Contacts of the helix formed by residues 6 - 24 (chain L) in PDB entry 4GGF
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 6 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K THR* 3.3 26.7 - - - -
41K GLU* 2.7 30.9 + - - -
4L LYS 3.4 2.9 + - - -
5L MET* 1.3 76.4 - - - +
7L GLN* 1.3 60.4 + - - +
8L LEU 3.3 1.9 + - - -
9L GLU* 2.9 26.9 + - - +
10L ARG* 2.9 30.9 + - - +
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Residues in contact with GLN 7 (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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11K SER* 2.7 34.5 + - - +
14K ASP* 4.2 12.7 + - - +
15K VAL* 3.4 18.9 - - + +
18K LYS* 2.5 37.2 + - - +
41K GLU* 3.7 9.3 + - - +
6L SER* 1.3 73.7 - - - +
8L LEU* 1.3 63.1 + - - +
10L ARG* 3.2 32.3 + - - +
11L ASN* 2.9 29.6 + - - +
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Residues in contact with LEU 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ILE* 4.0 33.4 - - + -
15K VAL* 4.1 12.5 - - + +
37K LEU* 5.0 3.4 - - + -
41K GLU* 3.3 35.8 + - + +
71K PHE* 4.4 22.7 - - + -
74K LEU* 5.3 0.2 - - + -
75K VAL* 4.4 9.4 - - + -
78K MET* 3.8 32.3 - - + -
6L SER* 3.2 0.8 - - - +
7L GLN* 1.3 78.6 - - - +
9L GLU* 1.3 63.6 + - - +
11L ASN* 3.1 7.7 + - - +
12L ILE* 3.0 33.0 + - + +
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Residues in contact with GLU 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K GLU 3.7 9.3 - - - +
42K SER 4.8 0.9 - - - -
43K PRO* 3.3 43.3 - - + +
78K MET* 4.6 4.5 - - + -
4L LYS 4.4 2.3 - - - +
5L MET* 3.4 27.8 - - + +
6L SER* 2.9 43.5 + - - +
8L LEU* 1.3 79.2 - - - +
10L ARG* 1.3 56.0 + - - +
12L ILE* 3.4 9.1 + - - +
13L GLU* 2.9 28.8 + - - +
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Residues in contact with ARG 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L MET* 3.2 44.4 + - + -
6L SER* 2.9 15.1 + - - +
7L GLN* 3.6 39.3 - - - +
9L GLU* 1.3 76.5 - - - +
11L ASN* 1.3 61.8 + - - +
13L GLU* 3.3 8.6 + - - +
14L THR* 2.9 31.5 + - - -
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Residues in contact with ASN 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ALA* 3.6 25.1 - - - +
11K SER* 2.7 53.3 + - - -
12K ILE* 3.5 15.3 - - + +
15K VAL* 4.1 0.6 - - - +
7L GLN* 2.9 26.7 + - - +
8L LEU* 3.1 8.9 + - - +
10L ARG* 1.3 77.5 - - - +
12L ILE* 1.3 64.1 + - - +
14L THR* 3.2 6.2 + - - -
15L ILE* 3.1 27.5 + - - +
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Residues in contact with ILE 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ILE* 5.1 1.1 - - + -
75K VAL* 4.2 16.8 - - + +
78K MET* 3.5 45.1 - - + -
79K GLY* 3.8 24.0 - - - +
82K ALA* 4.0 10.3 - - + -
8L LEU* 3.0 29.3 + - + +
9L GLU* 3.7 6.1 - - - +
11L ASN* 1.3 74.2 - - - +
13L GLU* 1.3 59.5 + - - +
15L ILE* 3.1 15.8 + - + +
16L ILE* 2.9 41.7 + - + +
76L PHE* 5.9 0.4 - - + -
80L ILE* 6.2 1.1 - - + -
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Residues in contact with GLU 13 (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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5L MET* 3.5 30.4 - - + +
9L GLU 2.9 17.8 + - - +
10L ARG* 3.5 11.4 - - - +
11L ASN 3.3 0.2 - - - -
12L ILE* 1.3 77.1 - - - +
14L THR* 1.3 50.7 + - - +
16L ILE* 3.2 9.7 + - + +
17L ASN* 2.8 60.1 + - - +
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Residues in contact with THR 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K GLU* 3.8 31.9 - - + +
5K LEU* 4.1 7.6 - - - +
8K ALA* 3.9 12.2 - - + +
10L ARG 2.9 15.5 + - - -
11L ASN* 3.5 9.7 + - - -
12L ILE 3.2 0.2 - - - -
13L GLU* 1.3 75.3 - - - +
15L ILE* 1.3 59.7 + - - +
17L ASN* 3.5 7.2 + - - +
18L THR* 2.7 42.4 + - - +
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Residues in contact with ILE 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K LEU* 3.9 22.4 - - + -
8K ALA* 4.8 2.0 - - + -
9K LEU* 3.7 25.4 - - + -
12K ILE* 3.9 17.0 - - + -
75K VAL* 5.6 2.9 - - + -
11L ASN 3.1 14.3 + - - +
12L ILE* 3.1 15.8 + - + +
14L THR* 1.3 75.6 - - - +
16L ILE* 1.3 64.2 + - - +
18L THR* 3.3 2.3 + - - -
19L PHE* 3.0 22.2 + - - +
76L PHE* 3.9 23.1 - - + -
79L PHE* 4.2 6.5 - - + -
80L ILE* 4.9 9.9 - - + -
83L MET* 3.8 29.2 - - + -
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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
----------------------------------------------------------
79K GLY 4.0 1.3 - - - +
82K ALA* 3.6 20.4 - - + +
83K HIS* 3.4 33.0 - - + +
86K SER* 4.4 12.1 - - - +
12L ILE* 2.9 24.6 + - + +
13L GLU* 3.7 9.0 - - - +
15L ILE* 1.3 75.3 - - - +
17L ASN* 1.3 69.5 + - - +
19L PHE* 3.4 3.6 + - - +
20L HIS* 3.0 48.3 + - + +
76L PHE* 3.6 27.4 - - + -
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Residues in contact with ASN 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L GLU* 2.8 46.2 + - - +
14L THR* 3.9 7.2 - - - +
16L ILE* 1.3 79.4 - - - +
18L THR* 1.3 57.1 + - - +
20L HIS* 3.3 7.9 + - - +
21L GLN* 2.9 47.8 + - - +
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Residues in contact with THR 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K LEU* 4.0 27.9 + - + +
14L THR* 2.7 31.9 + - - +
15L ILE 3.9 2.9 - - - -
16L ILE 3.2 0.2 - - - -
17L ASN* 1.3 72.3 - - - +
19L PHE* 1.3 67.1 + - - +
21L GLN* 3.4 17.6 + - - +
22L TYR* 3.2 30.7 - - + -
40L LEU* 4.2 7.2 - - + -
44L ASP* 3.6 32.5 - - + +
79L PHE* 6.0 0.7 - - - -
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Residues in contact with PHE 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K HIS* 4.9 0.2 - + - -
15L ILE 3.0 13.8 + - - +
16L ILE 3.5 7.4 - - - +
18L THR* 1.3 79.5 - - - +
20L HIS* 1.3 70.5 + + - +
22L TYR* 3.3 1.2 + - - -
23L SER* 2.9 36.6 + - - -
30L ASP* 3.5 31.0 - - - -
31L THR* 4.2 3.8 - - - -
32L LEU* 3.6 35.6 - - + +
40L LEU* 4.2 9.3 - - - +
74L LEU 3.5 13.0 - - - -
75L SER 3.8 3.6 - - - -
76L PHE* 3.4 49.6 - + + -
79L PHE* 3.7 21.9 - + + -
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Residues in contact with HIS 20 (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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83K HIS* 3.4 4.0 + + - -
86K SER* 3.6 17.3 - - - -
87K HIS* 3.0 16.4 + + - -
16L ILE* 3.0 34.6 + - + +
17L ASN* 3.3 8.4 + - - +
19L PHE* 1.3 83.5 - + - +
21L GLN* 1.3 66.5 + - + +
22L TYR 3.2 0.7 + - - -
23L SER* 3.5 11.1 + - - -
24L VAL* 3.3 26.9 + - - +
29L PRO 4.9 2.7 - - - -
30L ASP* 3.3 6.3 - - - -
201L MN 2.3 35.7 + - - -
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Residues in contact with GLN 21 (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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17L ASN* 2.9 40.9 + - - +
18L THR* 3.6 21.4 + - - +
19L PHE 3.3 0.4 - - - -
20L HIS* 1.3 76.3 - - - +
22L TYR* 1.3 71.7 + - + +
24L VAL* 3.5 15.7 - - - +
25L LYS* 3.5 15.7 - - - -
44L ASP* 4.9 1.7 - - - +
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Residues in contact with TYR 22 (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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18L THR* 3.2 25.6 - - + -
19L PHE 3.3 1.5 + - - +
20L HIS 3.1 0.2 - - - -
21L GLN* 1.3 87.8 + - + +
23L SER* 1.3 65.7 + - - +
24L VAL 3.1 2.2 - - - -
25L LYS* 3.1 22.1 + - + +
32L LEU* 3.7 17.9 - - + -
36L GLU* 3.0 28.8 - - + +
39L GLU* 3.5 44.0 - - + -
40L LEU* 3.6 31.6 - - + -
43L LYS* 3.7 18.3 - - + +
44L ASP* 2.6 31.8 + - - -
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Residues in contact with SER 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L PHE* 2.9 27.6 + - - -
20L HIS* 3.4 25.7 + - - -
22L TYR* 1.3 73.1 - - - +
24L VAL* 1.3 58.3 + - - +
26L LEU 3.8 0.2 - - - +
28L HIS 3.0 8.8 - - - +
29L PRO* 2.7 20.7 + - - +
30L ASP* 3.8 0.2 - - - -
31L THR 3.4 29.8 - - - -
32L LEU* 3.5 7.1 - - - +
36L GLU* 3.0 2.7 - - - +
205L CA 2.3 26.3 - - - -
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Residues in contact with VAL 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L HIS* 3.3 17.4 + - + +
21L GLN* 3.5 14.4 - - - +
23L SER* 1.3 80.7 + - - +
25L LYS* 1.3 71.4 + - + +
26L LEU 3.5 1.1 + - - -
27L GLY 5.4 0.9 - - - +
29L PRO* 3.5 28.6 - - + +
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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