Contacts of the helix formed by residues 3 - 20 (chain L) in PDB entry 3G5G
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 3 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K ILE* 5.1 0.2 - - - +
51K LYS* 4.1 27.8 - - - +
54K GLU* 2.8 24.4 + - - -
2L GLU* 1.3 71.2 - - - +
4L PHE* 1.3 63.0 + - - +
5L LEU* 4.4 0.2 - - - +
6L LEU* 3.2 30.6 + - - +
7L SER* 3.3 21.3 + - - -
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Residues in contact with PHE 4 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K GLU* 3.7 11.8 + - - +
64K ASP* 3.8 22.0 - - - -
2L GLU 3.5 5.8 + - - +
3L SER* 1.3 70.8 + - - +
5L LEU* 1.3 71.6 + - - +
7L SER* 2.9 21.9 + - - -
8L LYS* 3.1 47.0 + - + +
75L ILE* 4.4 22.2 - - + -
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Residues in contact with LEU 5 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K ILE* 3.7 29.4 - - + +
53K LEU* 4.5 8.1 - - + -
54K GLU* 3.1 22.2 + - + +
57K MET* 3.7 24.2 - - + -
64K ASP* 4.5 9.9 - - - +
68K PHE* 3.8 34.5 - - + -
3L SER 3.4 0.2 - - - -
4L PHE* 1.3 86.0 - - + +
6L LEU* 1.3 57.6 + - - +
8L LYS* 3.1 6.9 + - + +
9L VAL* 2.9 30.1 + - + +
71L LEU* 4.4 7.2 - - + -
75L ILE* 4.2 17.5 - - + -
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Residues in contact with LEU 6 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K ILE* 3.8 18.8 - - + +
51K LYS* 4.0 17.0 - - + -
3L SER* 3.2 23.4 + - - +
5L LEU* 1.3 77.6 - - - +
7L SER* 1.3 57.6 + - - +
9L VAL* 3.1 3.0 + - + +
10L SER* 2.9 33.1 + - - -
41L ILE* 5.7 0.4 - - + +
45L SER* 3.1 35.7 - - - +
46L ARG 3.7 16.6 - - - +
47L ASN* 3.9 17.0 - - - +
48L LEU* 3.9 24.9 - - + -
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Residues in contact with SER 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L SER 3.3 10.3 + - - -
4L PHE* 2.9 19.6 + - - -
6L LEU* 1.3 78.9 - - - +
8L LYS* 1.3 71.1 + - - +
10L SER* 3.7 7.3 + - - -
11L PHE* 3.1 26.0 + - - +
45L SER* 5.9 2.9 - - - -
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Residues in contact with LYS 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L PHE* 3.4 44.2 - - + +
5L LEU* 3.1 8.8 + - - +
7L SER* 1.3 87.9 + - - +
9L VAL* 1.3 64.9 + - - +
11L PHE* 3.3 7.3 + - + +
12L VAL* 3.1 27.0 + - - +
71L LEU* 3.6 20.4 - - + -
74L GLU* 4.1 35.3 + - + +
75L ILE* 3.8 19.0 + - + +
77L LYS 5.6 2.6 + - - -
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Residues in contact with VAL 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K ILE* 4.5 20.9 - - + -
68K PHE* 5.8 1.3 - - + -
5L LEU* 2.9 19.7 + - + +
6L LEU* 3.1 9.4 + - - +
8L LYS* 1.3 77.5 - - - +
10L SER* 1.3 61.7 + - - +
12L VAL* 3.3 3.1 + - - +
13L ILE* 3.2 30.2 + - + +
48L LEU* 3.9 27.6 - - + -
53L LEU* 4.4 17.3 - - + -
67L PHE* 4.0 9.6 - - + -
68L PHE* 6.3 0.7 - - + -
71L LEU* 4.3 25.1 - - + -
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Residues in contact with SER 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L LEU* 2.9 22.1 + - - -
7L SER* 3.7 9.4 + - - -
8L LYS 3.4 0.2 - - - -
9L VAL* 1.3 71.6 - - - +
11L PHE* 1.3 61.1 + - - +
13L ILE* 3.7 12.0 - - - +
14L LYS* 3.1 27.4 + - - +
41L ILE* 3.1 40.2 + - - -
42L GLU* 4.4 11.7 + - - +
45L SER* 6.1 0.2 - - - -
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Residues in contact with PHE 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L SER 3.1 20.0 + - - +
8L LYS* 3.5 7.2 - - + +
10L SER* 1.3 77.7 + - - +
12L VAL* 1.3 62.4 + - + +
14L LYS* 3.4 10.7 + - + +
15L LYS* 2.9 39.4 + - + +
74L GLU* 2.7 46.7 - - + -
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Residues in contact with VAL 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L LYS 3.1 16.2 + - - +
9L VAL* 3.3 4.2 + - - +
11L PHE* 1.3 77.9 - - + +
13L ILE* 1.3 56.3 + - - +
15L LYS* 3.6 5.2 - - + +
16L ILE* 3.0 43.8 + - + +
67L PHE* 3.5 31.0 - - + +
70L MET* 4.1 21.1 - - + +
71L LEU* 4.0 24.9 - - + +
74L GLU* 4.0 21.5 - - + +
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Residues in contact with ILE 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L VAL* 3.2 32.9 + - + +
10L SER* 3.7 7.4 - - - +
12L VAL* 1.3 73.8 - - - +
14L LYS* 1.3 59.5 + - - +
16L ILE* 4.0 0.5 - - - -
17L ARG* 3.0 27.4 + - - +
27L LEU* 4.1 20.0 - - + -
38L ILE* 6.0 0.9 - - + -
41L ILE* 4.0 24.7 - - + -
42L GLU* 4.0 18.8 - - + +
48L LEU* 4.6 2.9 - - + -
53L LEU* 4.4 6.7 - - + -
56L ILE* 4.0 31.0 - - + -
60L LEU* 4.2 8.2 - - + +
67L PHE* 4.0 16.4 - - + -
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Residues in contact with LYS 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F GLU* 3.2 32.7 + - - +
10L SER 3.1 15.6 + - - +
11L PHE* 3.7 10.3 - - + +
13L ILE* 1.3 76.8 - - - +
15L LYS* 1.3 67.5 + - - +
17L ARG* 3.2 12.8 + - - +
18L LEU* 3.0 44.3 + - + +
42L GLU* 3.5 43.3 - - + +
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Residues in contact with LYS 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L PHE* 2.9 28.0 + - + +
12L VAL* 3.6 6.7 - - + +
14L LYS* 1.3 78.4 - - - +
16L ILE* 1.3 58.3 + - - +
18L LEU* 3.4 8.6 + - - +
19L GLU* 3.0 49.4 + - + +
70L MET* 3.5 22.8 - - + +
74L GLU* 4.5 19.3 + - - +
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Residues in contact with ILE 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L VAL* 3.0 28.0 + - + +
15L LYS* 1.3 73.0 - - - +
17L ARG* 1.3 67.6 + - - +
19L GLU* 3.3 11.1 + - - +
20L LYS* 2.9 47.9 + - + +
60L LEU* 3.9 22.9 - - + -
62L VAL* 4.3 18.8 - - + -
67L PHE* 3.6 30.3 - - + -
70L MET* 3.6 29.2 - - + -
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Residues in contact with ARG 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L ILE 3.0 20.1 + - - +
14L LYS* 3.2 16.9 + - - +
16L ILE* 1.3 79.7 - - - +
18L LEU* 1.3 79.2 + - - +
20L LYS* 3.4 3.9 + - - +
21L GLY 3.2 4.0 + - - -
22L MET* 2.8 74.9 + - + +
23L THR* 3.5 26.4 - - - +
24L GLN* 3.5 20.3 - - - +
27L LEU* 4.0 18.2 - - + -
42L GLU* 2.8 40.7 + - - -
60L LEU* 3.7 15.4 - - + +
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Residues in contact with LEU 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L LYS* 3.0 37.8 + - + +
15L LYS* 3.8 7.2 - - - +
17L ARG* 1.3 101.9 - - - +
19L GLU* 1.3 61.5 + - - +
21L GLY* 2.9 21.1 + - - -
22L MET 4.8 1.8 - - - +
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Residues in contact with GLU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L LYS* 3.0 45.4 + - + +
16L ILE* 3.5 20.9 - - + +
18L LEU* 1.3 77.1 - - - +
20L LYS* 1.3 68.1 + - + +
21L GLY* 3.3 1.0 + - - -
70L MET* 4.5 8.8 - - - +
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Residues in contact with LYS 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L ILE* 2.9 33.5 + - + +
17L ARG 3.8 4.3 - - - +
19L GLU* 1.3 78.8 - - - +
21L GLY* 1.3 61.5 + - - +
22L MET* 3.5 22.7 + - + +
60L LEU* 3.3 20.7 + - + +
61L GLU* 3.3 28.5 + - + +
62L VAL* 4.3 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
------------------------------------------------------------
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