Contacts of the helix formed by residues 12 - 25 (chain B) in PDB entry 5UQ9
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 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B GLY 3.1 7.7 + - - +
11B LEU* 1.3 78.0 - - - +
13B VAL* 1.3 62.4 + - + +
14B MET* 3.1 8.3 - - + +
15B GLY 2.9 4.0 + - - +
16B GLN* 2.5 40.5 + - - +
38B LYS* 5.1 0.9 - - - +
74B LEU 5.5 5.4 - - - +
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Residues in contact with VAL 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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12B ALA* 1.3 75.3 - - + +
14B MET* 1.3 66.5 + - + +
16B GLN* 4.3 13.4 - - - +
17B ASN* 2.8 36.9 + - - +
132B GLU* 3.0 37.9 - - + +
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Residues in contact with MET 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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12B ALA* 3.1 5.0 - - + +
13B VAL* 1.3 84.1 - - + +
15B GLY* 1.3 64.6 + - - +
17B ASN* 3.9 3.9 - - - +
18B LEU* 3.3 31.6 + - + +
74B LEU* 4.1 27.4 - - + -
101B GLY 5.2 0.7 - - - +
128B VAL* 3.8 35.9 - - + +
129B SER 6.5 0.2 - - - -
131B GLY* 3.2 35.2 - - - +
132B GLU* 5.1 4.9 - - + -
135B ALA* 3.7 11.4 - - + +
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Residues in contact with GLY 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 LEU* 3.6 18.9 - - - +
10B GLY 3.5 18.6 + - - -
11B LEU* 5.2 0.2 - - - -
12B ALA* 2.9 8.5 + - - +
14B MET* 1.3 76.4 - - - +
16B GLN* 1.3 65.5 + - - +
18B LEU* 3.5 1.1 + - - -
19B ILE* 3.1 28.8 + - - +
74B LEU* 4.3 12.0 - - - +
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Residues in contact with GLN 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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11B LEU* 3.3 29.7 + - + +
12B ALA 2.5 25.3 + - - +
13B VAL* 4.2 13.3 - - - +
15B GLY* 1.3 73.1 - - - +
17B ASN* 1.3 58.7 + - - +
19B ILE* 3.1 5.7 + - - +
20B LEU* 2.9 36.4 + - + +
38B LYS* 4.4 10.3 - - - +
41B ASP* 5.9 0.6 + - - -
42B PHE* 3.5 44.8 - - + +
46B GLU* 3.8 20.0 + - - +
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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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13B VAL* 2.8 23.7 + - - +
14B MET 3.9 0.2 - - - +
15B GLY 3.3 0.2 - - - -
16B GLN* 1.3 78.0 - - - +
18B LEU* 1.3 57.4 + - - +
20B LEU* 3.7 6.5 - - - +
21B ASN* 2.8 24.9 + - - +
132B GLU* 2.9 38.2 + - - +
135B ALA* 2.9 31.3 - - + +
136B ARG* 3.4 27.0 + - - +
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Residues in contact with LEU 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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8B LEU* 3.9 13.0 - - + -
14B MET* 3.3 20.5 + - + +
15B GLY 3.8 4.5 - - - +
17B ASN* 1.3 76.8 - - - +
19B ILE* 1.3 57.7 + - - +
21B ASN* 3.4 2.9 + - + +
22B MET* 3.0 37.5 + - + +
72B ILE* 5.2 7.2 - - + -
74B LEU* 4.3 24.5 - - + -
128B VAL* 4.5 20.2 - - + -
135B ALA* 3.5 20.9 - - + +
139B PRO* 3.7 26.7 - - + -
141B LEU* 5.1 2.9 - - + -
160B ILE* 4.3 16.8 - - + -
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Residues in contact with ILE 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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8B LEU* 3.7 34.5 - - + -
11B LEU* 3.7 30.3 - - + -
15B GLY 3.1 11.3 + - - +
16B GLN 3.5 7.2 - - - +
18B LEU* 1.3 74.8 - - - +
20B LEU* 1.3 60.6 + - - +
22B MET* 3.2 9.6 + - - +
23B ASN* 2.9 26.3 + - - +
29B VAL* 3.7 21.6 - - + +
31B ALA* 3.8 14.6 - - + -
42B PHE* 4.1 9.6 - - + -
52B VAL* 3.9 28.7 - - + -
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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 GLN* 2.9 23.0 + - + +
17B ASN* 3.9 7.4 - - - +
19B ILE* 1.3 76.6 - - - +
21B ASN* 1.3 57.2 + - - +
23B ASN* 3.3 4.9 + - + +
24B ASP* 2.9 36.1 + - - +
42B PHE* 4.0 19.3 - - + -
46B GLU* 3.4 41.5 - - + +
47B ALA* 4.5 6.5 - - + -
50B THR* 5.0 6.3 - - + -
52B VAL* 5.0 7.2 - - + -
136B ARG* 3.5 41.7 - - - +
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Residues in contact with ASN 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 ASN 2.8 23.2 + - - +
18B LEU* 3.6 7.6 - - + +
19B ILE 3.2 0.2 - - - -
20B LEU* 1.3 73.5 - - - +
22B MET* 1.3 59.9 + - - +
24B ASP* 3.3 4.2 + - - +
25B HIS* 2.8 52.1 + - - -
135B ALA 3.5 7.8 + - - +
136B ARG* 3.0 33.6 + - - +
137B TYR* 3.3 3.1 - - - -
138B GLY 3.2 18.8 - - - +
139B PRO* 3.6 4.6 - - - +
160B ILE* 3.4 24.1 + - + +
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Residues in contact with MET 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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6B ILE* 3.6 27.1 - - + -
8B LEU* 4.2 15.9 - - + -
18B LEU* 3.0 26.8 + - + +
19B ILE* 3.7 13.9 - - - +
21B ASN* 1.3 75.5 - - - +
23B ASN* 1.3 60.6 + - - +
25B HIS 3.3 3.2 + - - +
27B PHE* 2.9 39.0 + - + +
29B VAL* 3.6 29.8 - - + -
72B ILE* 4.5 9.2 - - + -
156B ILE* 3.8 16.4 - - + -
160B ILE* 3.6 33.7 - - + -
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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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19B ILE 2.9 16.3 + - - +
20B LEU* 3.6 9.0 - - + +
21B ASN 3.2 0.2 - - - -
22B MET* 1.3 74.2 - - - +
24B ASP* 1.3 67.4 + - - +
25B HIS 3.1 2.0 - - - -
26B GLY* 2.9 20.1 + - - -
27B PHE 3.6 10.3 + - - +
29B VAL* 4.5 0.2 - - - +
50B THR* 3.4 29.3 - - + +
51B LYS* 2.9 43.6 + - - +
52B VAL* 3.4 17.2 + - + +
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Residues in contact with ASP 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* 2.9 15.8 + - - +
21B ASN* 3.3 6.9 + - - +
23B ASN* 1.3 84.3 + - - +
25B HIS* 1.3 66.1 + - + +
26B GLY 3.3 1.2 + - - -
136B ARG* 2.4 39.8 + - - +
137B TYR* 5.0 4.3 - - - -
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Residues in contact with HIS 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 ASN* 2.8 39.1 + - - +
22B MET 3.9 3.8 - - - +
23B ASN 3.1 1.2 - - - -
24B ASP* 1.3 83.9 - - + +
26B GLY* 1.3 58.8 + - - +
27B PHE* 3.5 31.4 + - + -
137B TYR* 5.0 8.5 - - - -
159B GLY* 3.0 33.1 + - - -
160B ILE* 4.0 5.6 - - + -
163B LYS* 5.4 0.6 + - - -
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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
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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