Contacts of the helix formed by residues 4 - 27 (chain B) in PDB entry 4L9T
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 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 3.4 27.8 - - + +
128A LYS* 3.8 2.7 - - - +
3B PHE* 1.3 78.8 - - - +
5B TYR* 1.3 62.4 + - - +
6B SER* 3.7 5.3 + - - -
7B TYR* 3.1 26.1 + - - +
8B LEU* 3.1 21.6 + - - +
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Residues in contact with TYR 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 2.9 26.6 + - - +
115A LEU* 3.8 27.1 - - + -
116A VAL* 4.0 15.5 - - + -
119A LEU* 4.2 1.4 - - - +
124A ASN* 2.6 36.2 + - - -
127A MET* 3.4 40.2 - - + +
128A LYS* 3.6 24.0 - - + +
131A LEU* 3.8 18.8 - - + -
4B THR* 1.3 69.0 - - - +
6B SER* 1.3 61.5 + - - +
8B LEU* 3.2 3.8 + - + +
9B PHE* 2.8 48.4 + + + -
134B MET* 3.8 17.3 - - + -
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Residues in contact with SER 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET* 4.8 21.3 - - - +
108A PHE* 4.2 22.0 + - - +
111A MET* 5.5 4.0 - - - +
112A GLU* 3.0 19.1 + - - +
115A LEU* 5.2 1.4 - - - +
4B THR* 3.3 5.1 - - - -
5B TYR* 1.3 76.6 - - - +
7B TYR* 1.3 61.3 + - - +
9B PHE* 4.2 0.7 - - - +
10B ARG* 3.1 26.7 + - - +
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Residues in contact with TYR 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.7 8.8 - - + +
3B PHE* 3.8 48.4 - + - -
4B THR* 3.1 23.1 + - - +
6B SER* 1.3 78.7 - - - +
8B LEU* 1.3 60.8 + - + +
10B ARG* 3.3 4.5 + - - +
11B MET* 2.9 69.2 + - + +
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS* 4.1 21.3 - - + +
131A LEU* 4.0 36.3 - - + +
132A THR* 3.7 32.1 - - - +
135A LEU* 4.4 13.7 - - + -
3B PHE* 3.8 33.7 - - + +
4B THR 3.1 18.6 + - - +
5B TYR* 3.2 5.4 + - + +
7B TYR* 1.3 82.2 - - + +
9B PHE* 1.3 57.0 + - - +
11B MET* 3.3 3.1 + - - +
12B ILE* 2.8 37.7 + - + +
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Residues in contact with PHE 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.8 30.6 - + + +
12A ILE* 3.9 30.7 - - + -
13A SER* 4.2 8.5 - - - +
16A MET* 4.1 21.3 - - + -
115A LEU* 4.3 2.5 - - + -
131A LEU* 4.0 16.4 - - + -
5B TYR* 2.8 42.0 + + + +
8B LEU* 1.3 73.6 - - - +
10B ARG* 1.3 56.9 + - - +
12B ILE* 3.8 4.3 - - + +
13B SER* 3.0 35.2 + - - -
131B LEU* 3.8 25.4 - - + -
134B MET* 3.6 33.7 - - + -
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Residues in contact with ARG 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 5.1 1.8 - - - -
16A MET* 5.3 3.0 - - + +
6B SER 3.1 20.2 + - - +
7B TYR* 3.7 4.3 - - - +
9B PHE* 1.3 77.5 - - - +
11B MET* 1.3 64.7 + - + +
13B SER* 3.4 5.6 + - - -
14B HIS* 3.0 28.8 + - - +
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Residues in contact with MET 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.8 24.7 - - + -
139A GLN* 5.7 3.4 - - - -
7B TYR* 2.9 60.8 + - + +
8B LEU 3.8 1.3 - - - +
10B ARG* 1.3 81.4 - - + +
12B ILE* 1.3 60.5 + - - +
14B HIS* 3.2 18.7 + - + +
15B GLU* 2.8 41.2 + - - +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.5 39.3 - - + -
131A LEU* 3.8 42.6 - - + +
134A MET* 5.0 2.7 - - + -
135A LEU* 4.0 28.3 - - + +
138A LEU* 4.3 13.9 - - + +
8B LEU* 2.8 28.6 + - + +
9B PHE* 3.8 7.4 - - + +
11B MET* 1.3 71.3 - - - +
13B SER* 1.3 63.1 + - - +
15B GLU* 3.2 3.7 + - - +
16B MET* 3.0 30.9 + - + +
115B LEU* 5.9 0.2 - - + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 4.2 12.0 + - - +
10A ARG* 5.2 1.9 - - - -
13A SER* 3.0 29.5 + - - -
9B PHE 3.0 13.8 + - - -
10B ARG* 3.8 5.2 - - - -
12B ILE* 1.3 76.5 - - - +
14B HIS* 1.3 61.8 + - - +
16B MET* 3.6 13.3 + - - +
17B LYS* 3.2 22.7 + - - +
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Residues in contact with HIS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG 3.0 18.3 + - - +
11B MET* 3.6 20.8 - - + +
13B SER* 1.3 77.4 - - - +
15B GLU* 1.3 71.3 + - - +
17B LYS* 3.3 9.7 + - + +
18B GLN* 2.9 51.7 + - + +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.5 20.6 - - + -
138A LEU* 4.1 21.2 - - + +
139A GLN* 3.7 34.8 + - + +
11B MET* 2.8 26.5 + - + +
12B ILE 3.2 3.3 + - - +
14B HIS* 1.3 88.5 + - - +
16B MET* 1.3 59.1 + - - +
18B GLN* 3.3 26.3 + - - +
19B LYS* 2.8 35.3 + - - +
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Residues in contact with MET 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 4.6 20.4 - - - +
9A PHE* 4.4 16.4 - - + -
10A ARG* 5.3 4.0 - - + +
138A LEU* 3.5 20.9 - - + -
12B ILE* 3.0 36.2 + - + +
13B SER* 4.1 12.6 - - - +
15B GLU* 1.3 73.0 - - - +
17B LYS* 1.3 64.4 + - - +
19B LYS* 3.6 0.4 + - - -
20B ALA* 3.3 19.1 + - - +
108B PHE* 5.1 1.8 - - - -
111B MET* 3.7 37.9 - - + +
115B LEU* 4.4 15.9 - - - -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER 3.2 14.1 + - - +
14B HIS* 3.3 12.5 + - + +
16B MET* 1.3 75.6 - - - +
18B GLN* 1.3 64.7 + - - +
20B ALA* 3.2 10.0 + - + +
21B ASP* 3.1 48.3 + - - +
31B ASN* 4.6 11.3 - - - +
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Residues in contact with GLN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B HIS* 2.9 36.2 + - + +
15B GLU* 3.3 30.6 + - - +
17B LYS* 1.3 76.8 - - - +
19B LYS* 1.3 56.4 + - + +
21B ASP* 3.1 10.1 + - + +
22B GLN* 2.8 54.4 + - + +
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.6 31.9 + - + +
140A HIS 5.3 6.3 + - - -
15B GLU* 2.8 22.1 + - - +
16B MET 3.8 0.2 - - - +
17B LYS 3.3 0.2 - - - -
18B GLN* 1.3 77.8 - - + +
20B ALA* 1.3 56.5 + - - +
22B GLN* 3.3 20.4 + - - +
23B LYS* 3.0 27.7 + - - +
26B GLN* 6.2 0.6 - - - +
107B ILE* 4.0 18.6 - - + +
110B GLU* 4.7 10.8 + - - -
111B MET* 3.6 35.0 - - + -
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET 3.3 10.6 + - - +
17B LYS* 3.2 16.3 + - + +
18B GLN 3.2 0.2 - - - -
19B LYS* 1.3 77.3 - - - +
21B ASP* 1.3 66.7 + - - +
23B LYS* 3.3 8.0 + - - +
24B LEU* 3.3 5.1 + - - +
104B PHE* 3.2 41.0 - - + -
107B ILE* 4.3 8.9 - - + +
108B PHE* 4.3 19.3 - - + -
111B MET* 5.3 0.2 - - + -
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 3.1 47.2 + - - +
18B GLN* 3.1 11.1 + - + +
20B ALA* 1.3 77.8 - - - +
22B GLN* 1.3 62.9 + - + +
24B LEU* 3.3 13.6 + - + +
25B GLU* 3.1 30.5 + - - +
31B ASN* 4.2 12.5 + - - -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLN* 2.8 48.7 + - + +
19B LYS* 3.7 28.5 + - + +
20B ALA 3.2 0.2 - - - -
21B ASP* 1.3 75.0 - - + +
23B LYS* 1.3 59.3 + - - +
25B GLU* 3.3 21.7 + - - +
26B GLN* 2.9 43.7 + - - +
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS 3.0 13.6 + - - +
20B ALA 3.6 8.7 - - - +
21B ASP 3.2 0.4 - - - -
22B GLN* 1.3 77.2 - - - +
24B LEU* 1.3 62.1 + - - +
26B GLN* 3.3 21.6 + - + +
27B LEU* 3.0 44.9 + - + +
103B ALA* 3.4 26.8 + - - +
104B PHE* 4.0 24.9 - - + -
106B SER* 4.7 5.6 + - - -
107B ILE* 4.1 27.8 - - + -
110B GLU* 4.6 11.3 + - - -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA 3.3 12.7 + - - +
21B ASP* 3.3 15.4 + - - +
22B GLN 3.3 0.6 - - - -
23B LYS* 1.3 77.1 - - - +
25B GLU* 1.3 61.0 - - + +
27B LEU* 3.1 4.8 + - - +
28B ASP 3.1 17.3 + - - -
29B ILE* 3.1 48.1 + - + +
30B THR 4.5 3.8 - - - +
31B ASN* 3.7 42.0 - - + +
34B GLY* 4.6 8.3 - - - -
104B PHE* 3.6 33.2 - - + -
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP* 3.1 19.6 + - - +
22B GLN* 3.5 27.5 - - - +
24B LEU* 1.3 78.8 - - + +
26B GLN* 1.3 59.9 + - + +
28B ASP* 3.0 19.9 + - - +
29B ILE 4.5 0.7 - - - +
201B SO4 3.6 26.1 + - - +
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS* 6.2 0.4 - - - +
22B GLN* 2.9 30.6 + - + +
23B LYS* 3.6 26.4 + - + +
24B LEU 3.2 0.2 - - - -
25B GLU* 1.3 76.7 - - + +
27B LEU* 1.3 62.5 + - + +
28B ASP* 3.2 3.7 + - - +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 3.0 36.1 + - + +
24B LEU* 3.1 6.0 + - - +
26B GLN* 1.3 77.7 - - + +
28B ASP* 1.3 67.6 + - - +
29B ILE* 3.3 18.9 + - + +
74B LYS* 4.7 1.0 + - - -
100B LEU* 3.8 41.8 - - + +
103B ALA* 4.3 8.1 - - + -
104B PHE* 3.9 36.6 - - + +
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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