Contacts of the helix formed by residues 39 - 59 (chain F) in PDB entry 3NBN
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 39 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F SER* 3.2 20.2 - - - +
36F THR* 3.9 5.8 - - - +
37F CYS 2.4 13.3 + - - -
38F GLU* 1.3 69.9 - - - +
40F ARG* 1.3 61.0 + - - +
42F GLU* 4.1 6.9 - - - +
43F ALA* 3.3 20.3 + - - +
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Residues in contact with ARG 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D PRO* 6.0 0.2 - - + -
2072E GLU 3.3 24.5 + - - -
2073E GLY* 3.5 24.7 + - - -
2074E SER* 3.9 7.3 - - - +
2075E TYR* 6.0 0.6 - - - +
2107E HIS* 3.4 31.5 - - - +
33F HIS* 5.8 1.6 - - - -
36F THR* 3.4 17.8 + - - +
37F CYS* 2.7 30.8 + - - +
39F ALA* 1.3 77.6 - - - +
41F TYR* 1.3 70.3 + - + +
43F ALA* 2.7 25.8 + - - +
44F VAL* 2.8 26.5 + - + +
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Residues in contact with TYR 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D THR 5.2 0.9 + - - -
339D PRO* 4.3 15.6 - - - +
365D THR* 3.2 29.1 + - + +
366D PRO* 3.6 32.8 - - + -
367D ASN* 3.1 40.3 + - + -
2105E ARG* 5.8 9.0 - - - -
37F CYS 3.1 2.2 + - - +
38F GLU* 4.6 2.7 - - - -
40F ARG* 1.3 88.4 - - + +
42F GLU* 1.3 65.2 + - - +
44F VAL* 3.4 7.5 - - + +
45F SER* 3.2 28.4 + - - -
48F ARG* 3.1 41.3 + - - -
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Residues in contact with GLU 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D ASN* 4.2 19.9 + - - +
417D ASN* 3.4 23.2 + - - +
38F GLU* 3.8 28.8 + - - +
39F ALA* 4.1 7.2 - - - +
40F ARG 3.2 0.4 - - - -
41F TYR* 1.3 82.9 - - - +
43F ALA* 1.3 62.6 + - - +
45F SER* 3.7 7.2 + - - +
46F PRO* 3.6 18.5 - - - +
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Residues in contact with ALA 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ALA 3.3 14.0 + - - +
40F ARG* 2.7 13.5 + - - +
42F GLU* 1.3 82.7 - - - +
44F VAL* 1.3 63.0 + - + +
45F SER 3.6 0.3 + - - -
46F PRO* 4.1 11.1 - - - +
47F GLU* 5.2 0.9 + - - +
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Residues in contact with VAL 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2105E ARG 4.3 11.4 - - - +
2106E MET* 3.5 36.6 - - + +
2107E HIS* 5.5 2.7 - - + +
2108E HIS* 5.1 0.7 - - - +
40F ARG* 2.8 29.8 + - + +
41F TYR* 3.4 17.3 - - + +
43F ALA* 1.3 80.1 - - + +
45F SER* 1.3 59.6 + - - +
46F PRO 3.5 0.4 - - - -
47F GLU* 3.2 18.6 + - - +
48F ARG* 2.9 34.3 + - - +
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Residues in contact with SER 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F TYR* 3.2 22.3 + - - -
42F GLU* 3.7 10.2 + - - +
43F ALA 3.3 1.8 - - - -
44F VAL* 1.3 71.8 - - - +
46F PRO* 1.4 75.5 - - - +
48F ARG* 3.7 27.3 - - - +
49F LEU* 2.6 41.0 + - - +
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Residues in contact with PRO 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F GLU 3.6 11.0 - - - +
43F ALA 4.1 9.0 - - - +
44F VAL 4.1 0.7 - - - +
45F SER* 1.4 102.0 - - - +
47F GLU* 1.3 62.1 + - - +
48F ARG 2.8 3.8 + - - -
49F LEU* 3.0 19.7 + - + +
50F GLU* 3.4 10.2 + - - +
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Residues in contact with GLU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2106E MET* 3.0 39.8 - - + +
2108E HIS* 3.2 30.1 + - - -
44F VAL* 3.2 15.1 + - - +
46F PRO* 1.3 77.4 - - - +
48F ARG* 1.3 58.6 + - - +
50F GLU* 3.3 19.9 - - + +
51F LEU* 4.4 1.9 + - - +
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Residues in contact with ARG 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D PRO* 5.9 2.0 - - - +
2104E GLU 4.2 10.3 - - - +
2105E ARG* 4.6 17.6 + - - +
2106E MET* 3.7 29.9 - - + +
41F TYR* 3.1 62.9 + - - -
44F VAL* 2.9 22.8 + - - +
45F SER* 3.6 22.5 + - - +
46F PRO 2.8 5.1 + - - -
47F GLU* 1.3 71.8 - - - +
49F LEU* 1.3 57.4 + - - +
50F GLU 2.9 9.6 + - - -
51F LEU* 3.8 9.5 + - - +
52F GLU* 4.2 6.1 + - - +
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D LEU* 3.8 11.9 - - + -
335D ALA* 3.8 19.7 - - + -
336D PRO* 5.4 2.7 - - + -
45F SER* 2.6 22.6 + - - +
46F PRO* 3.0 11.0 + - + +
48F ARG* 1.3 73.2 - - - +
50F GLU* 1.3 73.9 + - - +
51F LEU 3.6 0.4 - - - -
52F GLU* 3.2 11.4 + - - +
53F ARG* 2.9 69.3 + - + +
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PRO 3.4 7.2 + - - +
47F GLU* 3.3 20.6 - - + +
48F ARG 2.9 4.8 - - - -
49F LEU* 1.3 95.6 - - - +
51F LEU* 1.3 55.9 + - - +
52F GLU 3.1 4.9 + - - -
53F ARG* 3.8 12.9 - - - +
54F GLN* 3.5 31.1 + - - +
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F GLU 4.4 2.0 + - - +
48F ARG 3.8 6.7 + - - +
49F LEU 3.6 0.2 - - - -
50F GLU* 1.3 75.2 - - - +
52F GLU* 1.3 58.3 + - - +
54F GLN* 5.0 4.5 - - + -
55F HIS* 3.3 26.8 - - + +
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Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D LYS* 3.6 22.7 + - - +
138D ASP* 3.8 5.3 - - - +
140D GLY* 3.7 8.8 - - - -
141D VAL* 3.9 19.1 + - - +
336D PRO* 3.6 30.4 - - + +
338D THR* 4.5 4.5 - - - +
48F ARG 4.2 3.8 + - - +
49F LEU* 3.2 19.5 - - - +
50F GLU 3.1 0.4 - - - -
51F LEU* 1.3 81.8 - - - +
53F ARG* 1.3 59.0 + - - +
55F HIS* 4.0 6.5 + - - +
56F THR* 2.7 35.2 + - - -
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Residues in contact with ARG 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D SER 6.0 2.0 - - - -
138D ASP* 3.7 21.3 + - - +
334D LEU* 2.9 37.3 + - - +
335D ALA* 3.2 6.1 - - - +
336D PRO* 3.6 19.2 - - - +
49F LEU* 2.9 65.7 + - + +
50F GLU* 3.8 13.4 + - - +
52F GLU* 1.3 75.1 - - - +
54F GLN* 1.3 56.8 + - - +
55F HIS 2.5 16.6 + - - -
56F THR* 2.6 20.6 + - - -
57F PHE* 3.1 10.8 + - - +
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Residues in contact with GLN 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLU* 3.5 22.1 + - + +
51F LEU* 5.0 2.9 - - - -
53F ARG* 1.3 77.0 - - - +
55F HIS* 1.3 58.5 + - - +
57F PHE* 3.6 20.1 - - + +
58F ALA* 3.9 8.8 + - - +
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Residues in contact with HIS 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLU* 4.5 14.9 + - - -
98D MET* 3.9 28.9 - - - +
130D LYS* 4.6 12.9 - - + +
51F LEU* 3.3 29.2 + - + +
52F GLU* 3.9 8.7 + - - +
53F ARG 2.5 5.3 + - - -
54F GLN* 1.3 72.7 - - - +
56F THR* 1.3 56.2 + - - +
57F PHE 2.9 10.4 + - - -
58F ALA* 3.9 0.9 + - - +
59F LEU* 3.2 45.0 + - + +
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Residues in contact with THR 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D LYS* 3.3 17.3 - - - +
132D PHE* 3.5 38.0 - - + -
136D SER* 4.1 18.4 + - - +
138D ASP* 2.8 22.3 + - - +
52F GLU 2.7 22.7 + - - -
53F ARG* 2.6 13.5 + - - -
55F HIS* 1.3 70.4 + - - +
57F PHE* 1.3 55.5 + - - -
59F LEU* 4.6 4.7 - - - -
60F HIS* 3.3 22.3 + - - +
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Residues in contact with PHE 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D SER* 5.2 11.7 - - - -
53F ARG 3.1 7.7 + - - +
54F GLN* 3.6 17.9 - - + +
55F HIS 2.9 2.6 + - - -
56F THR* 1.3 75.7 - - - +
58F ALA* 1.3 68.2 + - + +
59F LEU 2.6 4.3 + - - -
60F HIS* 2.6 34.8 + - - +
61F GLN* 3.3 35.6 + - - +
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Residues in contact with ALA 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F GLN 3.9 7.4 + - - +
55F HIS 3.9 3.7 + - - +
57F PHE* 1.3 84.2 - - + +
59F LEU* 1.3 56.0 + - - +
61F GLN* 4.4 16.5 - - - +
62F ARG* 4.6 10.6 - - - -
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D PHE* 3.3 68.3 - - + -
97D GLU* 4.7 7.4 - - - +
98D MET* 4.6 10.8 - - + -
130D LYS* 3.9 24.2 - - + -
132D PHE* 4.0 9.6 - - + -
55F HIS* 3.2 41.0 + - + +
56F THR* 4.5 2.7 - - - -
57F PHE 2.6 5.5 + - - -
58F ALA* 1.3 76.4 - - - +
60F HIS* 1.3 60.9 + - - +
61F GLN 3.3 1.3 - - - -
62F ARG* 3.4 26.0 - - - +
63F CYS 3.5 0.3 + - - -
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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