Contacts of the helix formed by residues 6 - 24 (chain B) in PDB entry 5U07
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 ILE 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B TYR* 1.3 97.7 - - + +
7B LEU* 1.3 61.8 + - - +
8B GLN 3.1 1.0 + - - -
9B HIS* 3.2 11.8 + - - +
10B ALA* 2.9 19.4 + - + +
77B VAL* 4.3 17.5 - - + -
81B PHE* 4.1 19.6 - - + -
196B ILE* 5.2 0.7 - - + -
197B ARG* 4.5 17.0 - - + +
200B ALA* 4.3 25.1 - - + +
201B ARG* 6.3 1.3 - - + -
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Residues in contact with LEU 7 (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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5B TYR 2.3 17.5 + - - +
6B ILE* 1.3 72.9 - - - +
8B GLN* 1.3 56.8 + - + +
10B ALA* 3.5 4.8 - - + +
11B ASP* 2.9 37.4 + - - +
136B ARG* 3.2 32.8 - - - +
193B GLY* 3.8 35.7 - - - +
194B ILE* 4.3 3.1 - - + -
197B ARG* 3.7 41.1 - - + +
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 2.5 35.0 + - - +
7B LEU* 1.3 70.6 - - + +
9B HIS* 1.3 73.2 + - + +
11B ASP* 3.1 18.7 + - - +
12B ALA* 3.1 11.1 + - - +
15B LYS* 4.7 1.9 + - - -
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Residues in contact with HIS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.1 58.3 + - + +
15A GLN* 5.0 7.0 - - + +
5B TYR* 5.1 16.6 - + - -
6B ILE* 3.2 12.4 + - - +
8B GLN* 1.3 86.5 - - + +
10B ALA* 1.3 62.5 + - - +
12B ALA* 3.0 11.8 + - + +
13B LEU* 3.0 23.4 + - - +
54B TYR* 3.4 29.1 + - + +
55B VAL 5.7 0.8 - - - -
81B PHE* 4.2 11.1 - - + -
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Residues in contact with ALA 10 (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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6B ILE* 2.9 14.8 + - + +
7B LEU* 3.5 14.4 - - - +
8B GLN 3.1 0.2 - - - -
9B HIS* 1.3 77.4 - - - +
11B ASP* 1.3 58.0 + - - +
13B LEU* 3.2 4.2 + - - +
14B VAL* 2.9 33.6 + - - +
81B PHE* 3.6 11.6 - - + -
193B GLY* 4.3 11.2 - - - +
196B ILE* 3.9 33.5 - - + +
197B ARG 5.2 0.7 - - - +
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Residues in contact with ASP 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 2.9 35.1 + - - +
8B GLN* 3.1 10.6 + - - +
10B ALA* 1.3 74.1 - - - +
12B ALA* 1.3 65.8 + - - +
14B VAL* 3.0 16.2 - - + +
15B LYS* 3.0 37.6 + - + +
136B ARG* 4.5 9.9 + - - -
193B GLY* 4.6 6.8 - - - -
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Residues in contact with ALA 12 (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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14A ARG 6.1 0.7 - - - +
15A GLN 6.1 1.1 - - - +
16A THR* 5.5 4.7 - - + -
8B GLN 3.1 9.9 + - - +
9B HIS* 3.0 14.2 + - + +
11B ASP* 1.3 76.6 - - - +
13B LEU* 1.3 62.1 + - - +
15B LYS* 3.0 23.4 - - - +
16B ARG* 3.0 29.3 + - - +
54B TYR* 3.8 23.7 + - + +
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Residues in contact with LEU 13 (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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9B HIS 3.0 10.7 + - - +
10B ALA* 3.5 9.6 - - - +
12B ALA* 1.3 77.3 - - - +
14B VAL* 1.3 57.4 + - - +
16B ARG* 5.1 0.2 - - - -
17B VAL* 2.9 60.6 + - + +
50B VAL 5.0 2.0 - - - +
51B VAL* 4.2 24.0 - - + +
54B TYR* 3.5 32.1 - - + -
81B PHE* 3.3 47.3 - - + +
85B ALA* 4.6 9.0 - - + -
196B ILE* 4.8 7.0 - - + -
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Residues in contact with VAL 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 ALA 2.9 19.3 + - - +
11B ASP* 3.0 33.2 - - + +
13B LEU* 1.3 76.2 - - - +
15B LYS* 1.3 59.1 + - + +
17B VAL* 5.0 0.9 - - - -
18B SER* 2.7 35.6 + - - +
88B MET* 4.9 6.7 - - + +
192B TRP* 4.2 19.1 - - + -
193B GLY* 4.0 25.1 - - - +
196B ILE* 4.0 13.7 - - + -
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Residues in contact with LYS 15 (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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8B GLN 4.7 2.0 + - - -
11B ASP* 3.0 28.0 + - + +
12B ALA* 3.0 36.1 - - - +
14B VAL* 1.3 80.4 - - + +
16B ARG* 1.3 73.2 + - + +
18B SER* 3.5 4.3 - - - -
19B LYS* 2.9 24.5 + - - +
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Residues in contact with ARG 16 (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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11A LEU* 5.3 3.0 - - - +
16A THR* 4.8 2.8 + - - -
20A PHE* 4.0 31.1 + - - +
21A ARG* 4.7 16.4 + - + +
12B ALA 3.0 21.8 + - - +
13B LEU 4.2 0.7 - - - +
15B LYS* 1.3 77.7 - - + +
17B VAL* 1.3 63.8 + - + +
19B LYS* 3.2 6.6 + - - +
20B LEU* 3.0 42.1 + - + +
49B ARG 4.3 0.6 + - - -
50B VAL* 2.9 38.9 + - - +
53B PRO* 4.7 11.3 - - - +
54B TYR* 3.0 52.6 + - + +
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 2.9 49.8 + - + +
16B ARG* 1.3 72.3 - - + +
18B SER* 1.3 66.2 + - - +
19B LYS 3.0 1.6 - - - -
20B LEU* 3.1 6.4 + - + +
21B ILE* 2.9 54.9 + - + +
31B LEU* 4.2 13.2 - - + -
50B VAL* 4.6 10.1 - - + -
51B VAL* 4.4 10.3 - - + -
85B ALA* 4.6 9.9 - - + +
88B MET* 3.5 16.2 - - + -
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 2.7 24.4 + - - -
15B LYS* 3.5 5.2 - - - -
17B VAL* 1.3 76.4 - - - +
19B LYS* 1.3 60.1 + - - +
21B ILE* 5.2 1.6 - - - -
22B VAL* 3.3 29.1 + - - +
88B MET* 4.2 15.1 - - - +
192B TRP* 5.7 8.3 - - - -
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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
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170A ASP* 3.6 23.8 + - - +
15B LYS 2.9 12.5 + - - +
16B ARG* 3.4 10.1 - - - +
18B SER* 1.3 76.6 - - - +
20B LEU* 1.3 63.3 + - + +
22B VAL* 3.6 1.8 + - - +
23B ASN* 2.7 57.2 + - + +
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Residues in contact with LEU 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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20A PHE* 6.1 3.4 - - + +
21A ARG 5.5 9.4 - - - +
169A ASP* 5.7 2.5 - - - +
170A ASP 6.1 0.7 - - - +
16B ARG* 3.0 37.4 + - + +
17B VAL* 3.1 5.8 + - + +
19B LYS* 1.3 79.4 - - + +
21B ILE* 1.3 59.3 + - + +
23B ASN* 4.3 7.6 - - - +
24B GLU* 2.7 47.1 + - + +
27B ALA* 4.9 13.0 - - + -
28B ARG* 4.9 0.8 + - - -
31B LEU* 6.4 0.9 - - + -
50B VAL* 3.7 35.7 - - + -
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Residues in contact with ILE 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 VAL* 2.9 50.8 + - + +
18B SER* 4.7 1.8 - - - +
20B LEU* 1.3 80.1 - - + +
22B VAL* 1.3 68.1 + - + +
23B ASN 3.1 1.4 + - - -
24B GLU 4.0 4.5 + - - +
25B PRO* 5.2 0.7 - - - +
28B ARG* 3.9 19.5 - - + +
31B LEU* 4.0 16.2 - - + -
88B MET* 4.3 9.2 - - + +
89B ALA* 3.4 45.3 - - + +
91B GLN 6.1 0.2 - - - +
96B ARG* 3.2 41.0 + - + +
22I LEU* 5.6 0.7 - - - +
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Residues in contact with VAL 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 SER* 3.3 20.6 + - - +
19B LYS* 3.6 1.9 + - - +
20B LEU 3.5 0.2 - - - -
21B ILE* 1.3 77.3 - - + +
23B ASN* 1.3 61.1 + - - +
96B ARG* 3.7 44.7 + - + +
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Residues in contact with ASN 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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169A ASP* 3.3 17.0 + - - -
170A ASP* 2.9 56.0 + - - +
19B LYS* 2.7 41.0 + - + +
20B LEU* 4.1 5.9 - - - +
22B VAL* 1.3 81.3 - - - +
24B GLU* 1.3 60.4 + - + +
25B PRO* 3.4 10.7 - - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.4 19.0 - - + +
169A ASP* 4.3 30.7 - - + +
187A ALA* 5.2 7.6 - - + +
20B LEU* 2.7 35.9 + - + +
21B ILE 4.4 1.8 - - - -
23B ASN* 1.3 73.8 - - + +
25B PRO* 1.3 65.9 - - + +
26B ALA* 2.7 32.4 + - - +
27B ALA* 2.3 40.7 + - + +
28B ARG* 3.3 12.9 + - - +
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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