Contacts of the helix formed by residues 9 - 32 (chain P) in PDB entry 3E8E
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 GLY 9 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P LYS* 1.3 76.9 - - - +
10P SEP 1.3 64.5 + - - +
11P GLU 3.1 3.1 - - - -
12P GLN* 2.9 29.6 + - - +
13P GLU* 3.6 8.1 + - - +
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Residues in contact with SEP 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P LYS* 3.0 29.3 + - - +
8P LYS* 4.3 3.0 - - - +
9P GLY* 1.3 75.6 + - - +
11P GLU* 1.3 53.7 + - - -
13P GLU* 3.2 7.5 + - - +
14P SER* 2.7 45.3 + - - -
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Residues in contact with GLU 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P LYS* 3.2 34.8 + - - +
8P LYS 3.6 14.3 + - - +
9P GLY 3.0 1.4 + - - -
10P SEP 1.3 80.5 + - - -
12P GLN* 1.3 57.4 + - + +
14P SER* 3.6 9.0 - - - -
15P VAL* 2.9 39.7 + - + +
301P ASP* 5.5 0.3 - - - +
303P ILE* 3.1 39.6 - - + +
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Residues in contact with GLN 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P LYS 5.2 1.8 - - - +
9P GLY* 2.9 19.5 + - - +
11P GLU* 1.3 80.5 - - + +
13P GLU* 1.3 62.3 + - + +
15P VAL* 3.9 5.5 + - - +
16P LYS* 3.8 14.0 + - - +
289P ASN* 3.0 37.7 + - - +
293P ASN* 4.2 18.0 + - - +
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Residues in contact with GLU 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P GLY 3.6 7.3 + - - +
10P SEP 3.2 7.4 + - - +
12P GLN* 1.3 78.2 - - + +
14P SER* 1.3 60.2 + - - +
15P VAL 3.3 0.9 - - - -
16P LYS* 3.4 15.2 + - + +
17P GLU* 3.2 33.6 + - - +
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Residues in contact with SER 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P SEP 2.7 33.5 + - - -
11P GLU* 3.3 11.2 + - - -
13P GLU* 1.3 71.0 - - - +
15P VAL* 1.3 64.4 + - - +
17P GLU* 3.7 12.8 + - - +
18P PHE* 3.4 18.9 + - - +
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Residues in contact with VAL 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P GLU* 2.9 24.9 + - + +
12P GLN* 4.0 6.1 - - - +
14P SER* 1.3 76.8 - - - +
16P LYS* 1.3 58.2 + - - +
18P PHE* 3.3 10.7 + - + +
19P LEU* 2.9 41.9 + - + +
155P GLU* 3.8 27.6 - - - +
292P LYS* 4.3 15.9 - - - +
303P ILE* 6.2 3.6 - - + -
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Residues in contact with LYS 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P GLN 3.8 7.2 + - - +
13P GLU* 3.4 20.3 + - + +
14P SER 3.4 0.2 - - - -
15P VAL* 1.3 80.2 - - - +
17P GLU* 1.3 62.3 + - + +
19P LEU* 3.2 10.4 + - + +
20P ALA* 3.0 25.8 + - + +
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Residues in contact with GLU 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P GLU* 3.2 16.6 + - - +
14P SER* 3.9 12.5 - - - +
15P VAL 3.3 0.4 - - - -
16P LYS* 1.3 78.2 - - + +
18P PHE* 1.3 62.5 + - - +
20P ALA* 3.5 5.3 + - - +
21P LYS* 3.1 28.2 + - - +
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Residues in contact with PHE 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P SER 3.4 10.5 + - - +
15P VAL* 3.3 13.6 + - + +
16P LYS 3.3 0.4 - - - -
17P GLU* 1.3 79.5 - - - +
19P LEU* 1.3 72.5 + - + +
21P LYS* 3.4 6.6 + - + +
22P ALA* 2.9 35.9 + - + +
99P ASN 5.4 2.5 - - - -
100P PHE* 3.9 30.1 - + - -
156P TYR* 4.3 15.5 - + + -
306P TYR* 3.2 33.4 - + - -
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Residues in contact with LEU 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P VAL* 2.9 37.2 + - + +
16P LYS* 3.2 9.1 + - + +
18P PHE* 1.3 92.1 - - + +
20P ALA* 1.3 57.1 + - - +
22P ALA* 3.7 4.9 - - + +
23P LYS* 3.2 25.1 + - - +
155P GLU* 4.2 19.3 - - + +
156P TYR* 4.2 20.4 - - + +
159P SER* 3.5 36.6 + - - +
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Residues in contact with ALA 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P LYS* 3.0 17.5 + - + +
17P GLU* 3.8 7.0 - - - +
19P LEU* 1.3 73.2 - - - +
21P LYS* 1.3 64.9 + - - +
22P ALA 3.1 1.1 - - - -
23P LYS* 3.2 7.7 + - - +
24P GLU* 3.1 29.3 + - - +
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Residues in contact with LYS 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P GLU 3.1 16.2 + - - +
18P PHE* 3.7 7.9 - - + +
20P ALA* 1.3 77.8 - - - +
22P ALA* 1.3 61.3 + - - +
24P GLU* 3.4 24.2 + - + +
25P ASP* 3.2 22.0 + - - +
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Residues in contact with ALA 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P PHE* 2.9 27.2 + - + +
19P LEU* 3.7 11.0 - - + +
20P ALA 3.1 0.4 - - - -
21P LYS* 1.3 75.4 - - - +
23P LYS* 1.3 59.8 + - - +
25P ASP* 3.5 5.6 + - - +
26P PHE* 3.0 28.2 + - - +
156P TYR* 3.9 30.5 + - + -
160P LEU* 4.1 6.1 - - + +
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Residues in contact with LYS 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLU* 3.2 29.3 + - - +
32L ASN* 4.7 5.7 + - - +
19P LEU 3.2 14.0 + - - +
20P ALA* 3.2 8.5 + - - +
22P ALA* 1.3 75.2 - - - +
24P GLU* 1.3 65.6 + - + +
26P PHE* 3.7 1.7 - - + +
27P LEU* 3.0 53.2 + - + +
159P SER 4.2 16.8 - - - +
160P LEU* 3.5 21.3 - - + +
161P ASP* 4.4 5.8 - - - -
190P ARG* 4.3 11.4 - - - +
192P LYS* 4.9 1.3 - - - +
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Residues in contact with GLU 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P ALA* 3.1 17.4 + - - +
21P LYS* 3.5 31.3 + - + +
22P ALA 3.3 0.2 - - - -
23P LYS* 1.3 77.2 - - - +
25P ASP* 1.3 61.8 + - - +
27P LEU* 4.0 6.2 - - - +
28P LYS* 3.1 46.5 + - - +
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Residues in contact with ASP 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P LYS 3.2 12.7 + - - +
22P ALA* 4.1 5.4 - - - +
24P GLU* 1.3 77.4 - - - +
26P PHE* 1.3 64.0 + - - +
28P LYS* 3.7 13.6 + - - +
29P LYS* 3.1 57.2 + - - +
97P ALA 4.8 0.4 - - - -
99P ASN* 4.7 10.2 + - - +
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Residues in contact with PHE 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P ALA 3.0 18.1 + - - +
23P LYS* 3.7 4.7 - - + +
24P GLU 3.3 0.2 - - - -
25P ASP* 1.3 77.4 - - - +
27P LEU* 1.3 65.3 + - + +
29P LYS* 3.1 4.2 + - - +
30P TRP* 2.7 70.3 + + - +
94P ILE* 4.6 1.8 - - - -
97P ALA* 3.5 40.4 - - + +
98P VAL* 4.2 4.9 - - + -
156P TYR* 5.1 0.9 - - - +
160P LEU* 3.7 32.5 - - + -
162P LEU* 4.0 22.2 - - + -
190P ARG* 3.4 37.7 - - - -
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Residues in contact with LEU 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLU* 3.4 36.1 - - + +
23P LYS* 3.0 47.0 + - + +
24P GLU* 4.0 5.4 - - - +
26P PHE* 1.3 92.3 - - + +
28P LYS* 1.3 56.7 + - - +
30P TRP* 3.6 13.4 - - + +
31P GLU* 2.9 31.5 + - - +
190P ARG* 4.2 7.9 - - - +
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Residues in contact with LYS 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLU* 3.1 38.1 + - - +
25P ASP* 3.8 15.7 - - - +
26P PHE 3.3 0.2 - - - -
27P LEU* 1.3 76.0 - - - +
29P LYS* 1.3 62.0 + - + +
31P GLU* 3.7 6.2 - - - +
32P ASN* 3.5 22.7 + - - +
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Residues in contact with LYS 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P ASP* 3.1 42.5 + - - +
26P PHE 3.1 5.1 + - - +
28P LYS* 1.3 74.4 - - + +
30P TRP* 1.3 63.4 - - - +
31P GLU 3.1 2.0 - - - -
32P ASN 3.1 21.4 - - - +
96P GLN* 3.1 35.5 + - - +
97P ALA* 3.6 26.8 + - - +
98P VAL 4.3 3.2 + - - -
99P ASN* 4.0 23.8 - - - +
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Residues in contact with TRP 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLU* 5.4 1.3 - - - -
26P PHE* 2.7 46.6 + + + +
27P LEU* 3.6 20.6 - - + +
29P LYS* 1.3 73.3 - - - +
31P GLU* 1.3 62.6 + - - +
33P PRO* 4.4 4.5 - - - +
90P ASN* 5.8 4.5 - - - -
93P ARG* 3.4 95.8 + - + +
94P ILE* 3.8 17.5 - - + -
96P GLN* 4.2 2.9 + - - +
97P ALA* 3.9 4.0 - - + +
190P ARG* 3.9 42.1 - - + +
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Residues in contact with GLU 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L LYS* 3.4 12.3 + - - +
27L LEU* 3.4 30.3 - - + +
30L TRP* 5.7 0.3 - - - -
190L ARG* 3.2 34.9 + - - -
192L LYS* 3.0 36.4 + - - +
27P LEU 2.9 17.1 + - - +
28P LYS* 3.7 8.7 - - - +
29P LYS 3.1 0.2 - - - -
30P TRP* 1.3 79.9 - - - +
32P ASN* 1.3 71.3 + - - +
33P PRO* 3.3 9.7 - - - +
93P ARG* 5.6 0.2 - - - +
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Residues in contact with ASN 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L LYS* 4.8 4.6 + - - +
192L LYS* 3.5 16.4 + - - +
28P LYS 3.5 9.5 + - - +
29P LYS* 3.1 16.1 + - - +
31P GLU* 1.3 95.3 - - - +
33P PRO* 1.4 63.1 - - - +
34P ALA* 3.9 2.4 + - - +
96P GLN* 4.3 1.2 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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