Contacts of the helix formed by residues 71 - 88 (chain C) in PDB entry 3UF2
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 THR 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B THR* 4.2 3.6 - - - -
67C PHE* 4.1 5.9 - - - +
68C ARG* 2.8 40.1 + - + +
69C ASP 3.7 5.4 - - - +
70C ASN* 1.3 83.0 - - - +
72C PRO* 1.3 76.7 - - + +
73C ASN* 3.9 3.6 + - - +
74C ALA* 2.9 23.1 + - - +
75C ILE* 3.0 12.3 + - - +
24D ASP* 4.0 32.0 + - + -
25D SER* 5.7 0.7 - - - -
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Residues in contact with PRO 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 6.1 0.7 - - + -
36B GLU* 5.0 4.7 - - - +
105B THR* 3.1 33.1 - - + +
21C ARG* 6.2 4.7 - - - +
71C THR* 1.3 87.1 - - + +
73C ASN* 1.3 62.5 + - - +
75C ILE* 3.5 3.8 + - + +
76C ALA* 3.0 28.3 + - - +
24D ASP* 6.2 0.9 - - + -
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Residues in contact with ASN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER 5.1 0.7 - - - +
21C ARG* 4.3 3.8 - - - +
22C LEU* 3.6 32.5 + - + +
25C SER* 3.1 20.4 + - - -
26C GLN* 3.8 4.8 - - - +
67C PHE* 3.5 20.9 - - + -
71C THR* 3.2 4.1 + - - +
72C PRO* 1.3 81.9 - - - +
74C ALA* 1.3 65.4 + - - +
76C ALA* 3.5 5.5 - - - +
77C ILE* 3.2 26.3 + - - +
25D SER* 2.8 40.2 + - - -
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE* 3.9 20.8 - - + +
68C ARG 3.3 28.0 - - - +
69C ASP* 4.5 2.7 - - - +
70C ASN 4.3 5.6 - - - +
71C THR* 2.9 12.0 + - - +
73C ASN* 1.3 78.6 - - - +
75C ILE* 1.3 64.7 + - + +
77C ILE* 3.2 7.3 + - - +
78C VAL* 3.1 26.0 + - + +
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 4.0 10.3 - - + +
105B THR* 3.3 47.8 - - + +
106B PHE 4.1 1.6 - - - +
107B TYR* 3.3 54.5 - - + +
70C ASN* 4.5 14.1 - - - +
71C THR 3.0 10.6 + - - +
72C PRO* 4.0 4.5 - - + +
74C ALA* 1.3 73.3 - - + +
76C ALA* 1.3 65.0 + - - +
78C VAL* 3.6 9.1 - - + +
79C GLN* 3.0 27.2 + - - +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 4.2 29.8 + - - +
22C LEU* 4.3 11.0 - - + -
72C PRO 3.0 18.6 + - - +
73C ASN* 3.5 12.1 - - - +
75C ILE* 1.3 78.1 - - - +
77C ILE* 1.3 56.8 + - - +
79C GLN* 3.7 12.0 + - - +
80C LEU* 3.1 35.3 + - + +
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Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 4.0 16.2 - - + -
61C MET* 3.9 24.7 - - + +
65C MET* 3.4 36.6 - - + +
67C PHE* 3.8 17.7 - - + -
73C ASN 3.2 14.8 - - - +
74C ALA* 3.2 7.3 + - - +
75C ILE 3.2 0.4 - - - -
76C ALA* 1.3 76.4 - - - +
78C VAL* 1.3 55.3 + - + +
80C LEU* 3.0 14.7 + - + +
81C GLN* 2.7 56.5 + - + +
88H LYS* 5.7 1.1 - - - +
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Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 4.2 16.6 - - + -
74C ALA* 3.1 15.2 + - + +
75C ILE* 3.6 13.9 - - + +
77C ILE* 1.3 76.5 - - + +
79C GLN* 1.3 57.9 - - - +
81C GLN* 3.3 14.1 + - - +
82C GLU* 2.9 49.1 + - + +
85H LEU* 4.0 25.7 - - + +
86H ARG* 6.2 1.8 - - + -
88H LYS* 4.9 8.5 - - - +
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Residues in contact with GLN 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 5.4 5.3 + - - -
31A CYS* 6.3 1.2 - - - +
107A TYR* 5.3 0.5 + - - -
32B GLN 5.0 3.4 + - - -
33B ILE* 5.7 0.6 - - - +
34B THR* 4.0 15.0 + - - +
107B TYR* 3.3 38.8 + - + +
15C HIS* 4.3 17.4 + - + +
18C SER* 5.4 4.0 + - - -
75C ILE* 3.0 23.9 + - - +
76C ALA* 3.8 11.9 - - - +
78C VAL* 1.3 76.7 - - - +
80C LEU* 1.3 57.0 + - - +
82C GLU* 3.3 9.8 + - - +
83C LEU* 2.8 30.0 + - - +
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C HIS* 3.7 41.3 - - + +
18C SER* 4.9 4.5 - - - +
19C LEU* 3.8 35.4 - - + -
22C LEU* 6.2 0.7 - - + -
61C MET* 3.9 17.0 - - + -
76C ALA* 3.1 28.1 + - + +
77C ILE* 3.0 17.8 + - + +
79C GLN* 1.3 76.8 - - - +
81C GLN* 1.3 56.3 + - - +
83C LEU* 3.6 12.1 - - + +
84C SER* 2.4 37.9 + - - -
121C PHE* 4.3 14.3 - - + -
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Residues in contact with GLN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN 4.7 1.4 + - - -
61C MET* 3.8 21.6 - - + +
62C GLU* 2.8 44.9 + - - +
77C ILE* 2.7 40.6 + - + +
78C VAL* 3.7 4.9 - - - +
80C LEU* 1.3 70.8 - - - +
82C GLU* 1.3 59.5 + - - +
84C SER* 3.1 7.3 + - - -
85C LEU* 2.9 33.0 + - + +
85H LEU* 3.2 32.4 - - + +
88H LYS* 3.4 11.8 + - - -
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.9 19.2 + - - +
32B GLN* 3.8 13.9 - - - +
107B TYR* 3.0 25.8 + - - -
78C VAL* 2.9 34.0 + - - +
79C GLN* 3.6 5.3 - - - +
81C GLN* 1.3 72.6 - - - +
83C LEU* 1.3 65.7 + - - +
85C LEU* 3.3 17.8 + - - +
86C ARG* 3.6 14.4 + - - +
82H GLU* 2.6 39.2 - - - +
85H LEU* 3.5 16.5 - - + +
86H ARG* 5.0 5.2 + - - +
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLN* 4.4 4.9 - - - +
107A TYR* 4.0 15.6 - - + -
10C MET* 3.1 41.0 - - + +
11C ILE* 4.1 21.3 - - + +
15C HIS* 3.5 37.5 - - + +
79C GLN 2.8 18.3 + - - +
80C LEU* 3.6 13.9 - - + +
82C GLU* 1.3 74.7 - - - +
84C SER* 1.3 64.1 + - - +
86C ARG* 3.3 5.5 + - - +
87C LEU* 3.1 24.1 + - + +
121C PHE* 4.4 10.1 - - + -
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Residues in contact with SER 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 4.0 12.8 - - - -
58C GLN* 3.9 24.2 + - - +
61C MET* 3.7 11.0 - - - +
80C LEU 2.4 24.5 + - - -
81C GLN* 3.1 8.9 + - - -
83C LEU* 1.3 75.4 - - - +
85C LEU* 1.3 64.6 + - - +
87C LEU* 3.1 11.9 + - - +
88C LYS* 3.2 20.3 + - - +
121C PHE* 3.7 15.6 - - - -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLN* 2.9 19.1 + - + +
82C GLU* 3.3 11.2 + - - +
84C SER* 1.3 77.3 - - - +
86C ARG* 1.3 70.3 + - - +
88C LYS* 3.5 42.1 + - - +
89C SER 4.7 0.7 + - - -
62H GLU* 4.5 3.4 - - - +
78H VAL* 4.1 19.7 - - + +
81H GLN* 3.7 32.3 - - + +
82H GLU* 3.8 42.6 - - + +
85H LEU* 4.6 5.8 - - + -
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Residues in contact with ARG 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.4 33.6 + - - +
105A THR* 4.1 20.4 - - + +
107A TYR* 3.7 40.3 + - + -
6C TYR* 5.3 0.2 - - - -
10C MET* 3.7 18.6 - - + +
82C GLU* 3.6 12.4 + - - +
83C LEU 3.3 4.8 + - - +
84C SER 3.2 0.4 - - - -
85C LEU* 1.3 82.2 - - - +
87C LEU* 1.3 60.5 + - - +
88C LYS 3.2 3.0 + - - -
89C SER* 2.7 28.9 + - - -
90C CYS* 5.0 0.2 - - - -
78H VAL* 3.1 33.2 - - - +
82H GLU* 2.7 34.8 + - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C MET* 3.7 33.4 - - + +
11C ILE* 3.9 28.5 - - + -
54C PHE* 3.6 30.5 - - + -
83C LEU* 3.1 21.3 + - + +
84C SER* 3.1 6.0 + - - +
86C ARG* 1.3 72.4 - - - +
88C LYS* 1.3 59.5 + - - +
89C SER* 3.1 2.9 - - - -
90C CYS* 2.9 34.2 + - + +
91C PHE* 3.4 10.2 - - + -
121C PHE* 5.4 1.1 - - + -
124C THR* 4.3 7.9 - - + -
128C LEU* 3.8 20.2 - - + -
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 3.9 5.6 - - + -
55C LEU* 5.3 8.5 - - + -
58C GLN* 3.3 29.8 - - - +
84C SER 3.2 2.9 + - - +
85C LEU* 3.5 45.9 + - - +
86C ARG 3.2 0.6 - - - -
87C LEU* 1.3 77.8 - - - +
89C SER* 1.3 56.3 + - - +
90C CYS 3.0 0.4 - - - -
91C PHE* 2.8 39.2 + - + +
62H GLU* 3.5 29.4 + - - +
69H ASP* 4.8 1.4 - - - +
78H VAL* 5.6 4.0 - - - +
81H GLN* 3.9 9.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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