Contacts of the helix formed by residues 13 - 30 (chain A) in PDB entry 5GUF
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 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA 5.3 0.6 + - - -
12A ASP* 1.3 85.4 + - - +
14A ILE* 1.3 58.8 + - + +
15A LEU* 3.2 14.0 + - - +
16A GLU* 3.0 52.9 + - - +
17A ALA 3.0 23.0 + - - -
145A VAL* 3.6 13.0 - - - +
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASN* 1.3 74.9 - - + +
15A LEU* 1.3 62.4 + - + +
17A ALA* 3.4 3.5 + - + -
18A ILE* 2.8 47.6 + - + +
145A VAL* 4.4 4.6 - - - +
148A GLU* 3.8 26.3 + - + +
149A ALA* 3.5 42.2 - - + +
152A ALA* 4.5 6.1 - - + -
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA 6.1 2.2 - - - +
13A ASN* 3.2 9.7 + - - +
14A ILE* 1.3 85.6 - - + +
16A GLU* 1.3 56.4 + - - +
18A ILE* 3.1 15.9 + - + +
19A ILE* 2.9 54.4 + - + +
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA 3.6 20.9 - - - +
7A VAL* 3.3 9.1 - - + +
8A ASP* 2.6 33.5 + - - +
10A ARG 3.1 7.3 - - - +
11A ILE* 3.9 17.7 - - + -
12A ASP* 2.9 15.1 + - - +
13A ASN* 3.0 27.2 + - - +
15A LEU* 1.3 74.1 - - - +
17A ALA* 1.3 63.4 + - - +
19A ILE* 3.3 6.7 + - - +
20A LEU* 3.0 24.1 + - - +
203A MG 2.2 29.8 - - - -
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.7 13.8 - - + +
13A ASN 3.0 6.3 + - - -
14A ILE* 3.6 8.5 - - - +
16A GLU* 1.3 76.7 - - - +
18A ILE* 1.3 58.5 + - - +
20A LEU* 3.4 2.4 + - - +
21A MET* 2.9 35.4 + - - +
141A TRP* 3.5 31.4 - - + -
145A VAL* 3.8 13.5 - - + -
149A ALA* 4.2 12.6 - - + -
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 2.8 45.5 + - + +
15A LEU* 3.1 17.0 + - + +
17A ALA* 1.3 77.1 - - - +
19A ILE* 1.3 58.0 + - + +
21A MET* 4.7 0.2 - - - -
22A LEU* 2.9 50.7 + - + +
25A MET* 3.8 13.4 - - + +
149A ALA* 5.9 2.2 - - + -
152A ALA* 4.9 11.7 - - + -
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA 4.4 17.0 - - - +
7A VAL* 3.6 26.9 - - + -
15A LEU* 2.9 42.9 + - + +
16A GLU* 3.8 4.0 - - - +
18A ILE* 1.3 80.1 - - + +
20A LEU* 1.3 62.8 + - - +
21A MET 3.3 0.2 + - - -
22A LEU* 3.5 16.1 + - + +
23A PRO* 3.6 9.2 - - - +
76A ALA* 4.0 22.4 - - + +
79A ALA* 5.6 7.6 - - + -
80A SER* 4.3 8.1 - - - +
85A LEU* 3.9 13.7 - - + -
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.5 8.2 - - + +
11A ILE* 3.6 26.7 - - + -
16A GLU 3.0 18.0 + - - +
17A ALA* 3.8 3.6 - - - +
19A ILE* 1.3 78.5 - - - +
21A MET* 1.3 63.5 + - + +
23A PRO* 3.5 11.6 - - - +
85A LEU* 4.1 16.2 - - + -
88A HIS* 5.6 0.9 - - + -
89A SER* 5.1 2.3 + - - +
92A ILE* 3.8 30.5 - - + +
134A SER* 4.3 7.6 - - - -
139A TYR* 3.8 38.8 - - + +
141A TRP* 3.8 22.9 - - + -
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Residues in contact with MET 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA* 2.9 22.6 + - + +
20A LEU* 1.3 86.0 - - + +
22A LEU* 1.3 64.8 + - - +
23A PRO 3.3 3.1 - - - -
24A ALA* 2.9 18.5 + - + +
25A MET* 3.0 27.4 + - + +
92A ILE* 4.1 14.4 - - + -
126A PHE* 6.2 1.1 - - + -
127A TYR* 4.2 27.4 - - + -
130A ALA* 4.0 37.2 - - + +
131A LEU 4.3 2.5 - - - +
134A SER* 4.4 3.8 - - - -
141A TRP* 3.8 33.0 - - + -
149A ALA* 5.4 2.5 - - + -
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 2.9 39.4 + - + +
19A ILE* 4.0 10.3 - - + +
21A MET* 1.3 76.5 - - - +
23A PRO* 1.3 66.1 - - + +
25A MET* 3.4 25.1 + - + +
26A ILE* 2.9 48.1 + - + +
72A ALA* 4.9 0.7 - - + -
76A ALA* 5.9 1.3 - - + -
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Residues in contact with PRO 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE 3.6 7.4 - - - +
20A LEU 3.5 15.3 - - - +
22A LEU* 1.3 93.3 - - + +
24A ALA* 1.3 51.8 + - - +
26A ILE 3.4 0.5 + - - -
27A ALA* 2.7 35.4 + - - +
69A GLY* 3.6 22.6 - - - +
72A ALA* 4.0 14.6 - - + +
73A GLY* 3.9 14.1 - - - +
76A ALA* 4.4 6.1 - - + -
89A SER* 3.3 37.2 - - - +
92A ILE* 5.4 1.8 - - + -
93A ALA* 5.1 2.5 - - - +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A MET* 2.9 14.7 + - - +
23A PRO* 1.3 76.2 - - - +
25A MET* 1.3 56.5 + - - +
27A ALA* 3.2 3.2 + - - +
28A ASN* 2.7 37.2 + - - +
92A ILE* 4.0 11.4 - - + +
93A ALA* 4.7 3.1 - - - +
96A ALA* 3.6 17.1 - - + +
126A PHE* 4.1 8.7 - - + -
130A ALA* 3.6 31.6 - - + -
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Residues in contact with MET 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 3.8 19.3 - - + +
21A MET* 3.0 21.4 + - + +
22A LEU* 3.6 53.8 - - + +
24A ALA* 1.3 74.1 - - - +
26A ILE* 1.3 58.4 + - + +
28A ASN* 3.3 3.7 + - - +
29A ALA* 3.0 30.7 + - - +
126A PHE* 3.9 25.1 - - + -
153A VAL* 5.0 14.1 - - + -
156A LEU* 4.4 24.0 - - + -
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 2.9 34.9 + - + +
23A PRO 3.8 2.5 - - - +
25A MET* 1.3 75.2 - - + +
27A ALA* 1.3 65.6 + - - +
29A ALA* 4.2 4.0 - - - +
30A THR* 2.7 35.9 + - - +
68A ALA* 3.7 34.3 - - + +
72A ALA* 3.7 19.5 - - + -
75A LEU* 6.3 1.1 - - + -
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO 2.7 21.3 + - - +
24A ALA* 3.6 4.5 - - - +
26A ILE* 1.3 73.5 - - - +
28A ASN* 1.3 62.1 + - - +
31A PRO* 3.1 19.4 - - - +
65A GLY* 3.5 30.6 - - - +
69A GLY* 4.4 0.9 - - - +
93A ALA* 3.9 31.0 - - + +
96A ALA* 4.6 1.3 - - + -
97A LEU* 3.6 15.1 - - + +
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Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 2.7 20.8 + - - +
25A MET 3.7 4.8 + - - +
26A ILE 3.2 0.2 - - - -
27A ALA* 1.3 74.0 - - - +
29A ALA* 1.3 63.3 + - - +
31A PRO* 3.6 9.9 - - - +
32A VAL* 4.6 6.9 - - - +
96A ALA* 5.0 2.0 - - + +
97A LEU* 5.0 4.5 - - - -
100A ASP* 4.1 19.6 - - - +
122A ASP 5.6 1.9 + - - +
125A ASP* 5.0 0.5 - - - +
126A PHE* 3.4 53.0 - - + +
157A HIS* 4.3 16.2 + - - -
201A CTP 5.8 1.6 - - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A MET 3.0 16.6 + - - +
26A ILE* 4.2 4.3 - - - +
27A ALA 3.3 0.2 - - - -
28A ASN* 1.3 80.5 - - - +
30A THR* 1.3 61.8 + - - +
31A PRO 3.5 0.2 - - - -
32A VAL* 3.1 35.5 + - + +
33A VAL* 4.4 1.6 + - - +
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Residues in contact with THR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 2.7 25.5 + - - +
29A ALA* 1.3 78.2 - - - +
31A PRO* 1.3 67.6 - - - +
32A VAL 3.1 1.2 + - - -
33A VAL* 3.1 17.3 - - + +
34A ALA* 3.1 20.8 + - + -
64A ALA* 3.6 34.3 - - + +
65A GLY* 4.2 3.8 - - - -
68A ALA* 3.3 19.2 - - + +
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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
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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