Contacts of the helix formed by residues 62 - 76 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 3.6 11.1 + - - -
60A ASP* 2.8 31.3 + - - +
61A SER* 1.3 83.4 + - - +
63A VAL* 1.3 65.7 + - - +
64A ALA* 4.1 5.6 - - - -
65A VAL* 3.4 26.8 + - - +
66A SER* 3.5 9.7 + - - -
198A GLU* 5.0 12.0 + - - -
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Residues in contact with VAL 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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61A SER 3.3 0.6 + - - -
62A SER* 1.3 71.8 - - - +
64A ALA* 1.3 59.4 + - - +
66A SER* 3.1 5.5 + - - -
67A SER* 2.9 26.3 + - - +
198A GLU* 4.0 19.0 + - + +
199A GLY* 4.2 9.4 - - - -
207A ILE* 4.2 25.4 - - + -
236A VAL* 3.8 40.2 - - + -
250A PHE* 3.5 45.5 - - + +
273A VAL* 5.8 0.9 - - + -
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Residues in contact with ALA 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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22A SER* 5.7 1.3 - - - -
23A ALA* 3.8 23.1 - - + +
62A SER* 3.1 5.6 - - - -
63A VAL* 1.3 76.9 - - - +
65A VAL* 1.3 59.6 + - - +
67A SER* 3.7 8.5 - - - -
68A GLY* 2.7 34.1 + - - -
198A GLU* 3.8 8.7 + - - +
233A PHE* 4.2 4.0 - - + -
234A LYS* 3.8 28.9 - - + -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 4.5 5.2 - - + -
22A SER* 3.6 40.4 - - - +
23A ALA* 4.1 6.5 - - - +
26A ALA* 4.4 15.3 - - + +
54A GLU* 5.2 5.6 - - + +
57A CYS* 3.9 33.0 - - + +
58A GLY* 5.9 0.2 - - - -
60A ASP* 4.0 15.3 - - - +
62A SER* 3.4 15.9 + - - +
63A VAL 3.4 0.6 - - - -
64A ALA* 1.3 78.2 - - - +
66A SER* 1.3 62.7 + - - +
69A GLY* 3.1 20.4 + - - +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 5.9 0.7 - - - +
62A SER 3.5 7.7 + - - -
63A VAL 3.1 10.3 + - - -
65A VAL* 1.3 83.0 - - - +
67A SER* 1.3 58.7 + - - +
69A GLY* 3.7 0.9 - - - -
70A GLU* 3.0 28.9 + - - +
236A VAL* 5.6 2.7 - - - +
249A LYS* 4.7 7.3 + - - -
250A PHE* 4.2 21.7 - - - -
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL 2.9 19.6 + - - -
64A ALA* 3.5 1.9 + - - -
66A SER* 1.3 71.6 + - - +
68A GLY* 1.3 60.6 + - - +
70A GLU* 3.1 10.1 + - - +
71A LEU* 2.9 31.0 + - - +
233A PHE 2.6 23.1 + - - -
234A LYS* 3.7 10.9 + - - -
235A PHE 3.4 22.0 - - - -
236A VAL* 4.1 15.9 - - - +
304A TYR* 3.8 6.8 + - - -
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Residues in contact with GLY 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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23A ALA* 5.0 1.8 - - - -
27A ILE* 3.9 15.8 - - - +
64A ALA 2.7 21.3 + - - -
67A SER* 1.3 71.1 + - - +
69A GLY* 1.3 58.3 + - - +
71A LEU* 3.1 4.8 + - - +
72A PHE* 2.8 32.2 + - - +
100A PHE* 5.6 0.2 - - - -
233A PHE* 3.4 25.3 + - - -
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Residues in contact with GLY 69 (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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23A ALA* 6.0 0.4 - - - +
26A ALA* 6.3 1.8 - - - -
27A ILE* 4.7 4.1 - - - +
30A LEU* 4.6 7.6 - - - -
54A GLU* 4.4 17.7 - - - -
65A VAL* 3.1 20.4 + - - +
66A SER 3.7 0.7 - - - -
68A GLY* 1.3 77.0 - - - +
70A GLU* 1.3 61.3 + - - +
72A PHE* 3.2 6.1 + - - +
73A LEU* 3.1 29.6 + - - +
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Residues in contact with GLU 70 (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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54A GLU* 5.2 0.4 - - - +
66A SER* 3.0 15.7 + - - +
67A SER* 3.1 11.2 + - - +
69A GLY* 1.3 76.2 - - - +
71A LEU* 1.3 62.0 - - - +
73A LEU* 3.2 11.2 + - - +
74A ARG* 3.0 42.4 + - + +
237A ARG* 3.5 30.0 + - - +
304A TYR* 3.5 19.7 - - + -
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Residues in contact with LEU 71 (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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67A SER 2.9 18.6 + - - +
68A GLY* 3.6 4.3 - - - +
70A GLU* 1.3 75.1 - - - +
72A PHE* 1.3 64.2 + - - +
74A ARG* 3.5 7.1 + - + +
75A PHE* 3.0 23.7 + - - +
100A PHE* 3.9 16.5 - - + -
232A SER 4.2 0.9 - - - +
233A PHE* 3.9 26.5 - - + +
235A PHE 4.6 0.7 - - - +
303A LEU* 3.6 44.4 - - + +
304A TYR* 3.6 46.9 - - + +
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Residues in contact with PHE 72 (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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27A ILE* 3.7 22.2 - - + -
30A LEU* 3.3 40.2 - - + -
31A LEU* 4.1 24.2 - - + -
34A LEU* 4.7 5.2 - - + -
50A THR* 5.8 0.4 - - + -
68A GLY 2.8 19.7 + - - +
69A GLY 3.2 4.9 + - - +
71A LEU* 1.3 71.6 - - - +
73A LEU* 1.3 70.9 + - + +
75A PHE* 3.1 12.2 + - + +
76A ILE* 3.4 36.1 + - + +
97A GLY* 3.4 35.7 - - - -
100A PHE* 3.5 31.6 - + + -
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Residues in contact with LEU 73 (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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50A THR* 3.4 22.7 - - + -
51A SER* 4.4 17.3 - - - +
54A GLU* 3.0 38.8 - - + +
69A GLY 3.1 10.9 + - - +
70A GLU* 3.5 9.6 - - - +
72A PHE* 1.3 91.1 - - + +
74A ARG* 1.3 64.2 + - + +
76A ILE* 3.0 31.0 + - + +
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Residues in contact with ARG 74 (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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70A GLU* 3.0 31.6 + - + +
71A LEU* 3.8 8.1 - - + +
73A LEU* 1.3 77.1 - - + +
75A PHE* 1.3 60.6 + - - +
76A ILE 3.5 5.1 + - - +
77A SER 4.7 2.3 - - - -
237A ARG* 3.4 23.6 - - - +
304A TYR* 3.2 45.4 + - - +
305A LEU* 4.1 12.9 - - - +
307A ALA 3.7 14.9 - - - +
241B LEU* 3.9 21.2 - - - +
242B ASN* 4.8 6.9 - - - +
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Residues in contact with PHE 75 (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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71A LEU 3.0 14.3 + - - +
72A PHE* 3.4 10.1 - - - +
73A LEU 3.1 0.6 - - - -
74A ARG* 1.3 77.8 - - - +
76A ILE* 1.3 62.5 + - + +
77A SER 3.3 4.4 + - - -
96A ARG* 3.3 75.9 + - + -
97A GLY* 5.1 0.7 - - - -
99A LEU* 3.8 25.8 - - + -
100A PHE* 3.7 30.7 - + + -
306A ALA* 4.1 28.5 - - + -
307A ALA* 4.6 7.2 - - + -
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Residues in contact with ILE 76 (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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34A LEU* 3.7 22.0 - - + -
50A THR* 6.2 0.9 - - + -
72A PHE* 3.4 45.5 - - + +
73A LEU* 3.0 21.5 + - + +
74A ARG 4.1 2.1 - - - +
75A PHE* 1.3 74.8 - - + +
77A SER* 1.3 74.7 + - - +
90A LYS* 5.8 0.4 - - - -
93A MSE 3.3 51.6 - - + +
96A ARG* 4.7 4.0 - - - +
97A GLY* 4.8 6.5 - - - +
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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