Contacts of the helix formed by residues 46 - 62 (chain X) in PDB entry 3F6E
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 GLN 46 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X ASN* 4.9 0.4 - - - +
44X ALA 3.4 0.6 - - - -
45X LEU* 1.3 77.7 - - - +
47X GLU* 1.3 76.4 + - - +
48X ALA* 2.8 35.0 + - - +
49X CYS* 3.0 24.6 + - - +
50X VAL* 3.0 16.1 + - - +
77X ASN* 3.6 32.3 + - - +
433X TYR 5.3 4.0 - - - +
436X SER* 3.9 16.4 + - - +
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Residues in contact with GLU 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X ASN* 3.2 18.7 - - + +
46X GLN* 1.3 76.3 + - - +
48X ALA* 1.3 67.8 + - - +
49X CYS 3.1 1.1 - - - -
50X VAL* 3.6 6.2 - - - +
51X VAL* 3.0 28.9 + - - +
69X LEU* 3.7 20.4 - - + -
70X HIS* 5.0 0.9 + - - +
74X GLY* 3.3 38.7 - - - +
77X ASN* 2.9 27.3 + - + -
78X ALA* 4.0 7.9 - - + -
602X 8PA 2.7 33.9 + - - +
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Residues in contact with ALA 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X GLN* 2.8 18.0 + - - +
47X GLU* 1.3 79.2 - - - +
49X CYS* 1.3 57.5 + - - +
52X GLY* 2.9 25.6 + - - -
77X ASN 3.6 16.2 + - - +
78X ALA* 4.3 4.9 - - - +
81X ALA* 4.0 17.6 - - + +
404X GLY 4.8 2.3 - - - +
408X PRO* 4.4 3.3 - - - +
433X TYR 5.4 2.9 - - - +
434X SER* 4.1 15.4 + - - +
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Residues in contact with CYS 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X ALA* 4.0 13.9 - - + -
45X LEU 5.0 0.4 - - - +
46X GLN* 3.0 20.9 + - - +
48X ALA* 1.3 75.4 - - - +
50X VAL* 1.3 64.7 + - - +
53X ILE* 2.9 29.8 + - - +
408X PRO* 3.5 9.1 - - - +
434X SER* 3.7 25.1 - - - -
436X SER* 3.5 24.7 - - - -
437X ALA* 3.7 25.1 - - + -
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Residues in contact with VAL 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X PHE* 3.4 37.1 - - + +
22X GLY* 3.4 28.5 - - - +
23X ASN* 3.7 14.4 - - + +
42X ILE 5.4 0.4 - - - +
44X ALA* 3.7 15.9 - - + +
46X GLN 3.0 18.2 + - - +
47X GLU* 3.3 10.7 + - - +
49X CYS* 1.3 75.5 - - - +
51X VAL* 1.4 59.6 + - - +
53X ILE* 3.5 4.8 + - - +
54X ALA* 3.0 27.2 + - - +
67X ILE* 4.0 5.4 - - + -
69X LEU* 3.9 16.2 - - + -
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Residues in contact with VAL 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X GLU 3.0 12.0 + - - +
50X VAL* 1.4 75.9 - - - +
52X GLY* 1.3 58.5 + - - +
54X ALA* 3.3 5.9 + - - +
55X ASP* 2.8 29.1 + - + +
67X ILE* 4.1 26.0 - - + -
69X LEU* 4.2 6.7 - - + -
78X ALA* 3.5 26.2 - - + -
81X ALA* 3.7 25.6 - - + +
82X LEU* 4.0 24.9 - - + -
92X LEU* 4.0 15.3 - - + -
94X VAL* 5.3 0.9 - - + -
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Residues in contact with GLY 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X ALA 2.9 18.7 + - - -
49X CYS 3.9 0.4 - - - -
51X VAL* 1.3 75.1 - - - +
53X ILE* 1.3 62.9 + - - +
55X ASP* 3.3 6.4 + - - +
56X GLY 3.0 19.8 + - - -
81X ALA* 4.4 4.9 - - - +
404X GLY 5.4 1.3 - - - -
405X PHE* 4.8 9.0 - - - -
408X PRO* 4.0 11.0 - - - -
409X ALA* 3.1 18.0 - - - +
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Residues in contact with ILE 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X PHE* 3.6 26.0 - - + -
42X ILE* 4.6 7.2 - - + -
44X ALA* 3.9 22.7 - - + -
49X CYS 2.9 21.5 + - - +
50X VAL* 3.7 4.0 - - - +
52X GLY* 1.3 76.4 - - - +
54X ALA* 1.3 64.3 + - - +
55X ASP 3.2 0.3 + - - -
57X TYR* 2.9 19.8 + - - +
408X PRO* 3.2 28.9 - - + +
411X ILE* 4.3 10.8 - - + -
412X GLY* 3.3 21.7 - - - +
415X LEU* 5.4 1.8 - - + -
437X ALA* 4.8 6.1 - - + -
440X THR* 3.9 24.7 - - + -
446X ILE* 6.4 0.2 - - + -
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Residues in contact with ALA 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X PHE* 3.6 28.4 - - + -
50X VAL 3.0 13.6 + - - +
51X VAL 3.7 1.6 - - - +
53X ILE* 1.3 76.4 - - - +
55X ASP* 1.3 58.5 + - - +
57X TYR* 3.3 2.1 + - - +
58X ALA* 2.8 30.7 + - - +
65X ALA* 3.5 8.5 - - + +
67X ILE* 3.5 38.4 - - + -
92X LEU* 4.1 2.5 - - - -
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Residues in contact with ASP 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X VAL* 2.8 19.2 + - + +
52X GLY* 3.5 9.3 - - - +
53X ILE 3.1 0.2 - - - -
54X ALA* 1.3 75.5 - - - +
56X GLY* 1.3 61.4 + - - +
58X ALA* 3.2 1.4 + - - +
59X GLN* 2.8 46.5 + - - +
81X ALA 4.4 4.2 - - - +
84X ASN 4.6 0.5 - - - -
85X ALA* 3.7 25.8 + - - +
88X SER* 4.4 0.3 + - - -
90X SER* 2.6 31.4 + - - -
92X LEU* 3.9 13.4 - - + +
405X PHE* 3.6 18.6 - - + -
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Residues in contact with GLY 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X GLY 3.0 12.5 + - - -
53X ILE 3.8 0.4 - - - -
55X ASP* 1.3 76.6 - - - +
57X TYR* 1.3 63.0 + - - +
59X GLN* 4.0 6.2 - - - -
60X ALA* 3.0 27.7 + - - +
396X TYR* 6.1 0.2 - - - -
405X PHE* 5.1 1.1 - - - -
409X ALA* 3.7 26.5 - - - +
413X VAL* 3.6 16.6 - - - +
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Residues in contact with TYR 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X ASP* 4.6 5.0 + - - -
19X THR* 4.5 8.3 + - - -
21X PHE* 3.6 26.0 - + + -
40X ARG* 3.3 29.2 + - - -
53X ILE 2.9 14.7 + - - +
54X ALA 3.4 7.2 - - - +
56X GLY* 1.3 78.1 - - - +
58X ALA* 1.3 52.7 + - - +
61X SER* 2.6 44.9 + - - -
63X LYS* 2.9 47.0 - - - +
65X ALA* 4.3 0.7 - - + -
412X GLY* 3.5 22.0 - - - +
415X LEU* 4.0 15.3 - - + -
416X ALA* 3.7 27.7 - - + +
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Residues in contact with ALA 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X ALA 2.8 20.3 + - - +
55X ASP 3.2 3.6 + - - +
57X TYR* 1.3 75.4 - - - +
59X GLN* 1.3 59.0 + - - +
61X SER* 3.6 1.3 - - - -
62X ARG* 2.8 29.6 + - - -
63X LYS* 3.3 26.1 + - - +
65X ALA* 3.9 7.4 - - + +
90X SER* 5.1 1.1 - - - -
91X PRO* 4.1 15.8 - - + +
92X LEU* 3.8 19.5 - - + -
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Residues in contact with GLN 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X ASP* 2.8 41.9 + - - +
56X GLY* 4.1 3.1 - - - +
58X ALA* 1.3 76.5 - - - +
60X ALA* 1.4 62.2 + - - +
62X ARG* 3.5 9.4 + - - +
88X SER* 3.7 19.4 + - - +
90X SER* 3.4 22.7 + - - +
91X PRO* 5.7 2.7 - - + -
238X PRO* 5.0 1.6 - - - +
239X ARG* 2.9 58.9 + - - +
396X TYR* 3.6 19.9 - - + -
405X PHE* 3.7 21.6 - - - -
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Residues in contact with ALA 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X GLY 3.0 17.5 + - - +
59X GLN* 1.4 80.1 - - - +
61X SER* 1.3 61.5 + - - +
62X ARG* 3.5 17.0 + - - +
239X ARG* 4.8 0.2 - - - +
371X ILE* 5.8 0.2 - - + -
393X GLY* 6.1 0.4 - - - -
396X TYR* 3.5 17.4 + - - +
413X VAL* 4.0 20.2 - - + -
416X ALA* 3.7 19.7 - - + -
417X GLU* 4.1 19.2 - - + +
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Residues in contact with SER 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57X TYR* 2.6 30.3 + - - -
58X ALA 3.5 1.9 + - - -
60X ALA* 1.3 75.9 - - - +
62X ARG* 1.3 69.2 + - - +
63X LYS* 2.8 43.8 + - - +
416X ALA* 4.0 12.5 - - - +
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Residues in contact with ARG 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58X ALA 2.8 13.4 + - - -
59X GLN 3.7 10.8 - - - +
60X ALA 3.3 12.6 + - - +
61X SER* 1.3 78.7 - - - +
63X LYS* 1.3 57.1 + - - +
91X PRO* 5.4 2.7 - - - -
151X GLN* 5.4 7.4 + - - -
212X ASP* 2.9 46.4 + - - -
213X ALA* 3.1 21.7 + - - +
214X ALA 4.6 0.9 - - - -
215X ASN* 3.6 26.6 + - - +
239X ARG* 3.9 7.4 - - - +
392X PRO* 3.7 11.7 - - - +
393X GLY* 3.7 15.7 - - - +
396X TYR* 5.8 0.2 - - - -
417X GLU* 5.3 3.8 + - - -
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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
------------------------------------------------------------
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