Contacts of the helix formed by residues 61 - 78 (chain X) in PDB entry 2FSM
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 SER 61 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X PHE 4.0 0.2 - - - -
60X GLN* 1.3 81.4 - - - +
62X ILE* 1.3 60.7 + - - +
63X ILE* 3.3 11.7 + - - +
64X HIS* 2.8 27.0 + - - -
65X ALA* 2.8 31.5 + - - +
334X ILE* 3.4 13.6 - - - +
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Residues in contact with ILE 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61X SER* 1.3 74.7 - - - +
63X ILE* 1.3 65.2 + - + +
65X ALA* 3.3 3.0 + - - +
66X LYS* 2.9 32.7 + - + +
331X ASP* 6.1 1.3 - - - -
332X LEU 3.7 26.7 - - - +
333X LEU* 5.3 5.8 - - + -
334X ILE* 3.5 24.9 - - + +
337X TRP* 3.9 12.0 - - + +
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Residues in contact with ILE 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61X SER* 3.2 7.6 + - - +
62X ILE* 1.3 86.0 - - + +
64X HIS* 1.3 62.5 + - + +
66X LYS* 3.9 9.7 - - + +
67X ARG* 3.0 49.8 + - - +
70X ARG* 5.4 1.0 + - - -
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Residues in contact with HIS 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56X SER 5.0 1.6 + - - -
57X ARG* 3.4 30.7 + - + +
58X PRO* 3.2 11.4 - - + +
60X GLN* 3.9 27.4 + - + +
61X SER* 2.8 38.2 + - - +
63X ILE* 1.3 79.5 - - + +
65X ALA* 1.3 59.7 + - - +
67X ARG* 3.3 25.4 + - - +
68X THR* 2.9 32.6 + - - -
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Residues in contact with ALA 65 (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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58X PRO 3.3 10.1 + - - -
59X PHE* 3.8 22.7 - - + -
61X SER 2.8 18.8 + - - +
62X ILE* 3.7 3.8 - - - +
64X HIS* 1.3 77.2 - - - +
66X LYS* 1.3 58.7 + - - +
68X THR* 3.3 3.1 + - - -
69X TYR* 3.0 27.9 + - - +
334X ILE* 4.3 11.4 - - + +
337X TRP* 3.6 23.4 - - + +
341X THR* 4.3 2.8 + - - -
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Residues in contact with LYS 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62X ILE* 2.9 20.9 + - + +
63X ILE* 4.0 9.2 - - + +
65X ALA* 1.3 76.5 - - - +
67X ARG* 1.3 56.5 + - - +
69X TYR* 3.4 3.1 + - - +
70X ARG* 3.0 46.6 + - + +
327X SER 5.4 1.1 - - - +
328X GLU* 2.8 43.6 + - + +
329X SER 4.3 1.0 - - - -
330X ARG 2.8 23.9 + - - +
331X ASP* 4.4 5.7 + - - -
337X TRP* 3.6 42.1 - - + +
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Residues in contact with ARG 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X ILE* 3.0 38.9 + - - +
64X HIS* 3.3 32.2 + - - +
66X LYS* 1.3 71.4 - - - +
68X THR* 1.3 66.4 + - - +
70X ARG* 3.4 29.7 + - - +
71X GLU* 3.0 34.2 + - + +
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Residues in contact with THR 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X LEU* 3.7 27.4 - - + +
58X PRO* 2.7 41.1 + - + +
59X PHE* 4.0 15.0 - - + -
64X HIS 2.9 12.5 + - - -
65X ALA* 3.5 5.8 - - - -
67X ARG* 1.3 78.4 - - - +
69X TYR* 1.3 62.5 + - - +
71X GLU* 3.8 6.4 - - - +
72X LEU* 3.1 24.4 + - + +
102X VAL* 4.8 3.1 - - + -
341X THR* 4.1 11.4 - - + -
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Residues in contact with TYR 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65X ALA 3.0 11.8 + - - +
66X LYS 3.6 7.4 - - - +
68X THR* 1.3 78.7 - - - +
70X ARG* 1.3 60.8 + - - +
72X LEU* 3.4 3.9 + - - +
73X ARG* 3.0 53.5 + - - +
327X SER* 3.9 28.6 - - - -
330X ARG* 5.6 0.9 + - - -
337X TRP* 3.4 35.4 - + + +
340X LEU* 3.6 53.4 - - + +
341X THR* 3.5 17.7 + - - +
344X GLU* 3.7 20.0 + - + -
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Residues in contact with ARG 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X ILE 5.4 0.8 + - - -
66X LYS* 3.0 36.6 + - + +
67X ARG* 3.8 36.6 + - - +
68X THR 3.3 0.4 - - - -
69X TYR* 1.3 81.6 - - - +
71X GLU* 1.3 56.7 + - - +
73X ARG* 3.4 1.1 + - - +
74X LEU* 3.0 39.1 + - + +
323X TYR* 3.6 10.7 + - - +
327X SER 5.3 1.8 - - - +
328X GLU* 3.0 47.1 + - + +
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Residues in contact with GLU 71 (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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53X LYS* 3.0 29.9 + - - +
55X LEU* 4.3 14.8 - - - +
67X ARG* 3.0 26.9 + - + +
68X THR* 3.8 5.6 - - - +
70X ARG* 1.3 73.4 - - - +
72X LEU* 1.3 60.4 + - - +
74X LEU* 3.5 7.6 + - - +
75X LEU* 2.9 47.3 + - + +
104X LEU* 3.6 19.8 - - + +
168X ASP* 4.5 12.3 - - - +
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Residues in contact with LEU 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68X THR* 3.1 17.4 + - + +
69X TYR* 3.8 4.0 - - + +
71X GLU* 1.3 80.4 - - - +
73X ARG* 1.3 61.8 + - - +
75X LEU* 4.0 3.3 - - - -
76X LYS* 3.0 35.1 + - + +
86X LEU* 3.8 24.7 - - + -
89X VAL* 4.1 9.4 - - + -
102X VAL* 5.2 4.7 - - + -
104X LEU* 3.8 20.9 - - + -
341X THR* 3.9 25.4 - - + +
344X GLU* 3.8 24.5 - - + -
345X VAL* 4.1 14.4 - - + +
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Residues in contact with ARG 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69X TYR* 3.0 52.0 + - + +
70X ARG* 3.8 1.6 - - - +
72X LEU* 1.3 77.9 - - - +
74X LEU* 1.3 63.9 + - - +
76X LYS* 3.3 7.1 + - - +
77X HIS* 3.1 22.7 + - - +
323X TYR* 3.3 36.1 - - + +
324X ASP* 2.9 43.9 + - - +
327X SER* 3.8 8.8 + - - -
344X GLU* 3.8 30.4 + - + +
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Residues in contact with LEU 74 (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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70X ARG* 3.0 28.3 + - + +
71X GLU* 3.8 7.0 - - - +
73X ARG* 1.3 76.5 - - - +
75X LEU* 1.3 65.0 + - + +
77X HIS* 3.0 12.5 + - - +
78X MET* 3.2 30.4 + - + +
146X ILE* 3.3 41.5 - - + -
168X ASP* 6.0 6.1 - - + -
323X TYR* 3.5 22.4 + - + -
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Residues in contact with LEU 75 (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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71X GLU* 2.9 30.7 + - + +
72X LEU* 4.1 2.7 - - - +
74X LEU* 1.3 78.2 - - + +
76X LYS* 1.3 63.0 + - - +
77X HIS 3.4 0.3 + - - -
78X MET* 3.5 20.6 + - + +
84X ILE* 4.1 29.6 - - + +
85X GLY* 4.7 2.8 - - - -
86X LEU* 3.8 37.2 + - + +
104X LEU* 3.7 31.4 - - + -
106X THR* 5.4 6.5 - - + -
168X ASP* 3.7 24.9 - - + +
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Residues in contact with LYS 76 (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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72X LEU* 3.0 34.3 + - + +
73X ARG* 3.8 4.7 - - - +
74X LEU 3.2 0.4 - - - -
75X LEU* 1.3 78.8 - - - +
77X HIS* 1.3 61.5 + - - +
78X MET 3.6 0.2 + - - -
79X LYS* 3.6 23.2 - - - +
86X LEU* 3.6 21.1 - - + -
344X GLU* 2.8 55.4 + - - +
347X SER* 3.1 16.7 + - - -
348X PHE* 3.9 29.2 - - + +
349X VAL 5.5 0.2 - - - +
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Residues in contact with HIS 77 (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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73X ARG 3.1 12.5 + - - +
74X LEU* 3.0 10.3 + - + +
76X LYS* 1.3 78.0 - - - +
78X MET* 1.3 83.4 + - + +
79X LYS* 3.3 10.7 + - - +
140X TYR* 3.4 6.3 + - - -
144X ALA* 4.2 2.3 - - + +
320X ALA* 4.3 5.8 - - + +
321X ASP* 2.7 40.0 + - + -
322X PRO 3.6 14.1 - - - -
323X TYR* 3.7 32.6 - + + +
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Residues in contact with MET 78 (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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74X LEU* 3.2 23.9 + - + +
75X LEU* 3.5 14.4 + - + +
76X LYS 3.3 2.0 - - - -
77X HIS* 1.3 107.7 - - + +
79X LYS* 1.3 63.8 + - - +
80X HIS 3.9 3.2 + - - -
83X VAL* 4.0 20.2 - - + -
84X ILE* 3.7 18.4 - - + +
85X GLY* 3.9 15.4 - - - -
86X LEU 4.8 0.5 + - - -
140X TYR* 3.6 23.8 - - + -
141X ILE* 4.4 11.4 - - - -
144X ALA* 4.3 6.5 - - + -
146X ILE* 4.0 22.9 - - + -
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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
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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