24.0 - - + -
94A LEU* 4.5 5.2 - - + -
95A PRO* 3.8 32.3 - - + +
96A SER 4.5 2.2 - - - +
97A ALA* 3.5 14.8 - - - +
98A LEU* 3.4 58.4 - - + +
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Residues in contact with ALA 65 (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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61A ILE 2.9 16.5 + - - +
62A TRP 3.9 0.4 - - - +
64A LEU* 1.3 74.9 - - - +
66A ASP* 1.3 61.1 + - - +
67A MSE 2.8 14.6 + - - +
73A MSE 3.6 15.7 - - + -
77A GLU* 3.2 40.7 - - - +
80A ILE* 4.0 11.2 - - + -
81A ALA* 3.7 20.0 - - + +
84A LEU* 4.8 0.7 - - + -
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Residues in contact with ASP 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 TRP* 2.9 44.1 + - + +
63A ALA* 3.9 8.3 + - - +
64A LEU 3.4 0.4 - - - -
65A ALA* 1.3 72.0 - - - +
67A MSE 1.3 63.0 + - - +
68A ASN* 3.2 5.0 - - - +
69A ASN* 2.9 28.7 + - - +
70A ASP* 3.3 4.3 + - - +
71A GLY* 2.9 29.5 + - - -
72A ARG 3.9 0.9 - - - -
73A MSE 4.3 2.4 - - - +
77A GLU* 3.9 5.2 - - - -
201A CA 2.3 32.2 - - - -
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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