Contacts of the helix formed by residues 6 - 30 (chain A) in PDB entry 4DJ9
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 THR 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE 3.4 1.2 - - - +
5A HIS* 1.3 98.5 + - + +
7A ARG* 1.3 59.2 + - - +
8A THR* 3.9 6.8 + - - -
9A ILE* 3.2 29.4 + - - +
10A GLU* 3.0 28.6 + - - +
127A ASP* 3.5 24.5 + - - +
178A ARG* 3.8 13.7 - - - +
181A GLU* 3.4 13.9 - - + +
182A LEU* 4.2 4.5 - - + -
183A THR* 3.5 6.0 - - - +
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Residues in contact with ARG 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 1.3 69.7 - - - +
8A THR* 1.3 61.8 + - - +
10A GLU* 3.8 10.0 - - - +
11A SER* 2.9 31.4 + - - -
180A GLN* 3.6 26.9 + - - +
181A GLU* 2.9 24.8 + - + +
182A LEU 5.5 2.0 - - - -
183A THR* 3.5 14.4 - - + +
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Residues in contact with THR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.3 7.2 + - - -
7A ARG* 1.3 76.7 - - - +
9A ILE* 1.3 68.7 + - + +
11A SER* 2.9 21.9 + - - -
12A ILE* 3.1 31.9 + - + +
123A LEU* 5.7 2.5 - - + -
181A GLU* 6.2 0.7 - - - +
2081B ILE* 4.0 22.0 - - + -
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Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.6 29.2 - - + -
5A HIS* 3.7 28.0 - - + +
6A THR* 3.2 22.2 + - - +
8A THR* 1.3 76.6 - - + +
10A GLU* 1.3 53.9 + - - +
12A ILE* 3.8 0.2 - - - -
13A LEU* 2.8 49.5 + - + +
120A SER* 5.9 1.1 - - - +
123A LEU* 3.9 40.8 - - + +
124A LEU* 4.0 18.4 - - + -
127A ASP* 4.4 4.9 - - + -
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Residues in contact with GLU 10 (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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3A VAL 5.7 2.4 + - - -
4A PHE* 3.7 19.7 - - + +
6A THR 3.0 18.6 + - - +
7A ARG* 3.8 11.9 - - - +
9A ILE* 1.3 74.8 - - - +
11A SER* 1.4 63.3 + - - +
14A GLU* 2.9 59.2 + - + +
15A PRO* 3.7 1.2 - - - +
183A THR* 4.1 22.2 - - + +
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Residues in contact with SER 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG 2.9 19.2 + - - -
8A THR* 2.9 14.6 + - - +
10A GLU* 1.4 75.5 + - - +
12A ILE* 1.3 76.9 + - - +
15A PRO* 3.3 19.6 - - - +
2085B LYS* 5.9 1.2 - - - -
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 3.1 25.8 + - + +
9A ILE 4.0 2.2 - - - +
11A SER* 1.3 88.8 + - - +
13A LEU* 1.3 67.3 + - + +
15A PRO* 4.2 3.3 - - - +
16A VAL* 4.1 3.8 + - - +
123A LEU* 3.8 24.2 - - + -
2081B ILE* 3.8 37.2 - - + +
2084B VAL* 4.2 4.5 - - + -
2085B LYS* 4.0 46.4 - - + -
2088B ALA* 3.6 20.0 - - + +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.9 18.2 - - + -
9A ILE* 2.8 30.6 + - + +
12A ILE* 1.3 87.4 - - + +
14A GLU* 1.3 53.1 + - - +
15A PRO* 3.5 3.4 - - - -
16A VAL* 3.3 6.0 - - + +
17A ALA* 2.8 35.4 + - - +
116A LEU* 4.0 16.1 - - + +
119A THR* 3.5 24.7 - - - +
120A SER* 3.6 37.2 - - - +
123A LEU* 3.9 16.6 - - + -
2088B ALA* 4.4 9.4 - - + -
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 4.8 9.7 + - - -
4A PHE* 3.7 30.5 - - + -
10A GLU* 2.9 50.0 + - + +
13A LEU* 1.3 69.6 - - - +
15A PRO* 1.4 66.7 - - + +
17A ALA* 4.2 1.1 - - + -
18A GLN* 3.0 51.3 + - + +
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Residues in contact with PRO 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU 3.7 3.1 - - - +
11A SER* 3.3 24.5 - - - +
12A ILE 4.2 3.4 - - - +
13A LEU 3.6 3.1 - - - -
14A GLU* 1.4 91.6 - - + +
16A VAL* 1.4 59.8 + - - +
18A GLN* 3.5 12.0 + - - +
19A GLN* 3.3 27.5 + - - +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE 4.1 7.4 - - - +
13A LEU* 3.3 22.9 - - + +
15A PRO* 1.4 76.4 - - - +
17A ALA* 1.4 58.0 + - - +
19A GLN* 3.3 15.6 + - - +
20A ILE* 3.1 35.6 + - + +
116A LEU* 4.0 13.2 - - + -
2088B ALA* 4.1 22.2 - - + +
2091B LEU* 3.8 34.5 - - + -
2092B GLY* 4.1 12.3 - - - +
2095B ILE* 4.2 3.8 - - + -
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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
----------------------------------------------------------
4A PHE* 3.8 24.5 - - + -
13A LEU 2.8 22.8 + - - +
14A GLU* 3.4 5.1 + - + +
16A VAL* 1.4 72.6 - - - +
18A GLN* 1.4 57.6 + - + +
20A ILE* 3.7 2.3 + - - +
21A SER* 3.2 26.3 + - - -
116A LEU* 3.8 27.5 - - + +
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Residues in contact with GLN 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 GLU* 3.0 52.3 + - + +
15A PRO* 3.7 9.4 - - - +
17A ALA* 1.4 75.5 - - + +
19A GLN* 1.4 63.1 + - - +
21A SER* 2.8 24.0 + - - +
22A HIS* 3.1 13.5 + - + +
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Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO* 3.3 11.0 + - - +
16A VAL* 3.3 19.6 + - - +
18A GLN* 1.4 76.6 - - - +
20A ILE* 1.4 52.3 + - - +
22A HIS* 3.3 8.1 + - - +
23A LEU* 2.9 35.3 + - - +
2092B GLY* 3.3 39.4 + - - -
2095B ILE* 3.8 21.4 - - + +
2096B SER* 4.1 18.6 - - - +
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.1 29.7 + - + +
17A ALA* 4.0 4.9 - - - +
19A GLN* 1.4 70.8 - - - +
21A SER* 1.3 65.6 + - - +
23A LEU* 3.2 9.2 + - + +
24A VAL* 3.0 29.0 + - + +
109A ILE* 5.0 2.7 - - + +
112A SER* 3.6 36.1 - - - +
113A ARG* 3.9 27.4 - - + +
116A LEU* 3.8 27.1 - - + -
2091B LEU* 4.2 1.8 - - + -
2095B ILE* 3.7 17.5 - - + -
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Residues in contact with SER 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 3.2 14.9 + - - -
18A GLN* 2.8 22.8 + - - +
20A ILE* 1.3 73.4 - - - +
22A HIS* 1.4 58.8 + - - +
24A VAL* 3.2 9.1 + - - +
25A ILE* 3.0 41.7 + - - +
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Residues in contact with HIS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.1 11.1 + - + +
19A GLN* 3.4 11.4 - - - +
21A SER* 1.4 82.2 + - - +
23A LEU* 1.3 50.6 + - - +
25A ILE* 3.2 10.4 + - + -
26A MET* 2.9 73.8 + - + +
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Residues in contact with LEU 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 GLN 2.9 11.7 + - - +
20A ILE* 3.4 12.1 - - + +
22A HIS* 1.3 74.8 - - - +
24A VAL* 1.4 55.9 + - - +
26A MET* 3.5 6.2 + - - +
27A HIS* 3.0 30.0 + - - +
108A LEU* 5.2 7.4 - - + -
109A ILE* 3.7 28.3 - - + +
112A SER* 4.6 9.4 - - - +
2095B ILE* 4.0 39.3 - - + -
2098B THR* 4.0 7.4 - - + +
2099B LYS* 3.5 41.3 + - + +
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Residues in contact with VAL 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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20A ILE* 3.0 25.1 + - + +
21A SER* 3.5 10.5 - - - +
23A LEU* 1.4 72.3 - - - +
25A ILE* 1.4 62.9 + - + +
27A HIS* 3.3 4.6 + - - +
28A GLU* 3.0 31.3 + - + +
109A ILE* 3.8 19.7 - - + -
113A ARG* 3.5 45.1 - - - +
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Residues in contact with ILE 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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21A SER* 3.0 30.4 + - - +
22A HIS* 3.7 11.2 - - + +
24A VAL* 1.4 76.5 - - + +
26A MET* 1.4 75.4 + - + +
28A GLU* 3.4 7.5 + - - +
29A GLU* 3.2 25.6 + - + +
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Residues in contact with MET 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 HIS* 2.9 56.0 + - + +
23A LEU* 3.7 8.1 - - - +
25A ILE* 1.4 94.4 - - + +
27A HIS* 1.3 56.7 + - - +
29A GLU* 4.3 2.5 - - - +
30A GLY* 3.0 28.6 + - - -
2099B LYS* 4.8 19.5 - - + +
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Residues in contact with HIS 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 LEU 3.0 18.2 + - - +
24A VAL* 3.3 7.4 + - - +
26A MET* 1.3 73.0 - - - +
28A GLU* 1.4 67.6 - - - +
30A GLY 3.8 14.3 - - - -
102A VAL* 5.1 6.1 - - + -
105A ARG* 3.8 31.8 + - + +
106A ASP* 3.3 29.2 + - - -
109A ILE* 4.6 17.9 - - + +
2099B LYS* 5.9 0.6 - - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.0 20.1 + - + +
25A ILE* 3.6 8.5 - - + +
27A HIS* 1.4 79.3 - - - +
29A GLU* 1.4 63.0 + - - +
30A GLY 4.6 1.0 - - - -
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Residues in contact with GLU 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 ILE* 3.2 14.2 + - + +
26A MET* 4.4 2.5 - - - +
28A GLU* 1.4 78.9 - - - +
30A GLY* 1.3 61.9 + - - +
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Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET 3.0 18.0 + - - -
27A HIS* 3.8 14.8 - - - -
28A GLU 4.6 0.9 - - - -
29A GLU* 1.3 80.5 - - - +
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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