Contacts of the helix formed by residues 68 - 79 (chain P) in PDB entry 1E3C
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 LEU 68 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66P VAL* 3.2 2.8 + - + -
67P SER* 1.3 84.6 - - - +
69P SER* 1.3 62.4 + - - +
71P PRO* 3.3 17.4 - - + +
72P SER* 3.1 26.7 + - - -
90P GLY* 3.8 28.5 - - - +
91P VAL* 4.1 9.4 - - + -
282P ASN* 3.3 9.6 - - - -
302P LYS* 4.3 17.9 - - - +
303P GLY* 4.5 6.7 - - - -
378P SER* 3.6 38.8 - - - +
379P TYR* 5.6 0.7 - - + -
405P HIS* 4.4 17.3 - - + +
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Residues in contact with SER 69 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P LEU* 1.3 72.2 - - - +
70P THR* 1.3 62.0 + - - +
72P SER* 3.7 0.7 - - - -
73P ARG* 2.8 61.0 + - - +
91P VAL* 4.1 4.9 - - - +
123P LYS* 3.2 9.2 - - - -
125P HIS* 2.8 30.5 + - - -
281P ASP* 3.6 10.8 - - - -
282P ASN* 3.4 3.0 + - - -
302P LYS* 5.6 1.6 - - - +
603P MG 3.4 15.4 - - - -
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Residues in contact with THR 70 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P SER* 1.3 76.4 - - - +
71P PRO* 1.3 77.5 - - + +
73P ARG* 3.0 3.5 + - - +
74P ALA* 2.8 20.4 + - - +
87P MET* 3.2 39.3 - - + +
90P GLY 4.5 0.7 - - - +
91P VAL* 3.5 12.3 - - - +
92P LEU* 3.3 29.2 + - + +
125P HIS* 3.2 33.6 + - - +
126P LEU* 3.8 1.5 - - + +
477P VAL* 6.0 2.0 - - + -
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Residues in contact with PRO 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P VAL* 3.7 22.4 - - + -
68P LEU* 3.3 26.2 - - + +
70P THR* 1.3 96.8 - - + +
72P SER* 1.3 57.5 + - - +
74P ALA* 3.3 1.6 + - - +
75P ALA* 3.0 22.5 + - - +
82P PRO* 3.1 32.5 - - + +
87P MET* 3.6 22.2 - - + +
90P GLY 3.8 16.8 - - - +
91P VAL* 4.4 0.2 - - + -
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Residues in contact with SER 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P PHE* 3.8 6.8 - - - -
64P VAL* 3.9 10.6 - - - +
65P PRO* 5.3 4.5 - - - -
66P VAL* 3.8 10.3 + - - -
68P LEU 3.1 20.6 + - - -
69P SER 3.8 2.5 - - - -
70P THR 3.2 0.6 - - - -
71P PRO* 1.3 74.0 - - - +
73P ARG* 1.3 66.4 + - - +
75P ALA* 3.1 7.8 + - - +
76P LEU* 3.0 22.9 + - - +
281P ASP* 2.5 39.6 + - - +
333P SER* 5.1 1.7 + - - -
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Residues in contact with ARG 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P PHE* 3.7 29.0 + - + -
28P ALA 4.2 3.6 + - - -
29P ASP* 3.2 23.0 + - - +
69P SER* 2.8 41.0 + - - +
70P THR 3.6 2.5 - - - +
72P SER* 1.3 72.6 - - - +
74P ALA* 1.4 61.3 + - - +
76P LEU* 3.4 1.9 + - - +
77P LEU* 3.2 27.0 + - - +
123P LYS* 3.5 34.3 + - - +
124P TRP 3.6 16.8 - - - +
125P HIS* 3.9 5.8 - - - -
126P LEU* 4.0 19.7 - - + -
222P TYR* 4.0 8.1 + - - +
224P ALA* 3.8 16.2 - - - +
225P SER 4.6 3.0 + - - -
281P ASP* 3.0 26.1 + - + +
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Residues in contact with ALA 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P THR 2.8 15.7 + - - +
71P PRO 3.6 7.4 - - - +
73P ARG* 1.4 73.2 - - - +
75P ALA* 1.3 63.4 + - - +
77P LEU* 3.3 1.6 + - - -
78P THR* 2.8 32.9 + - - +
80P ARG 4.7 0.2 - - - -
82P PRO* 4.8 2.0 - - + -
85P MET* 4.4 7.6 - - - -
87P MET* 3.9 29.8 - - + -
100P LEU* 4.2 11.9 - - + -
126P LEU* 3.7 14.0 - - + +
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Residues in contact with ALA 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P PRO* 4.0 22.0 - - + -
71P PRO 3.0 16.7 + - - +
72P SER 3.1 3.8 + - - +
74P ALA* 1.3 78.4 - - - +
76P LEU* 1.3 61.8 + - - +
79P GLY* 2.9 24.8 + - - -
80P ARG 3.4 22.2 - - - +
82P PRO* 4.0 3.6 - - + +
333P SER* 4.1 3.6 - - - +
334P LEU* 3.5 19.8 - - + +
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Residues in contact with LEU 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P LEU* 4.4 14.1 - - + -
27P PHE* 3.8 45.5 - - + -
72P SER 3.0 15.6 + - - +
73P ARG* 3.8 3.4 - - - +
75P ALA* 1.3 79.2 - - - +
77P LEU* 1.3 70.7 + - + +
79P GLY 3.8 4.0 + - - -
107P VAL* 4.3 6.1 - - + +
222P TYR* 3.9 22.4 - - + +
279P THR* 5.2 0.2 - - - +
333P SER* 3.8 29.5 + - - +
336P LEU* 3.6 33.3 - - + +
337P LEU 4.5 9.2 + - - -
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Residues in contact with LEU 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P LEU* 5.4 2.0 - - + -
73P ARG 3.2 11.7 + - - +
74P ALA* 4.2 2.0 - - - +
76P LEU* 1.3 88.2 - - + +
78P THR* 1.3 67.4 + - + +
100P LEU* 5.2 1.8 - - + -
106P THR* 3.2 16.7 - - + -
107P VAL* 2.8 49.5 + - + +
124P TRP* 3.7 20.6 - - + -
126P LEU* 3.3 31.9 - - + -
141P PHE* 4.8 10.8 - - + -
220P PHE* 5.6 0.4 - - + -
222P TYR* 4.3 35.4 - - + +
337P LEU* 3.7 2.6 - - - +
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Residues in contact with THR 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74P ALA 2.8 18.2 + - - +
77P LEU* 1.3 83.5 - - + +
79P GLY* 1.4 58.9 + - - +
80P ARG* 3.0 25.0 + - - -
85P MET* 3.4 21.8 - - + +
100P LEU* 4.2 17.5 - - + -
104P GLU* 4.0 30.5 - - + -
105P VAL 3.8 15.5 - - - +
106P THR* 4.8 0.9 - - - -
337P LEU* 3.7 15.0 - - - +
353P LEU* 3.8 6.4 - - - +
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Residues in contact with GLY 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75P ALA 2.9 14.4 + - - -
76P LEU 3.8 3.4 + - - -
77P LEU 3.7 1.6 - - - -
78P THR* 1.4 76.4 - - - +
80P ARG* 1.3 59.1 + - - +
334P LEU* 3.7 24.9 - - - +
337P LEU* 4.3 11.7 - - - +
338P PRO* 4.8 1.6 - - - -
353P LEU* 3.7 4.7 - - - +
354P ASP* 2.8 28.1 + - - +
355P GLY 3.9 2.8 + - - -
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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
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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