Contacts of the helix formed by residues 51 - 65 (chain A) in PDB entry 6FWF
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 LYS 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.9 25.6 - - + +
37A PRO 2.8 23.3 + - - +
38A GLU* 3.1 35.5 + - + +
50A ALA* 1.3 69.2 - - - +
52A ASP* 1.3 58.0 + - - +
54A ILE* 4.2 8.3 - - - -
55A LEU* 2.8 64.3 + - + +
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Residues in contact with ASP 52 (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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38A GLU 4.7 2.3 - - - +
50A ALA* 4.1 13.8 - - + +
51A LYS* 1.3 78.3 - - - +
53A ASP* 1.3 59.8 + - - +
55A LEU* 4.2 2.2 - - - +
56A ALA* 2.8 39.7 + - - +
188A LYS* 4.9 4.9 - - - +
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Residues in contact with ASP 53 (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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49A MET* 3.7 4.2 - - - -
50A ALA* 2.8 36.9 + - - +
52A ASP* 1.3 73.6 - - - +
54A ILE* 1.3 59.1 + - - +
57A GLY 2.8 23.2 + - - -
181A PRO* 5.7 2.3 - - - +
183A GLN* 3.7 25.9 - - - +
188A LYS* 3.1 54.2 + - + +
191A ASP* 3.8 21.1 - - + +
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.4 29.2 - - + -
37A PRO* 3.8 19.3 - - + +
40A VAL* 5.2 0.4 - - + -
49A MET* 3.8 29.4 - - + -
50A ALA 2.8 28.5 + - - +
51A LYS* 3.9 4.7 - - - +
53A ASP* 1.3 73.4 - - - +
55A LEU* 1.3 56.5 + - - +
57A GLY 3.6 0.2 - - - -
58A GLN* 2.8 27.1 + - - +
191A ASP 4.3 2.5 - - - +
192A PHE* 3.5 18.8 - - + +
195A TRP* 3.5 43.7 - - + -
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Residues in contact with LEU 55 (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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36A TYR* 3.3 22.9 - - + -
51A LYS* 2.8 49.2 + - + +
52A ASP* 4.2 2.7 - - - +
54A ILE* 1.3 72.0 - - - +
56A ALA* 1.3 58.2 + - - +
58A GLN* 3.2 25.9 + - - +
59A SER* 2.8 27.4 + - - -
474A GLU 4.5 1.6 - - - +
475A LYS* 3.3 45.9 - - + +
476A SER 3.8 7.4 - - - +
477A PRO* 4.8 1.6 - - + -
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Residues in contact with ALA 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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52A ASP 2.8 22.8 + - - +
55A LEU* 1.3 72.3 - - - +
57A GLY* 1.3 54.6 + - - +
59A SER* 2.7 23.3 + - - +
60A ALA* 2.8 22.1 + - - +
188A LYS* 3.5 31.0 - - + +
475A LYS* 4.1 10.9 - - - +
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Residues in contact with GLY 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 ASP 2.8 19.3 + - - -
54A ILE 3.6 1.6 - - - -
56A ALA* 1.3 74.8 - - - +
58A GLN* 1.3 56.6 + - - +
60A ALA* 4.0 4.2 - - - +
61A TRP* 2.8 32.0 + - - +
188A LYS* 3.5 22.8 - - - +
189A LEU* 3.8 8.8 - - - +
192A PHE* 3.7 9.3 - - - -
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Residues in contact with GLN 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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36A TYR* 2.5 33.1 + - - -
54A ILE 2.8 16.5 + - - +
55A LEU* 3.2 13.0 - - - +
57A GLY* 1.3 73.8 - - - +
59A SER* 1.3 59.2 + - - +
61A TRP* 3.2 8.1 + - + +
62A GLN* 2.8 47.9 + - - +
192A PHE* 3.9 19.7 - - + -
474A GLU 3.5 7.9 + - - +
476A SER 2.6 26.6 + - - +
478A ILE* 4.1 7.2 - - + +
481A MET* 3.0 29.5 - - - +
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Residues in contact with SER 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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55A LEU 2.8 17.2 + - - -
56A ALA* 2.7 20.4 + - - +
58A GLN* 1.3 74.1 - - - +
60A ALA* 1.3 51.3 + - - +
62A GLN* 3.3 14.4 + - - +
63A THR* 2.8 36.6 + - - -
474A GLU* 3.8 21.0 + - - +
475A LYS* 3.3 30.6 + - - -
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Residues in contact with ALA 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 ALA 2.8 21.8 + - - +
57A GLY* 4.0 8.3 - - - +
59A SER* 1.3 71.9 + - - +
61A TRP* 1.3 57.4 + - - +
62A GLN 3.2 0.2 - - - -
63A THR* 3.4 9.4 - - + -
64A THR* 2.8 43.4 + - + +
185A ALA 5.4 5.8 - - - +
189A LEU* 5.1 10.1 - - + -
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Residues in contact with TRP 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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57A GLY 2.8 21.2 + - - +
58A GLN* 3.2 7.6 - - + +
60A ALA* 1.3 75.1 - - - +
62A GLN* 1.3 66.3 + - + +
64A THR* 2.6 22.5 + - - -
65A GLY* 2.8 16.6 + - - -
66A GLY* 3.3 32.4 + - - -
67A MET* 3.3 36.7 - - + +
70A GLY 3.2 22.7 - - - -
72A VAL* 3.6 33.1 - - + +
83A TRP* 3.7 19.3 - + - -
189A LEU* 4.3 8.2 - - + +
192A PHE* 3.5 31.4 - + + -
193A PHE* 4.0 20.0 - + - -
409A GLY* 4.8 1.2 + - - +
410A TYR* 5.9 0.6 - + - -
478A ILE* 4.7 6.5 - - + +
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Residues in contact with GLN 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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58A GLN* 2.8 35.5 + - - +
59A SER* 3.5 6.2 - - - +
60A ALA 3.2 0.2 - - - -
61A TRP* 1.3 80.8 - - + +
63A THR* 1.3 62.3 + - - +
65A GLY 3.8 2.4 + - - -
402A ASN* 5.3 1.3 - - - -
403A PHE* 5.2 1.6 - - + -
407A HIS 2.9 23.6 - - - +
408A GLN 3.4 17.3 - - - +
409A GLY* 3.7 11.6 - - - -
410A TYR* 2.9 31.5 + - + +
474A GLU* 2.9 44.7 + - + +
478A ILE* 4.7 0.9 - - - +
481A MET* 3.1 20.8 - - - +
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Residues in contact with THR 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 SER* 2.8 21.8 + - - -
60A ALA* 3.4 13.3 - - + +
62A GLN* 1.3 76.6 - - - +
64A THR* 1.3 67.4 + - + +
65A GLY* 3.2 0.7 + - - -
392A ALA* 3.7 23.6 - - - +
395A HIS* 3.8 30.5 - - + +
399A PRO* 4.5 3.7 + - + +
402A ASN* 2.7 46.6 + - - +
407A HIS* 4.6 3.3 - - - +
474A GLU* 4.8 1.2 + - - -
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Residues in contact with THR 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 ALA* 2.8 25.4 + - + +
61A TRP* 2.6 29.3 + - - -
63A THR* 1.3 77.1 - - + +
65A GLY* 1.3 58.8 + - - +
66A GLY* 3.4 9.7 + - - -
69A VAL* 5.9 0.5 - - - +
189A LEU* 5.2 14.3 - - + +
329A ALA* 5.4 0.3 - - - +
392A ALA 5.2 2.0 - - - -
393A LEU* 3.1 23.8 - - - +
395A HIS* 5.7 4.5 - - - +
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Residues in contact with GLY 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 TRP 2.8 10.0 + - - -
62A GLN 3.8 2.7 - - - -
63A THR 3.2 2.6 - - - -
64A THR* 1.3 78.9 - - - +
66A GLY* 1.3 52.9 + - - +
67A MET 3.0 5.8 - - - -
68A GLU* 2.8 35.5 + - - +
69A VAL* 4.1 2.9 - - - +
393A LEU* 3.9 5.3 - - - +
407A HIS* 3.1 30.6 - - - -
409A GLY* 4.3 2.0 - - - -
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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