Contacts of the helix formed by residues 9 - 29 (chain B) in PDB entry 6P1A
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 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ASN 5.5 1.1 - - - +
8B LEU* 1.3 77.5 - - - +
10B LYS* 1.3 67.0 + - - +
11B GLU* 3.8 4.5 + - - +
12B GLN* 3.0 41.2 + - - +
13B HIS* 2.9 21.2 + - - +
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Residues in contact with LYS 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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109A LYS* 5.8 9.3 - - - +
201A EDO 5.8 0.7 - - - +
8B LEU 3.9 0.2 + - - -
9B THR* 1.3 75.9 - - - +
11B GLU* 1.3 63.4 + - - +
13B HIS* 3.3 5.5 + - - +
14B GLU* 2.9 57.5 + - + +
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Residues in contact with GLU 11 (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 THR* 3.3 5.1 + - - +
10B LYS* 1.3 81.3 - - - +
12B GLN* 1.3 65.8 + - - +
14B GLU* 3.2 27.2 + - - +
15B TRP* 3.0 24.6 + - - +
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.7 16.1 - - + +
9B THR* 3.0 45.2 + - - +
11B GLU* 1.3 77.0 - - + +
13B HIS* 1.3 63.8 + - - +
15B TRP* 3.3 5.2 + - - +
16B LEU* 3.0 25.6 + - - +
142B TYR* 3.4 50.6 + - + +
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Residues in contact with HIS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A EDO 4.0 23.7 + - - -
8B LEU* 4.3 18.6 - - + +
9B THR 2.9 18.0 + - - +
10B LYS* 3.5 6.5 - - - +
12B GLN* 1.3 78.2 - - - +
14B GLU* 1.3 57.0 + - - +
16B LEU* 3.4 2.7 + - - +
17B ASN* 2.8 39.0 + - - +
135B ASN* 5.3 5.0 + - - -
138B LEU* 3.4 32.1 - - + +
201B EDO 3.7 29.8 + - - -
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Residues in contact with GLU 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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109A LYS* 5.0 3.0 + - - +
201A EDO 3.5 38.8 + - - +
10B LYS* 2.9 50.8 + - + +
11B GLU* 3.2 31.1 + - - +
13B HIS* 1.3 76.8 - - - +
15B TRP* 1.3 62.0 + - - +
17B ASN 3.3 0.2 + - - -
18B GLY* 2.9 21.7 + - - -
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Residues in contact with TRP 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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11B GLU 3.0 16.5 + - - +
12B GLN* 3.6 4.0 - - - +
14B GLU* 1.3 78.1 - - - +
16B LEU* 1.3 83.6 + - + +
18B GLY* 3.3 1.2 + - - -
19B TRP* 3.0 53.7 + + - +
142B TYR* 3.3 42.2 - + + -
145B LEU* 3.9 33.2 - - + -
146B ASP* 4.2 20.4 - - + -
149B PHE* 3.8 14.4 - + + -
202B CL 3.9 6.2 - - - +
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Residues in contact with LEU 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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8B LEU* 4.1 4.0 - - + -
12B GLN 3.0 17.6 + - - +
13B HIS* 3.9 4.0 - - - +
15B TRP* 1.3 90.9 - - + +
17B ASN* 1.3 57.0 + - - +
19B TRP* 3.3 2.2 + - - +
20B LEU* 2.9 42.8 + - + +
138B LEU* 3.2 48.2 - - + +
141B ILE* 3.9 15.9 - - + -
142B TYR* 3.8 19.7 - - + +
145B LEU* 3.6 28.0 - - + -
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Residues in contact with ASN 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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117A ARG* 5.6 6.1 - - - +
118A ILE* 5.7 0.8 - - - +
201A EDO 3.2 36.6 + - - +
13B HIS* 2.8 26.5 + - + +
14B GLU 3.8 0.2 - - - +
15B TRP 3.2 0.2 - - - -
16B LEU* 1.3 73.7 - - - +
18B GLY* 1.3 62.9 + - - +
20B LEU 3.3 0.5 + - - -
21B GLU* 2.9 41.2 + - - +
87B TYR* 4.5 5.5 + - - -
88B TYR* 2.8 35.7 + - - +
138B LEU* 5.0 1.3 - - + +
201B EDO 4.2 9.0 + - - -
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Residues in contact with GLY 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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201A EDO 4.4 1.8 + - - -
14B GLU 2.9 15.0 + - - -
15B TRP 3.3 2.7 + - - -
17B ASN* 1.3 79.6 - - - +
19B TRP* 1.3 61.3 + - - +
21B GLU* 3.3 6.4 + - - +
22B LEU* 3.0 29.2 + - - +
202B CL 4.0 14.8 - - - -
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Residues in contact with TRP 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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15B TRP* 3.0 66.0 + + - +
16B LEU 3.7 6.7 - - - +
18B GLY* 1.3 75.8 - - - +
20B LEU* 1.3 59.1 + - + +
22B LEU* 3.4 24.6 + - + +
23B TRP* 2.9 29.3 + - - +
58B CYS* 4.4 7.0 - - + -
62B ASP* 3.6 29.2 - - + -
66B ILE* 3.7 24.5 - - + +
145B LEU* 4.2 14.1 - - + -
149B PHE* 3.6 29.9 - + - -
202B CL 4.0 3.0 - - + +
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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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16B LEU* 2.9 36.8 + - + +
19B TRP* 1.3 73.9 - - - +
21B GLU* 1.3 60.1 + - - +
23B TRP* 3.6 25.5 - - + -
24B GLY* 2.8 25.8 + - - -
66B ILE* 4.3 8.1 - - + -
70B VAL* 4.1 20.4 - - + -
84B LEU* 4.4 5.6 - - + -
88B TYR* 3.6 36.4 - - + +
138B LEU* 3.5 36.3 - - + -
141B ILE* 4.9 9.0 - - + -
145B LEU* 5.4 1.8 - - + -
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Residues in contact with GLU 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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117A ARG* 3.6 35.0 + - - +
17B ASN* 2.9 32.7 + - - +
18B GLY* 3.6 7.2 - - - +
20B LEU* 1.3 73.5 - - - +
22B LEU* 1.3 67.2 + - + +
24B GLY* 3.3 1.4 + - - -
25B ALA* 3.0 23.6 + - - +
55B ARG* 4.3 12.6 + - - +
56B PRO 5.0 0.4 - - - -
87B TYR* 4.5 1.0 - - - +
88B TYR* 3.6 33.0 - - - +
91B GLY* 5.5 0.5 - - - -
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Residues in contact with LEU 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 GLY 3.0 21.0 + - - +
19B TRP* 3.7 26.7 - - + +
21B GLU* 1.3 77.5 - - + +
23B TRP* 1.3 57.4 + - - +
25B ALA* 3.3 4.0 + - - +
26B TRP* 2.9 27.9 + - - +
56B PRO* 3.3 43.3 - - + +
57B MET* 3.7 9.8 - - - +
58B CYS* 4.0 18.6 - - + +
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Residues in contact with TRP 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 TRP 2.9 18.1 + - - +
20B LEU* 3.6 27.1 - - + +
22B LEU* 1.3 76.1 - - - +
24B GLY* 1.3 71.8 + - - +
26B TRP* 3.2 5.0 + + - +
27B VAL* 2.8 43.1 + - + +
40B ILE* 4.0 21.8 - - + -
58B CYS* 4.1 9.6 - - - -
63B GLY 3.8 5.8 - - - -
66B ILE* 3.3 38.8 - - + -
67B SER* 3.0 31.2 + - - +
70B VAL* 4.0 23.3 - - + -
81B PHE* 4.7 0.7 - + - -
84B LEU* 4.6 11.9 - - + -
85B LEU* 3.5 29.2 - - + -
88B TYR* 4.5 13.2 - - + -
89B ALA 5.4 0.2 - - - -
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Residues in contact with GLY 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 LEU 2.8 18.1 + - - -
21B GLU 3.8 0.2 - - - -
23B TRP* 1.3 83.0 - - - +
25B ALA* 1.3 59.6 + - - +
27B VAL* 4.4 1.1 - - - -
28B TYR* 2.9 31.4 + - - +
88B TYR 3.7 7.4 - - - -
89B ALA* 3.4 29.2 - - - +
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Residues in contact with ALA 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 GLU 3.0 11.7 + - - +
22B LEU 3.6 3.8 - - - +
24B GLY* 1.3 76.3 - - - +
26B TRP* 1.3 61.9 + - - +
29B SER* 3.2 18.4 + - - -
53B MET* 3.2 12.9 - - + +
55B ARG* 3.9 34.5 - - + +
56B PRO 3.2 28.3 - - - +
57B MET* 3.7 9.3 - - + +
88B TYR 4.2 1.6 + - - -
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Residues in contact with TRP 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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22B LEU 2.9 15.1 + - - +
23B TRP* 3.2 8.7 + + - +
25B ALA* 1.3 76.6 - - - +
27B VAL* 1.3 82.5 + - + +
29B SER* 2.4 23.3 + - - -
30B GLY 3.7 2.9 + - - -
31B ARG* 3.5 43.8 + - + +
32B LEU* 3.8 26.7 - - + -
57B MET* 3.6 12.9 - - + +
58B CYS* 3.5 32.1 - - - -
59B ASN 3.6 3.6 + - - -
60B ASP* 3.1 33.2 + - + -
63B GLY* 3.4 31.2 - - - -
64B MET* 3.7 9.6 - - + -
67B SER* 3.2 24.0 - - - -
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Residues in contact with VAL 27 (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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23B TRP* 2.8 49.0 + - + +
24B GLY* 3.9 5.6 - - - +
26B TRP* 1.3 92.2 - - + +
28B TYR* 1.3 63.9 + - - +
30B GLY* 2.9 19.9 + - - -
31B ARG 4.4 0.4 + - - +
32B LEU* 4.3 14.4 + - + +
40B ILE* 3.7 25.8 - - + -
44B MET* 3.4 21.8 - - + +
67B SER* 4.2 2.0 - - - +
85B LEU* 4.9 4.3 - - + -
89B ALA* 4.6 9.2 - - + -
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Residues in contact with TYR 28 (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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24B GLY 2.9 17.7 + - - +
25B ALA 3.8 4.5 - - - +
27B VAL* 1.3 77.9 - - - +
29B SER* 1.3 50.5 + - - +
43B PHE* 4.7 0.4 - + - -
44B MET* 3.8 19.1 - - + +
47B VAL* 3.8 32.1 - - + +
48B GLU* 4.8 5.4 + - - +
51B ARG* 2.4 63.3 + - + -
52B VAL 5.8 1.6 - - - -
53B MET* 3.8 16.4 - - + -
55B ARG* 4.1 4.7 - - - +
89B ALA* 3.3 24.7 - - + +
90B HIS* 3.3 39.6 + + + -
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Residues in contact with SER 29 (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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25B ALA 3.2 10.6 + - - -
26B TRP 2.4 27.7 + - - -
28B TYR* 1.3 72.9 - - - +
30B GLY* 1.3 59.3 + - - +
31B ARG* 3.6 17.4 + - - +
51B ARG* 3.2 14.2 + - - +
53B MET* 3.8 15.2 - - - +
57B MET* 3.7 24.1 - - - -
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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
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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