Contacts of the helix formed by residues 70 - 83 (chain A) in PDB entry 5UFL
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 ALA 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A SER* 1.3 76.8 - - - +
71A SER* 1.3 63.4 + - - +
73A ILE* 3.5 18.2 - - - +
74A LEU* 3.3 18.9 - - - +
113A THR* 5.3 13.9 - - + -
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Residues in contact with SER 71 (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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30A LEU* 3.7 27.1 - - - +
69A SER 3.5 0.2 - - - -
70A ALA* 1.3 78.4 - - - +
72A LEU* 1.3 63.9 + - - +
74A LEU* 3.6 16.6 - - - +
75A SER* 3.5 22.2 + - - -
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Residues in contact with LEU 72 (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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17A TYR* 3.1 41.1 - - + +
26A ALA* 4.3 25.6 - - + +
29A LEU* 3.7 32.5 - - + -
30A LEU* 4.4 10.1 - - + -
33A LEU* 5.4 1.8 - - + -
62A LEU* 4.9 11.9 - - + -
69A SER* 3.6 21.0 + - - +
70A ALA 3.3 1.0 - - - -
71A SER* 1.3 78.6 - - - +
73A ILE* 1.3 64.9 + - - +
75A SER* 2.7 21.5 + - - +
76A ILE* 3.2 17.8 + - + +
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 5.8 2.5 - - + -
63A LEU* 4.9 19.3 - - + -
69A SER* 3.2 33.8 + - - +
70A ALA* 3.5 11.2 - - - +
72A LEU* 1.3 76.7 - - + +
74A LEU* 1.3 64.6 + - - +
76A ILE* 3.4 21.2 - - + +
77A ILE* 3.4 20.6 + - + +
106A VAL* 5.2 14.6 - - + -
109A ARG* 6.3 1.6 - - - +
113A THR* 4.4 9.2 - - + +
116A VAL* 3.8 35.4 - - + -
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Residues in contact with LEU 74 (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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70A ALA* 3.3 18.4 - - + +
71A SER* 3.6 22.4 - - - +
73A ILE* 1.3 83.1 - - + +
75A SER* 1.3 64.8 + - - +
77A ILE* 3.3 25.2 - - + +
78A GLY* 3.9 2.8 + - - -
115A SER* 5.8 5.2 - - - +
116A VAL* 4.9 12.6 - - + -
119A GLN* 5.2 10.2 - - + +
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Residues in contact with SER 75 (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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30A LEU* 3.5 23.4 - - - +
33A LEU* 3.9 16.1 - - - +
71A SER 3.5 13.9 + - - -
72A LEU* 2.7 21.9 + - - -
74A LEU* 1.3 82.9 - - - +
76A ILE* 1.3 66.0 + - - +
78A GLY* 3.1 12.0 + - - -
79A LEU* 3.4 21.0 + - - +
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Residues in contact with ILE 76 (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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29A LEU* 6.3 1.1 - - + -
33A LEU* 3.9 19.7 - - + -
59A LEU* 3.8 45.2 - - + +
62A LEU* 4.7 15.0 - - + -
63A LEU* 3.5 40.8 - - + -
72A LEU* 3.5 15.3 - - + +
73A ILE* 3.4 18.6 - - + +
75A SER* 1.3 79.1 + - - +
77A ILE* 1.3 68.2 + - + +
79A LEU* 3.4 8.2 + - - +
80A LEU* 3.2 27.2 + - + +
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Residues in contact with ILE 77 (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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63A LEU* 5.4 2.7 - - + -
73A ILE* 3.4 16.6 - - + +
74A LEU* 3.3 21.8 - - - +
76A ILE* 1.3 80.6 - - + +
78A GLY* 1.3 72.8 + - - +
80A LEU* 3.5 15.1 - - + +
81A SER* 2.9 31.0 + - - -
103A LEU* 4.5 21.5 - - + -
116A VAL* 5.9 4.3 - - + -
119A GLN* 3.6 49.6 - - + +
120A CYS* 5.3 7.2 - - + -
123A LEU* 3.9 15.8 - - + +
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Residues in contact with GLY 78 (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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74A LEU 4.5 2.2 - - - -
75A SER 3.1 9.5 + - - -
77A ILE* 1.3 90.0 - - - +
79A LEU* 1.3 60.4 + - - +
81A SER* 2.6 20.8 + - - -
82A GLN* 3.1 17.1 + - - +
119A GLN* 6.0 0.2 - - - -
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Residues in contact with LEU 79 (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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33A LEU* 3.4 55.2 - - + +
34A GLU* 5.6 0.9 - - - -
36A ILE* 3.7 25.4 - - + +
37A SER* 4.5 13.2 - - - +
45A PHE* 5.2 11.7 - - + -
59A LEU* 5.7 6.1 - - + -
75A SER* 3.5 16.6 - - - +
76A ILE* 3.4 9.0 + - - +
78A GLY* 1.3 77.8 - - - +
80A LEU* 1.3 60.6 + - - +
82A GLN* 3.2 18.6 + - - +
83A LEU* 3.3 16.8 + - - +
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Residues in contact with LEU 80 (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 LEU* 6.3 2.7 - - + -
59A LEU* 5.4 8.3 - - + +
60A VAL* 5.6 5.4 - - + -
63A LEU* 4.9 14.4 - - + -
76A ILE* 3.2 23.4 + - + +
77A ILE* 3.5 17.3 - - + +
79A LEU* 1.3 76.0 - - - +
81A SER* 1.3 60.5 - - - +
83A LEU* 3.4 31.7 - - + +
84A ALA* 3.5 9.2 + - - +
93A LEU* 4.7 10.8 - - + +
99A LEU* 4.1 28.0 - - + -
103A LEU* 5.0 5.4 - - + -
123A LEU* 3.3 37.8 - - + +
127A LEU* 5.2 1.9 - - + +
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Residues in contact with SER 81 (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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77A ILE* 2.9 17.3 + - - +
78A GLY* 2.6 26.2 + - - -
80A LEU* 1.3 73.8 - - - +
82A GLN* 1.3 59.7 + - - +
83A LEU 3.2 0.2 - - - -
84A ALA* 2.9 25.9 + - - +
85A VAL* 4.0 3.3 + - - +
123A LEU* 3.5 30.1 - - - -
126A LYS* 6.5 0.4 - - - -
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Residues in contact with GLN 82 (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 SER* 2.7 37.9 + - - +
43A ARG* 3.3 44.0 - - + +
78A GLY 3.1 11.8 + - - +
79A LEU* 3.2 14.1 + - - +
81A SER* 1.3 80.5 + - - +
83A LEU* 1.3 56.9 + - - +
84A ALA 3.4 0.2 - - - -
85A VAL* 3.4 21.5 - - + +
86A ASP* 4.0 3.3 - - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 6.4 0.7 - - + -
45A PHE* 4.2 36.8 - - + -
56A LEU* 4.7 22.7 - - + -
79A LEU 3.3 12.6 + - - +
80A LEU* 3.4 22.7 - - + +
81A SER 3.2 0.8 - - - -
82A GLN* 1.3 75.7 - - - +
84A ALA* 1.3 56.5 + - - +
85A VAL 3.6 0.2 - - - -
86A ASP* 3.1 22.1 - - - +
89A THR* 2.5 51.1 + - + +
90A ARG* 4.8 1.0 + - - -
93A LEU* 4.2 18.1 - - + +
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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