Contacts of the helix formed by residues 53 - 68 (chain A) in PDB entry 1F0C
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 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ILE* 1.3 69.9 - - - +
54A PRO* 1.4 68.2 - - - +
55A PRO* 3.8 3.6 - - - +
56A SER* 3.1 18.4 + - - -
57A ILE* 3.3 11.7 + - - +
112A PHE* 4.9 0.2 - - - -
188A VAL* 3.5 16.1 - - - +
334A HIS* 3.0 13.5 + - - -
336A THR* 4.4 0.4 - - - +
349A ALA* 3.5 23.8 - - - -
383B LEU 3.1 14.1 + - - -
384B PHE* 3.5 18.5 - - - -
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Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET* 4.9 7.0 - - + -
37A ILE* 5.7 7.4 - - + +
52A ILE* 3.4 22.6 - - + +
53A SER* 1.4 83.7 - - - +
55A PRO* 1.3 74.7 - - + +
57A ILE* 3.3 10.7 + - + +
58A SER* 2.9 25.2 + - - -
382B ILE* 4.4 8.7 - - + +
383B LEU 3.7 5.8 - - - +
384B PHE* 4.0 2.5 - - - -
385B VAL* 3.6 26.7 - - + -
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Residues in contact with PRO 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 3.6 3.8 - - - +
54A PRO* 1.3 90.9 - - + +
56A SER* 1.3 56.8 + - - +
58A SER* 3.1 8.0 + - - +
59A SER* 2.8 33.6 + - - -
81A GLU* 4.7 6.1 - - - -
112A PHE* 4.3 13.0 - - + -
188A VAL* 5.4 1.8 - - + -
381B LYS* 3.8 29.6 - - - +
382B ILE 3.2 27.4 - - - +
383B LEU* 3.4 19.1 - - - +
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 3.1 21.8 + - - -
55A PRO* 1.3 78.8 - - - +
57A ILE* 1.3 61.9 + - - +
59A SER* 3.4 2.0 + - - -
60A VAL 3.3 16.5 + - - -
186A SER* 2.7 36.2 + - - -
188A VAL* 4.1 14.8 - - - +
334A HIS* 3.8 7.0 - - - -
349A ALA* 4.2 1.6 + - - -
350A ALA* 4.0 4.2 - - - -
351A THR* 2.8 29.4 + - - -
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.5 44.6 - - + -
52A ILE* 4.2 12.3 - - + -
53A SER 3.3 6.5 + - - +
54A PRO* 3.3 6.9 + - + +
55A PRO 3.3 0.2 - - - -
56A SER* 1.3 76.0 - - - +
58A SER* 1.3 65.0 + - - +
60A VAL* 3.1 4.5 + - - +
61A LEU* 3.1 34.4 + - + +
299A LEU* 3.7 30.5 - - + -
303A LEU* 5.4 1.3 - - + -
332A MET* 4.0 3.3 - - + +
334A HIS* 3.6 40.4 - - + +
351A THR* 3.9 8.3 - - - +
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 6.3 0.9 - - - -
54A PRO 2.9 17.7 + - - -
55A PRO* 3.6 7.7 + - - -
57A ILE* 1.3 81.0 - - - +
59A SER* 1.3 58.3 + - - +
61A LEU* 3.4 8.9 + - - +
62A THR* 2.8 32.9 + - - -
79A TYR* 3.2 24.0 + - - +
81A GLU* 4.1 19.1 + - - -
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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 PRO 2.8 15.3 + - - -
56A SER* 3.5 0.7 + - - -
57A ILE 3.2 0.2 - - - -
58A SER* 1.3 74.7 + - - +
60A VAL* 1.3 66.5 + - - +
62A THR* 3.5 8.4 + - - -
63A ILE* 3.3 24.7 + - - +
116A ASN* 2.7 35.9 + - - -
186A SER* 3.4 14.3 + - - -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER 3.3 1.2 + - - +
57A ILE 3.1 7.3 + - - +
59A SER* 1.3 76.0 + - - +
61A LEU* 1.3 67.3 + - - +
63A ILE* 2.9 18.4 + - + +
64A LEU* 3.1 12.8 + - + +
184A ALA* 3.7 20.4 - - + +
185A ILE 4.1 1.6 - - - -
186A SER* 3.6 20.9 - - - +
332A MET* 4.0 14.4 - - + -
351A THR* 3.4 32.8 - - - +
353A ALA* 3.6 32.8 - - + +
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Residues in contact with LEU 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 ILE* 3.1 34.6 + - + +
58A SER* 3.8 5.4 - - - +
59A SER 3.3 0.2 - - - -
60A VAL* 1.3 77.9 - - - +
62A THR* 1.3 56.0 - - - +
64A LEU* 3.4 14.2 + - + +
65A TYR* 2.9 26.2 + - - +
76A LEU* 3.8 27.0 - - + +
79A TYR* 3.9 40.6 - - + -
80A VAL* 5.8 0.4 - - - -
303A LEU* 4.0 21.1 - - + -
308A LEU* 4.6 4.0 - - + -
312A PHE* 4.9 2.2 - - + -
332A MET* 3.5 30.1 - - + -
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Residues in contact with THR 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 SER* 2.8 23.4 + - - -
59A SER* 3.7 9.3 - - - -
60A VAL 3.1 0.2 - - - -
61A LEU* 1.3 76.3 - - - +
63A ILE* 1.3 67.2 + - + +
65A TYR* 3.0 8.3 + - - +
66A TYR* 3.0 52.2 + - + +
79A TYR 3.7 0.7 + - - -
80A VAL* 3.6 38.4 - - + -
81A GLU 4.2 2.5 + - - +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER 3.3 17.3 + - - +
60A VAL* 2.9 12.5 + - + +
62A THR* 1.3 74.3 - - + +
64A LEU* 1.3 66.9 + - + +
66A TYR* 2.9 32.5 + - + +
67A GLY 3.5 2.9 + - - -
116A ASN* 4.7 19.3 - - + +
117A LYS 5.7 0.4 - - - +
118A VAL* 3.9 22.2 - - + -
130A PHE* 3.8 12.5 - - + -
134A ILE* 3.8 28.3 - - + -
141A ASN* 6.3 0.2 - - + -
182A LEU* 5.6 1.3 - - + -
184A ALA* 3.7 29.8 - - + -
185A ILE 5.8 0.9 - - - +
321A MET* 5.9 0.7 - - + -
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Residues in contact with LEU 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 VAL* 3.5 12.1 - - + +
61A LEU* 3.4 26.2 - - + +
63A ILE* 1.3 81.8 - - + +
65A TYR* 1.3 60.6 + - - +
67A GLY 3.2 2.5 + - - +
68A ALA* 3.1 23.0 + - - +
76A LEU* 4.0 10.5 - - + -
184A ALA* 5.1 8.3 - - + -
311A VAL* 4.8 7.9 - - + -
312A PHE* 4.9 0.7 - - + -
318A TYR* 3.5 15.8 - - + +
321A MET* 4.6 10.8 - - + -
329A VAL* 4.0 33.7 - - + -
332A MET* 4.8 2.7 - - - -
353A ALA* 4.1 25.6 - - + -
355A VAL* 4.2 13.0 - - + -
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Residues in contact with TYR 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 LEU 2.9 14.9 + - - +
62A THR* 3.0 12.5 + - - +
64A LEU* 1.3 72.9 - - - +
66A TYR* 1.3 85.8 + + - +
67A GLY 3.1 1.6 + - - -
68A ALA* 3.1 16.9 + - - +
73A ALA* 3.2 39.9 - - + +
76A LEU* 4.0 11.9 - - + +
77A SER* 3.7 26.9 - - - -
80A VAL* 3.5 26.0 - - + -
133A LYS* 5.3 0.5 + - - -
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Residues in contact with TYR 66 (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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62A THR* 3.0 41.3 + - + +
63A ILE* 2.9 23.0 + - + +
65A TYR* 1.3 90.6 - + - +
67A GLY* 1.3 57.2 + - - +
68A ALA 4.9 0.6 - - - +
80A VAL* 5.6 2.2 - - + +
130A PHE* 3.8 14.1 - - + -
133A LYS* 3.0 79.9 + - + +
134A ILE* 4.0 13.7 - - + -
320A ASN* 3.9 8.8 - - - +
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Residues in contact with GLY 67 (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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63A ILE 3.5 3.4 + - - -
64A LEU 3.2 8.4 + - - -
65A TYR 3.0 0.8 - - - -
66A TYR* 1.3 79.6 - - - +
68A ALA* 1.3 59.1 + - - +
130A PHE* 3.7 7.6 - - - -
318A TYR* 3.0 26.4 - - - +
320A ASN* 3.2 20.1 + - - -
321A MET* 3.4 22.5 + - - -
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Residues in contact with ALA 68 (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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64A LEU 3.1 14.2 + - - +
65A TYR 3.1 11.8 + - - +
66A TYR 4.9 0.2 - - - +
67A GLY* 1.3 81.7 - - - +
69A ASN* 1.3 61.6 + - - +
72A THR* 3.7 22.7 - - + -
73A ALA* 3.6 21.9 - - - +
76A LEU* 4.0 3.8 - - + -
133A LYS* 5.9 0.2 + - - -
317A ASP 3.3 12.8 - - - +
318A TYR* 3.7 4.0 - - + -
320A ASN* 3.4 13.1 - - - +
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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