Contacts of the helix formed by residues 45 - 64 (chain B) 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 ASP 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.6 2.8 - - + +
44B LYS* 1.3 76.5 - - - +
46B PRO* 1.3 76.9 - - - +
47B VAL* 3.6 5.4 + - - +
48B CYS* 2.9 37.4 + - + +
49B TYR* 3.0 23.0 + - - +
137B LYS* 3.0 27.8 + - - -
142B SER* 3.7 18.6 + - - +
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Residues in contact with PRO 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LYS 3.1 9.6 - - - +
45B ASP* 1.3 91.9 - - - +
47B VAL* 1.3 64.3 + - + +
49B TYR* 3.3 9.6 + - + +
50B LEU* 3.3 27.4 + - + +
127B LEU* 6.2 2.2 - - + -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 3.4 10.8 + - - +
46B PRO* 1.3 82.7 - - + +
48B CYS* 1.3 64.8 + - - +
50B LEU* 3.2 8.5 + - - +
51B LYS* 3.1 24.0 + - + +
127B LEU* 5.2 4.5 - - + -
134B ILE* 3.9 38.1 - - + +
135B PHE* 3.9 23.5 - - + -
137B LYS* 3.9 30.5 - - + +
139B CYS* 4.6 0.4 - - - -
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Residues in contact with CYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.8 23.8 - - + +
45B ASP* 2.9 25.8 + - - +
46B PRO 3.4 0.2 - - - -
47B VAL* 1.3 78.2 - - - +
49B TYR* 1.3 62.0 + - - +
51B LYS* 3.2 4.3 + - - +
52B LYS 3.1 17.8 + - - -
137B LYS* 4.1 4.5 - - - -
139B CYS* 2.0 60.3 - - + -
142B SER* 3.5 13.2 - - - -
143B PHE* 3.8 10.4 - - + -
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Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.3 26.5 - + - -
38B VAL* 3.6 32.5 + - + +
40B GLN* 3.1 39.3 - - + +
43B LEU* 3.8 17.0 - - + +
44B LYS 5.3 0.4 - - - +
45B ASP 3.0 15.2 + - - +
46B PRO* 3.3 13.7 - - + +
47B VAL 3.2 0.2 - - - -
48B CYS* 1.3 77.6 - - - +
50B LEU* 1.3 74.2 + - + +
52B LYS* 3.9 1.2 - - - +
53B ALA* 2.8 44.0 + - + +
116B LYS* 5.3 4.0 - - - +
120B VAL* 4.9 4.9 - - + +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 3.7 13.9 - - + +
47B VAL* 3.2 7.4 + - - +
49B TYR* 1.3 90.8 - - + +
51B LYS* 1.3 65.9 + - - +
53B ALA* 4.2 1.8 - - - -
54B PHE* 2.9 28.2 + - - +
91B PHE* 4.2 2.2 - - - -
119B ASN 4.6 0.7 - - - +
120B VAL* 4.1 27.0 - - + +
123B GLU* 3.9 31.4 - - + -
124B THR* 4.2 4.7 - - - +
127B LEU* 3.7 30.7 - - + -
135B PHE* 3.7 21.3 - - + -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.1 18.6 + - + +
48B CYS* 3.2 8.9 + - - +
50B LEU* 1.3 77.9 - - - +
52B LYS* 1.3 59.0 + - - +
54B PHE* 3.8 3.5 - - - +
55B LEU* 3.6 23.0 + - - +
91B PHE* 4.0 23.9 - - + +
92B THR* 2.7 30.8 + - - +
94B ASP* 3.0 14.9 + - - +
97B GLU* 4.3 8.8 - - - +
135B PHE* 3.2 37.7 + - + +
137B LYS 3.0 22.7 + - - +
139B CYS* 3.5 22.7 - - - -
143B PHE* 4.4 7.6 - - + -
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 4.0 13.7 - - + -
43B LEU* 4.3 4.0 - - + -
48B CYS 3.1 11.5 + - - +
49B TYR 4.0 0.7 - - - +
51B LYS* 1.3 77.5 - - - +
53B ALA* 1.3 66.5 + - - +
54B PHE 3.1 1.3 - - - -
55B LEU* 2.9 20.9 + - + +
56B LEU* 3.1 19.7 + - + +
97B GLU* 4.8 8.9 - - + +
98B HIS 4.8 5.7 - - - +
99B ASP* 2.7 33.7 + - - +
101B ALA* 3.0 29.4 + - - +
102B CYS* 4.2 9.9 - - + -
103B VAL* 4.4 8.6 - - + +
143B PHE* 3.8 44.2 - - + -
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.8 15.2 - - + -
38B VAL* 3.4 15.5 - - + +
49B TYR* 2.8 29.2 + - + +
50B LEU* 3.9 3.1 - - - +
52B LYS* 1.3 75.4 - - - +
54B PHE* 1.3 53.1 + - - +
56B LEU* 3.1 4.0 + - - +
57B VAL* 2.8 39.3 + - - +
120B VAL* 3.6 24.5 - - + -
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Residues in contact with PHE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU 2.9 19.9 + - - +
51B LYS 3.8 4.0 - - - +
53B ALA* 1.3 76.2 - - - +
55B LEU* 1.3 74.3 + - + +
57B VAL* 3.3 6.0 - - + +
58B GLN* 3.3 48.4 + - + +
84B SER* 3.9 10.5 - - - -
87B LEU* 3.4 45.1 - - + -
88B LYS* 4.3 13.0 - - + -
91B PHE* 3.9 39.5 - + + -
120B VAL* 4.0 21.4 - - + +
121B PHE* 4.5 9.6 - + - -
124B THR* 5.0 4.0 - - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LYS 3.6 12.1 - - - +
52B LYS* 2.9 12.1 + - + +
54B PHE* 1.3 89.4 - - + +
56B LEU* 1.3 67.2 + - + +
58B GLN* 3.1 22.5 + - + +
59B ASP* 3.3 11.5 - - - +
88B LYS* 6.3 2.5 - - + -
91B PHE* 6.1 3.6 - - + -
93B LYS* 6.3 2.9 - - - -
97B GLU* 3.2 55.2 - - + +
98B HIS* 4.1 31.7 - - + +
62F GLU* 4.4 7.2 - - - +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU* 4.3 19.6 - - + +
37B PHE* 3.7 17.3 - - + -
38B VAL* 3.5 44.6 - - + +
52B LYS* 3.1 13.1 + - + +
53B ALA 3.1 6.1 + - - +
55B LEU* 1.3 75.7 - - + +
57B VAL* 1.3 65.9 + - - +
59B ASP* 3.3 15.2 + - + +
60B ILE* 3.1 26.9 + - - +
98B HIS* 6.1 4.7 - - - -
103B VAL* 3.8 23.8 - - + -
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.9 17.5 - - + -
53B ALA 2.8 17.0 + - - +
54B PHE* 3.3 11.9 - - - +
56B LEU* 1.3 75.3 - - - +
58B GLN* 1.3 61.9 + - - +
60B ILE* 3.0 9.4 + - - +
61B MET* 2.8 42.5 + - + +
117B VAL* 4.1 20.2 - - + -
120B VAL* 4.1 22.2 - - + -
121B PHE* 3.8 29.6 - - + -
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PHE* 3.4 41.6 + - + +
55B LEU* 3.1 10.7 + - + +
57B VAL* 1.3 80.5 - - - +
59B ASP* 1.3 62.6 + - - +
61B MET* 3.4 19.4 + - - +
62B GLU* 3.2 21.5 + - - +
81B GLN* 4.6 7.3 + - - +
84B SER* 2.9 43.0 + - - -
85B LEU* 5.8 2.4 - - - +
121B PHE* 4.7 0.4 - - - -
62F GLU* 3.1 36.7 - - + +
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU 3.3 17.3 - - - +
56B LEU* 3.3 17.7 + - + +
57B VAL 3.2 0.4 - - - -
58B GLN* 1.3 76.9 - - - +
60B ILE* 1.3 54.7 + - + +
62B GLU* 3.0 5.3 + - - -
63B ASP* 2.7 49.9 + - - +
98B HIS* 4.4 4.7 + - - -
59F ASP* 4.0 9.7 - - - +
62F GLU* 4.5 3.5 - - - +
63F ASP* 2.7 42.3 - - - +
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 4.8 9.2 - - + -
36B GLU 3.7 13.9 - - - +
37B PHE* 3.6 33.2 - - + -
56B LEU 3.1 16.7 + - - +
57B VAL* 3.0 10.4 + - - +
59B ASP* 1.3 77.4 - - + +
61B MET* 1.3 57.3 + - - +
64B THR* 3.1 16.8 + - - +
65B MET* 2.9 49.8 + - + +
113B LEU* 4.0 33.7 - - + -
117B VAL* 4.2 6.3 - - + -
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Residues in contact with MET 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B VAL* 2.8 25.3 + - + +
58B GLN* 3.4 36.6 - - - +
60B ILE* 1.3 76.5 - - - +
62B GLU* 1.3 59.1 + - - +
65B MET* 3.3 43.0 - - + +
77B ILE* 3.6 15.5 - - + +
80B LEU* 3.5 32.8 - - - -
81B GLN* 4.1 27.2 + - + +
84B SER* 3.5 15.0 - - - +
117B VAL* 5.0 2.0 - - + -
121B PHE* 4.1 11.7 - - + -
88F LYS* 5.2 1.7 + - - -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLN 3.2 11.6 + - - +
59B ASP* 3.0 8.8 + - - +
61B MET* 1.3 80.9 - - - +
63B ASP* 1.3 74.8 + - - +
66B ARG* 4.1 13.6 - - - +
81B GLN* 3.3 14.3 + - - +
55F LEU* 4.0 12.0 - - - +
58F GLN* 3.0 40.8 + - + +
59F ASP* 3.6 12.1 - - - +
62F GLU* 6.6 0.4 - - + -
88F LYS* 3.3 29.4 + - - +
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASP* 2.7 31.7 + - - +
62B GLU* 1.3 79.7 - - - +
64B THR* 1.3 63.4 + - - +
66B ARG* 3.3 23.8 + - - +
59F ASP* 2.8 40.4 - - - +
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Residues in contact with THR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MET* 4.2 9.3 - - + +
28A GLU 4.2 10.0 - - - +
29A THR* 5.6 1.3 - - + +
33B ILE* 3.9 28.9 - - + -
34B THR 4.4 13.6 + - - +
35B PHE* 4.6 7.0 - - + +
60B ILE* 3.1 21.2 + - - +
63B ASP* 1.3 82.9 - - - +
65B MET* 1.3 61.3 + - - +
66B ARG* 3.0 13.7 + - - +
113B LEU* 4.0 12.3 - - + -
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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