Contacts of the helix formed by residues 10 - 25 (chain B) in PDB entry 6Q3W
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 ALA 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B VAL* 1.3 81.0 - - + +
11B GLU* 1.3 53.3 + - - +
12B LEU 3.2 1.2 - - - +
13B LEU* 3.6 18.7 - - - +
14B ALA* 2.8 35.5 + - - +
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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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8B GLN* 3.6 21.5 - - + -
9B VAL 2.8 8.9 + - - +
10B ALA* 1.3 71.2 - - - +
12B LEU* 1.3 60.0 + - - +
14B ALA* 3.9 6.2 - - - +
15B GLU* 3.1 29.0 + - - +
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Residues in contact with LEU 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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8B GLN* 3.3 17.8 - - + +
9B VAL* 3.8 10.7 - - - +
11B GLU* 1.3 80.0 - - - +
13B LEU* 1.3 57.6 + - - +
15B GLU* 3.4 15.8 + - - +
16B ALA* 3.1 26.0 + - - +
60B MET* 3.6 44.0 - - + +
62B VAL* 3.8 11.9 - - + -
130B VAL* 3.7 32.0 - - + +
131B SER 4.0 16.8 - - - +
132B SER* 3.9 14.4 - - - +
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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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10B ALA* 3.3 20.3 + - - +
12B LEU* 1.3 77.6 - - - +
14B ALA* 1.3 60.0 + - - +
16B ALA* 3.1 5.4 + - - +
17B ARG* 2.9 60.0 + - - +
31B ALA* 4.1 13.0 - - + -
62B VAL* 4.1 16.3 - - + +
64B VAL* 3.6 27.8 - - + -
390B LEU* 4.4 19.3 - - + -
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Residues in contact with ALA 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 2.8 22.5 + - - +
11B GLU* 3.9 7.2 - - - +
13B LEU* 1.3 73.1 - - - +
15B GLU* 1.3 58.9 + - - +
17B ARG* 3.3 9.1 + - - +
18B ARG* 2.9 33.0 + - - +
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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
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11B GLU 3.1 19.1 + - - +
12B LEU* 3.6 14.1 - - - +
13B LEU 3.2 0.2 - - - -
14B ALA* 1.3 75.4 - - - +
16B ALA* 1.3 61.1 + - - +
18B ARG* 4.0 5.4 - - - +
19B ALA* 3.1 24.8 + - + +
78B THR* 2.7 35.3 + - - +
130B VAL* 4.2 10.0 - - + +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU 3.1 14.9 + - - +
13B LEU* 3.1 10.1 + - - +
15B GLU* 1.3 77.0 - - - +
17B ARG* 1.3 56.6 + - - +
19B ALA 3.3 0.9 + - - -
20B PHE* 3.0 28.6 + - - +
62B VAL* 4.4 2.0 - - + -
64B VAL* 4.0 25.8 - - + +
128B VAL* 3.7 13.3 - - + +
130B VAL* 3.8 28.0 - - + -
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Residues in contact with ARG 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 LEU* 2.9 49.7 + - + +
14B ALA* 3.8 7.0 - - - +
16B ALA* 1.3 74.1 - - - +
18B ARG* 1.3 63.8 + - - +
20B PHE* 3.5 2.1 + - - +
21B ARG* 3.2 24.9 + - - +
27B GLU* 4.5 23.0 + - - +
28B PRO* 4.4 8.0 - - + +
64B VAL* 4.2 17.3 - - + -
390B LEU* 5.2 2.2 - - - +
392B LEU* 3.8 45.5 + - + +
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Residues in contact with ARG 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 ALA 2.9 18.0 + - - +
15B GLU* 4.2 4.5 - - - +
17B ARG* 1.3 76.5 - - - +
19B ALA* 1.3 59.6 + - - +
21B ARG* 4.3 4.5 - - - +
22B GLU* 3.5 21.3 + - - +
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Residues in contact with ALA 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 GLU* 3.1 20.5 + - + +
16B ALA 3.7 4.0 - - - +
17B ARG 3.2 0.2 - - - -
18B ARG* 1.3 78.4 - - - +
20B PHE* 1.3 63.9 + - - +
21B ARG 3.3 0.2 - - - -
22B GLU* 3.5 4.2 + - - +
23B GLU* 3.1 25.6 + - - +
76B LEU* 4.3 5.1 - - + +
78B THR* 4.1 24.9 - - + -
128B VAL* 4.0 11.7 - - + +
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Residues in contact with PHE 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 ALA 3.0 17.6 + - - +
17B ARG 3.9 4.5 - - - +
19B ALA* 1.3 77.7 - - - +
21B ARG* 1.3 52.7 + - - +
24B PHE* 2.8 72.6 + + + +
26B ALA* 3.4 23.6 - - + -
27B GLU 4.2 1.8 - - - -
28B PRO* 3.7 23.1 - - + -
64B VAL* 3.2 24.5 - - + -
65B GLY* 3.4 12.8 - - - -
66B SER* 4.0 11.7 - - - -
126B SER* 3.4 39.3 - - - -
128B VAL* 3.5 12.5 - - + +
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Residues in contact with ARG 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 ARG 3.2 14.9 + - - +
18B ARG* 4.3 5.2 - - - +
20B PHE* 1.3 79.2 - - - +
22B GLU* 1.3 59.4 + - - +
25B GLY* 2.8 34.6 + - - +
26B ALA 3.6 17.3 - - - +
27B GLU* 4.4 18.2 - - - +
28B PRO* 5.3 0.2 - - + -
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Residues in contact with GLU 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 ARG 3.5 17.3 + - - +
19B ALA* 3.9 6.5 - - - +
20B PHE 3.3 0.2 - - - -
21B ARG* 1.3 79.9 - - - +
23B GLU* 1.3 60.9 + - - +
25B GLY* 4.3 2.3 + - - -
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Residues in contact with GLU 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 ALA 3.1 18.6 + - - +
22B GLU* 1.3 79.9 - - - +
24B PHE* 1.3 78.6 + - + +
25B GLY 3.6 0.2 - - - -
76B LEU* 4.0 22.4 - - + -
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Residues in contact with PHE 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 PHE* 2.8 70.3 + + + +
23B GLU* 1.3 86.2 - - + +
25B GLY* 1.3 57.3 + - - +
26B ALA* 3.0 11.8 + - + +
74B SER* 3.2 31.4 - - - -
75B LEU 4.8 0.4 - - - -
76B LEU* 4.7 9.0 - - + -
126B SER* 3.6 22.2 - - - -
127B ALA 4.0 12.6 - - - -
128B VAL* 3.7 17.3 - - + -
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Residues in contact with GLY 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 ARG* 2.8 24.9 + - - +
22B GLU 4.3 1.5 + - - -
23B GLU 3.6 2.0 - - - -
24B PHE* 1.3 73.4 - - - +
26B ALA* 1.3 59.5 + - - -
27B GLU* 5.7 0.3 - - - +
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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