Contacts of the helix formed by residues 62 - 75 (chain F) in PDB entry 3ECS
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 62 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F SER* 4.6 8.6 - - - -
60F ASP* 2.5 31.5 + - - +
61F SER* 1.3 76.9 - - - +
63F VAL* 1.3 65.9 + - - +
64F ALA* 3.3 16.8 + - - +
65F VAL* 3.5 23.0 + - - +
66F SER* 3.8 8.1 + - - -
198F GLU* 4.6 13.9 + - - -
250F PHE* 4.1 0.2 - - - -
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Residues in contact with VAL 63 (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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62F SER* 1.3 70.1 + - - +
64F ALA* 1.3 61.9 + - - +
66F SER* 2.8 22.3 + - - -
67F SER* 3.1 12.3 + - - +
198F GLU* 3.6 22.1 + - + +
199F GLY* 3.9 13.5 - - - -
207F ILE* 4.4 20.9 - - + -
234F LYS 4.6 0.2 - - - +
236F VAL* 4.0 30.7 - - + -
250F PHE* 3.4 46.9 - - + -
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Residues in contact with ALA 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F SER* 6.0 0.2 - - - -
23F ALA* 3.5 23.6 - - + +
62F SER* 3.3 9.3 + - - +
63F VAL* 1.3 80.1 - - - +
65F VAL* 1.3 54.6 + - - +
67F SER* 3.2 10.5 - - - -
68F GLY* 2.6 33.6 + - - -
198F GLU 3.5 6.9 + - - +
233F PHE* 4.0 4.0 - - + +
234F LYS* 3.8 29.8 - - + -
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Residues in contact with VAL 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F PHE* 4.9 1.1 - - + -
22F SER* 4.1 23.6 - - - +
23F ALA* 4.4 5.8 - - - +
26F ALA* 4.1 17.8 - - + +
54F GLU* 5.1 2.7 - - - +
57F CYS* 4.1 29.6 - - + +
58F GLY* 4.7 4.0 - - - +
60F ASP* 3.9 21.5 - - + +
62F SER* 3.5 28.8 + - - +
63F VAL 3.1 1.0 - - - -
64F ALA* 1.3 76.9 - - - +
66F SER* 1.3 59.5 + - - +
69F GLY* 3.0 24.3 + - - +
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Residues in contact with SER 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F GLY* 6.0 1.6 - - - -
62F SER 3.9 7.6 + - - -
63F VAL* 2.8 11.1 + - - -
65F VAL* 1.3 76.6 - - - +
67F SER* 1.3 54.0 + - - -
69F GLY* 3.2 1.6 + - - -
70F GLU* 2.6 40.0 + - - +
236F VAL* 5.7 4.3 - - - -
250F PHE* 3.9 20.4 - - - -
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Residues in contact with SER 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F VAL* 3.1 13.7 + - - +
64F ALA* 3.2 7.8 - - - -
66F SER* 1.3 75.0 - - - +
68F GLY* 1.3 59.6 + - - +
70F GLU* 3.8 4.7 - - - +
71F LEU* 2.8 35.7 + - - +
233F PHE 2.8 23.1 + - - -
234F LYS* 3.8 5.4 + - - -
235F PHE 3.4 25.6 - - - -
236F VAL* 4.2 12.3 - - - +
304F TYR* 4.0 7.2 - - - -
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Residues in contact with GLY 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ALA* 4.6 2.2 - - - -
27F ILE* 3.8 25.6 - - - +
64F ALA 2.6 21.8 + - - -
67F SER* 1.3 73.7 + - - +
69F GLY* 1.3 61.6 + - - +
71F LEU* 3.7 2.5 - - - +
72F PHE* 2.9 25.3 + - - +
100F PHE* 5.5 0.2 - - - -
233F PHE* 3.4 17.6 + - - -
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Residues in contact with GLY 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ALA* 6.2 0.2 - - - +
26F ALA* 6.2 1.5 - - - +
27F ILE* 4.4 4.0 - - - +
30F LEU* 4.3 10.8 - - - -
54F GLU* 3.1 28.9 - - - +
65F VAL 3.0 21.3 + - - -
66F SER 3.5 0.7 - - - -
68F GLY* 1.3 78.0 - - - +
70F GLU* 1.3 61.9 + - - +
72F PHE* 3.3 3.3 + - - +
73F LEU* 3.2 18.2 + - - +
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Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLU* 4.8 0.7 - - - -
66F SER* 2.6 23.1 + - - +
67F SER* 3.8 6.1 - - - +
69F GLY* 1.3 71.2 - - - +
71F LEU* 1.3 65.2 + - - +
72F PHE 3.2 0.2 + - - -
73F LEU* 3.2 11.1 + - + +
74F ARG* 3.0 43.1 + - - +
237F ARG* 3.2 30.5 + - - +
304F TYR* 3.8 13.3 + - + -
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Residues in contact with LEU 71 (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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67F SER 2.8 27.6 + - - +
68F GLY* 3.7 3.6 - - - +
70F GLU* 1.3 73.0 - - - +
72F PHE* 1.3 62.2 + - - +
74F ARG* 3.2 7.2 + - - +
75F PHE* 3.0 25.3 + - - +
100F PHE* 3.7 17.3 - - + -
232F SER 4.0 1.8 - - - +
233F PHE* 3.8 30.3 - - + +
235F PHE 4.3 7.6 - - - +
303F LEU* 3.4 42.6 - - + +
304F TYR* 3.6 33.9 - - + -
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Residues in contact with PHE 72 (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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27F ILE* 3.5 26.5 - - + -
30F LEU* 3.5 38.6 - - + -
31F LEU* 4.2 22.0 - - + -
34F LEU* 4.8 8.7 - - + -
50F THR* 5.1 7.9 - - - -
54F GLU* 5.2 0.2 - - - -
68F GLY 2.9 13.8 + - - +
69F GLY* 3.4 10.1 - - - +
71F LEU* 1.3 76.2 - - - +
73F LEU* 1.3 66.6 + - + +
74F ARG 3.1 1.2 + - - -
75F PHE* 3.1 12.5 + - - +
76F ILE* 3.7 34.7 - - + +
97F GLY* 3.6 33.7 - - - -
100F PHE* 3.7 22.2 - + + -
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Residues in contact with LEU 73 (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 ALA* 4.1 15.7 - - + +
50F THR* 3.4 32.8 - - + +
51F SER* 4.6 9.6 - - - +
54F GLU* 5.0 9.0 - - + +
69F GLY 3.2 8.2 + - - +
70F GLU* 3.2 13.1 + - + +
72F PHE* 1.3 85.8 - - + +
74F ARG* 1.3 63.6 + - + +
76F ILE* 3.2 30.1 + - + +
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Residues in contact with ARG 74 (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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241D LEU* 3.8 20.8 - - - +
242D ASN* 5.4 6.3 - - - +
245D ASP* 5.8 0.4 + - - -
70F GLU* 3.0 40.6 + - - +
71F LEU* 3.4 13.5 - - + +
73F LEU* 1.3 81.2 - - + +
75F PHE* 1.3 58.2 + - - +
76F ILE* 2.8 17.3 + - - +
77F SER* 4.6 0.5 + - - -
237F ARG* 4.3 5.5 - - - +
304F TYR* 3.1 50.1 + - - +
305F LEU* 5.5 4.0 - - - +
307F ALA* 4.3 11.4 - - - +
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Residues in contact with PHE 75 (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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71F LEU 3.0 9.6 + - - +
72F PHE 3.1 4.2 + - - +
74F ARG* 1.3 73.8 - - - +
76F ILE* 1.3 60.4 + - + +
77F SER 4.2 0.4 - - - -
96F ARG* 3.3 81.9 + - + -
99F LEU* 4.0 25.4 - - + -
100F PHE* 3.6 35.9 - + + -
103F ARG* 4.5 16.4 - - - -
306F ALA* 4.5 23.8 - - + -
307F ALA* 4.8 12.1 - - + +
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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
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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