Contacts of the helix formed by residues 4 - 20 (chain I) in PDB entry 5GAG
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 ASN 4 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1043A C 4.2 18.8 + - - -
1044A C 4.5 6.6 + - - -
2I ALA 4.0 2.0 + - - -
3I LEU* 1.3 77.3 - - - +
5I LEU* 1.3 70.8 + - - +
6I GLN* 3.2 29.6 + - - +
7I ASP* 2.9 33.5 + - - +
8I LYS* 3.2 14.4 + - - -
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Residues in contact with LEU 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044A C 4.0 10.7 + - - +
1045A C 5.3 2.2 - - - +
1046A A 3.8 41.1 - - + +
4I ASN* 1.3 78.4 - - - +
6I GLN* 1.3 56.4 + - - +
8I LYS* 3.5 17.2 + - - +
9I GLN* 3.0 51.4 + - - +
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Residues in contact with GLN 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I ASN* 3.4 17.1 + - - +
5I LEU* 1.3 77.4 - - - +
7I ASP* 1.3 64.0 + - - +
9I GLN* 3.3 19.7 + - - +
10I ALA* 2.9 28.4 + - + +
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Residues in contact with ASP 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I ALA 4.2 3.5 - - - +
3I LEU* 3.4 29.9 - - + +
4I ASN* 2.9 38.5 + - - +
6I GLN* 1.3 81.4 - - - +
8I LYS* 1.3 58.5 + - - +
10I ALA* 3.0 10.6 + - - +
11I ILE* 2.9 34.9 + - + +
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Residues in contact with LYS 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044A C 4.3 13.9 + - - -
1045A C 3.4 8.5 + - - -
1046A A 2.5 65.0 + - - +
1047A G 4.3 4.2 + - - -
3I LEU* 4.4 11.2 + - + -
4I ASN 3.2 8.7 + - - +
5I LEU* 3.6 30.0 - - - +
7I ASP* 1.3 77.4 - - - +
9I GLN* 1.3 56.5 + - - +
11I ILE* 3.4 8.8 + - - +
12I VAL* 2.9 25.6 + - - +
56I ARG* 3.1 33.4 - - - +
59I LEU* 4.3 14.2 - - + +
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Residues in contact with GLN 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046A A 3.6 38.2 + - + +
5I LEU* 3.0 39.8 + - + +
6I GLN* 3.3 24.5 - - - +
7I ASP 3.2 0.2 - - - -
8I LYS* 1.3 74.3 - - - +
10I ALA* 1.3 64.7 + - - +
12I VAL* 3.4 4.9 + - - +
13I ALA* 3.0 23.3 + - - +
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Residues in contact with ALA 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 2.9 14.5 + - + +
7I ASP* 3.0 13.9 + - - +
9I GLN* 1.3 76.2 - - - +
11I ILE* 1.3 55.8 + - + +
13I ALA* 3.4 8.8 - - - +
14I GLU* 3.0 42.7 + - - +
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Residues in contact with ILE 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I LEU* 3.6 33.2 - - + -
7I ASP* 2.9 26.5 + - + +
8I LYS* 3.8 6.1 - - - +
10I ALA* 1.3 75.7 - - + +
12I VAL* 1.3 58.4 + - - +
13I ALA 3.1 1.6 - - - -
14I GLU* 4.0 16.2 - - - +
15I VAL* 2.9 30.0 + - - +
53I ARG* 3.2 24.0 - - - +
55I VAL* 4.4 5.6 - - + -
59I LEU* 3.7 22.7 - - + -
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Residues in contact with VAL 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046A A 3.4 31.6 - - + +
8I LYS 2.9 13.2 + - - +
9I GLN 3.8 3.6 - - - +
11I ILE* 1.3 74.4 - - - +
13I ALA* 1.3 59.8 + - - +
16I SER* 2.9 39.5 + - - +
59I LEU* 3.4 37.2 - - + +
62I ARG* 3.8 28.0 - - + +
63I ALA* 3.9 4.2 - - - +
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Residues in contact with ALA 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I GLN 3.0 14.9 + - - +
10I ALA* 3.4 13.0 - - - +
11I ILE 3.1 0.2 - - - -
12I VAL* 1.3 80.3 - - + +
14I GLU* 1.3 57.0 + - + +
16I SER* 3.8 4.4 - - - -
17I GLU* 2.9 31.2 + - - +
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Residues in contact with GLU 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I ALA* 3.0 41.3 + - - +
11I ILE* 3.2 15.3 + - - +
13I ALA* 1.3 73.3 - - + +
15I VAL* 1.3 60.7 + - - +
17I GLU* 3.3 11.8 + - - +
18I VAL* 3.0 36.3 + - + +
51I TYR* 4.5 5.2 - - - +
53I ARG* 3.9 23.7 + - - +
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Residues in contact with VAL 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ILE 2.9 14.6 + - - +
14I GLU* 1.3 75.1 - - - +
16I SER* 1.3 57.3 + - - +
18I VAL* 3.6 2.7 + - - +
19I ALA* 2.9 28.1 + - - +
51I TYR* 4.5 6.3 - - + +
53I ARG* 3.2 33.0 - - - +
55I VAL* 3.9 20.4 - - + -
59I LEU* 4.9 0.7 - - + -
60I LEU* 3.5 24.5 - - + -
63I ALA* 3.8 13.5 - - + -
82I ILE* 4.0 15.9 - - + -
84I TYR* 3.8 12.3 + - + +
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Residues in contact with SER 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 2.9 27.6 + - - +
13I ALA* 3.9 5.4 - - - -
15I VAL* 1.3 76.0 - - - +
17I GLU* 1.3 58.1 + - - +
19I ALA* 3.3 7.0 - - - +
20I LYS* 3.0 43.5 + - - +
62I ARG 4.0 4.0 + - - -
63I ALA* 3.0 27.9 + - - +
66I GLY* 4.8 6.3 - - - -
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Residues in contact with GLU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I ALA 2.9 20.0 + - - +
14I GLU* 3.3 11.0 + - - +
16I SER* 1.3 74.6 - - - +
18I VAL* 1.3 65.4 + - - +
19I ALA 3.3 0.4 + - - -
20I LYS* 4.1 21.2 + - - +
21I GLY* 3.8 13.7 + - - -
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Residues in contact with VAL 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I GLU* 3.0 17.3 + - + +
15I VAL 3.8 1.3 - - - +
17I GLU* 1.3 81.6 - - + +
19I ALA* 1.3 57.4 - - - +
21I GLY* 3.9 2.6 - - - +
22I ALA* 3.1 31.2 + - - +
51I TYR* 3.5 55.9 - - + +
84I TYR* 4.0 6.1 - - + -
86I THR* 3.6 25.4 - - + -
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Residues in contact with ALA 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I VAL 2.9 14.8 + - - +
16I SER* 3.3 11.7 - - - +
17I GLU 3.3 0.4 - - - -
18I VAL* 1.3 75.1 - - - +
20I LYS* 1.3 63.9 + - + +
21I GLY 3.1 5.4 + - - -
22I ALA 3.4 9.0 + - - +
63I ALA 4.4 9.4 - - - +
66I GLY 5.8 1.6 - - - +
67I THR 4.8 2.8 - - - +
68I PRO* 5.5 0.9 - - - +
69I PHE* 3.0 31.6 - - + -
84I TYR* 3.0 30.3 - - - +
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Residues in contact with LYS 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I SER* 3.0 31.0 + - - +
17I GLU* 4.2 23.2 - - - +
19I ALA* 1.3 75.8 - - + +
21I GLY* 1.3 56.0 - - - +
22I ALA 3.6 0.8 - - - +
66I GLY* 4.0 20.4 - - - +
67I THR 4.7 5.8 - - - +
68I PRO* 6.0 1.1 - - - -
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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
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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