Contacts of the helix formed by residues 12 - 26 (chain U) in PDB entry 5GJQ
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 HIS 12 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10U VAL* 6.1 3.1 - - + +
11U VAL* 1.3 75.4 - - - +
13U PRO* 1.3 71.8 - - + +
14U LEU 3.2 3.5 + - - +
15U VAL* 3.1 23.3 - - - +
16U LEU* 4.0 2.8 + - - +
49U ASP* 5.0 10.5 - - - +
50U VAL 2.3 33.7 + - - +
51U SER* 3.1 37.0 + - - +
162U ILE* 4.5 1.6 - - - -
163U GLY* 2.9 24.1 + - - -
164U ALA 5.1 0.2 - - - -
165U GLU* 3.9 32.3 + - + +
168U GLU* 4.6 10.7 - - - +
43V LYS* 5.0 1.9 - - - -
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Residues in contact with PRO 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U HIS* 1.3 86.2 - - + +
14U LEU* 1.3 59.4 + - - +
15U VAL 3.3 0.2 - - - -
16U LEU* 3.0 17.8 + - + +
17U LEU* 3.0 29.5 + - - +
162U ILE* 4.1 17.9 - - + -
163U GLY 4.1 9.4 - - - +
164U ALA* 4.4 4.5 - - - -
168U GLU* 3.5 32.1 - - + -
172U VAL* 4.2 11.9 - - + -
39V LEU* 4.4 5.4 - - + -
217V LEU* 4.1 24.2 - - + -
220V LEU* 5.1 3.1 - - + -
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Residues in contact with LEU 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U HIS* 3.2 2.3 - - + -
13U PRO* 1.3 79.3 - - - +
15U VAL* 1.3 61.0 + - - +
17U LEU* 4.6 2.4 - - - +
18U SER* 2.8 39.5 + - - +
51U SER 4.2 11.9 - - - +
52U ASN* 3.4 26.9 - - - +
53U SER 4.9 0.9 - - - +
168U GLU* 4.1 9.6 - - - +
36V LEU* 5.2 0.9 - - - +
39V LEU* 3.9 15.9 - - + +
40V LYS* 3.2 58.8 - - + +
43V LYS* 3.7 25.8 - - + -
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Residues in contact with VAL 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11U VAL* 4.8 7.2 - - + -
12U HIS 3.1 19.9 + - - +
14U LEU* 1.3 73.4 - - - +
16U LEU* 1.3 77.4 + - + +
18U SER* 2.6 20.0 + - - -
19U VAL* 2.9 15.8 + - - +
39U LEU* 5.9 1.8 - - + -
50U VAL* 3.5 31.0 - - + -
51U SER 3.2 25.6 - - - +
52U ASN* 3.7 15.3 - - - +
53U SER* 3.9 9.0 + - - +
95U TYR* 5.9 0.2 - - - -
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Residues in contact with LEU 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11U VAL* 5.7 1.6 - - + -
12U HIS 4.2 7.4 - - - +
13U PRO* 3.0 20.3 + - + +
15U VAL* 1.3 87.4 - - + +
17U LEU* 1.3 67.5 + - + +
19U VAL* 3.0 3.7 + - - +
20U VAL* 2.9 27.9 + - - +
124U ILE* 4.1 18.3 - - + +
134U PRO* 5.7 2.9 - - + -
135U THR* 3.4 29.6 - - + -
162U ILE* 3.8 30.5 - - + -
216V MET* 3.6 31.4 - - + +
217V LEU* 5.9 1.6 - - + -
219V ASN* 5.5 2.2 - - - +
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Residues in contact with LEU 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U PRO 3.0 12.3 + - - +
14U LEU* 4.6 1.6 - - - +
16U LEU* 1.3 81.0 - - + +
18U SER* 1.3 63.2 + - - +
20U VAL* 3.4 16.5 + - + +
21U ASP* 2.9 24.1 + - - +
35V SER* 3.5 28.0 - - - +
36V LEU* 4.1 19.7 - - + +
39V LEU* 3.8 26.2 - - + -
213V GLU* 4.0 33.0 - - + +
216V MET* 4.7 7.4 - - - -
217V LEU* 4.1 24.0 - - + -
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Residues in contact with SER 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U LEU* 2.8 26.6 + - - -
15U VAL 2.6 22.7 + - - -
17U LEU* 1.3 76.4 - - - +
19U VAL* 1.3 57.4 + - - +
21U ASP* 3.1 8.6 + - - +
22U HIS* 2.9 26.1 + - - +
53U SER* 2.7 26.2 + - - -
95U TYR* 5.3 0.2 - - - -
36V LEU* 4.5 7.0 - - - +
40V LYS* 5.5 7.9 - - - -
104V ARG* 3.9 17.3 + - - +
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Residues in contact with VAL 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15U VAL 2.9 16.2 + - - +
16U LEU* 3.6 3.8 - - - +
18U SER* 1.3 78.4 + - - +
20U VAL* 1.3 64.7 + - - +
22U HIS* 3.0 8.5 + - - +
23U PHE* 2.9 20.6 + - - +
35U VAL* 4.8 1.4 - - - +
95U TYR* 3.6 42.1 + - + +
97U THR* 5.9 4.5 - - - -
124U ILE* 4.8 14.8 - - + -
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Residues in contact with VAL 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U LEU 2.9 23.0 + - - +
17U LEU* 3.5 19.3 - - + +
19U VAL* 1.3 74.1 - - - +
21U ASP* 1.3 58.1 + - - +
23U PHE* 2.6 37.2 + - - +
24U ASN* 3.0 15.9 + - - -
124U ILE* 5.3 3.1 - - + +
126U VAL* 4.7 20.2 - - + +
210V ASN* 5.9 4.5 - - - +
212V LEU* 5.7 10.8 - - + -
213V GLU* 6.1 5.2 - - + +
216V MET* 4.2 23.3 - - + -
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Residues in contact with ASP 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U LEU 2.9 14.5 + - - +
18U SER 3.6 8.1 - - - +
20U VAL* 1.3 77.1 - - - +
22U HIS* 1.3 50.0 + - - +
24U ASN* 4.7 4.6 - - - +
25U ARG* 2.5 73.2 + - - +
36V LEU* 4.6 11.7 - - + -
70V ILE* 4.1 6.6 - - - +
71V ASP* 4.1 1.3 - - - -
104V ARG* 2.5 38.8 + - - +
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Residues in contact with HIS 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18U SER 2.9 11.9 + - - +
19U VAL* 3.0 14.1 - - - +
20U VAL 2.9 0.2 - - - -
21U ASP* 1.3 76.5 - - - +
23U PHE* 1.3 54.4 + - - +
25U ARG* 3.7 3.4 - - - +
26U ILE* 2.6 50.0 + - + +
35U VAL* 2.0 42.6 - - + +
36U VAL 3.3 17.6 + - - -
55U ALA* 3.3 30.8 - - + +
56U VAL 4.6 6.2 + - - -
57U PRO* 5.9 1.3 - - + -
95U TYR* 3.9 15.5 - + - +
102V THR* 5.1 12.3 + - + -
104V ARG* 4.8 5.8 - - - +
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Residues in contact with PHE 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U VAL 2.9 9.9 + - - +
20U VAL* 2.6 14.7 + - - +
22U HIS* 1.3 74.5 - - - +
24U ASN* 1.3 61.4 + - - +
26U ILE* 3.2 3.6 - - - +
27U GLY 3.0 22.7 + - - -
28U LYS* 2.4 35.6 + - + -
29U VAL 3.9 9.2 - - - -
30U GLY* 4.5 2.7 - - - -
33U LYS 5.4 2.2 - - - -
34U ARG* 5.9 0.7 - - - -
35U VAL* 3.7 16.3 - - + +
97U THR* 3.9 24.0 - - - -
126U VAL* 2.1 60.1 - - + -
127U LYS* 3.9 20.0 - - - -
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Residues in contact with ASN 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U VAL* 3.0 20.0 + - + +
21U ASP* 4.9 4.9 - - - +
23U PHE* 1.3 83.8 - - - +
25U ARG* 1.3 65.1 + - - +
26U ILE 3.3 0.2 - - - -
27U GLY* 3.7 9.9 + - - +
126U VAL* 5.3 4.3 - - - -
210V ASN* 5.6 7.9 - - - -
212V LEU* 6.4 1.8 - - - -
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Residues in contact with ARG 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U ASP* 2.5 50.4 + - - +
22U HIS* 3.7 6.7 - - - +
24U ASN* 1.3 81.2 - - - +
26U ILE* 1.3 59.1 + - - +
27U GLY 3.3 0.7 + - - -
70V ILE* 2.9 36.7 - - - +
71V ASP* 3.0 21.9 + - - -
102V THR 4.2 5.6 - - - +
103V GLY* 3.4 27.8 + - - +
104V ARG* 3.4 32.8 + - + +
106V GLU* 3.8 15.6 + - - +
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Residues in contact with ILE 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U HIS* 2.6 42.5 + - + +
23U PHE 3.2 6.1 - - - +
25U ARG* 1.3 76.5 - - - +
27U GLY* 1.3 60.5 + - - +
28U LYS* 3.0 32.4 + - + +
35U VAL* 3.8 8.3 - - + -
102V THR 4.8 9.9 - - - +
103V GLY* 6.4 0.2 - - - -
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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
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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