Contacts of the helix formed by residues 12 - 25 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10H GLY 3.4 7.8 + - - +
11H LEU* 1.3 74.9 - - - +
13H VAL* 1.3 63.1 + - + +
14H MET* 3.1 6.3 - - + +
15H GLY 3.7 5.1 - - - +
16H GLN* 2.6 40.6 + - - +
74H LEU 5.4 5.6 - - - +
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Residues in contact with VAL 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ALA* 1.3 75.4 - - + +
14H MET* 1.3 61.1 + - + +
16H GLN* 3.6 14.1 - - - +
17H ASN* 2.2 46.2 + - - +
132H GLU* 4.5 25.1 - - + -
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Residues in contact with MET 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ALA* 3.1 3.4 - - + +
13H VAL* 1.3 82.6 - - + +
15H GLY* 1.3 62.8 + - - +
17H ASN* 3.5 0.7 + - - +
18H LEU* 3.3 37.1 + - + +
74H LEU* 4.7 14.4 - - + -
128H VAL* 4.3 31.0 - - + +
129H SER* 6.2 0.4 - - - -
130H GLY 5.8 1.8 - - - +
131H GLY 3.5 31.9 - - - +
132H GLU* 4.5 7.6 - - + -
135H ALA* 3.6 17.6 - - + +
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Residues in contact with GLY 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LEU* 3.4 21.3 - - - +
10H GLY 3.8 15.3 - - - -
11H LEU* 5.3 0.2 - - - -
12H ALA* 3.1 9.4 + - - +
14H MET* 1.3 80.7 - - - +
16H GLN* 1.3 60.1 + - - +
18H LEU 3.5 1.0 + - - -
19H ILE* 3.4 14.7 + - - +
74H LEU* 3.6 24.5 - - - +
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Residues in contact with GLN 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H LEU* 3.6 17.5 - - + +
12H ALA 2.6 29.2 + - - +
13H VAL* 3.6 18.5 + - - +
15H GLY* 1.3 69.9 - - - +
17H ASN* 1.3 76.4 + - - +
19H ILE* 3.2 6.0 + - - +
20H LEU* 3.0 28.7 + - + +
42H PHE* 3.4 37.7 - - + +
46H GLU* 3.8 24.3 + - + +
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Residues in contact with ASN 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H VAL* 2.2 41.0 + - - +
14H MET* 3.5 2.9 + - - +
15H GLY 3.3 0.4 - - - -
16H GLN* 1.3 90.3 + - - +
18H LEU* 1.3 52.4 + - - +
20H LEU* 3.0 12.5 + - - +
21H ASN* 2.3 39.4 + - - -
132H GLU 4.1 10.9 + - - -
135H ALA* 3.7 4.7 - - + +
136H ARG* 3.3 46.6 + - - +
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Residues in contact with LEU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LEU* 4.0 9.4 - - + -
14H MET* 3.3 23.8 + - + +
15H GLY 3.8 6.3 - - - +
16H GLN 3.3 0.2 - - - -
17H ASN* 1.3 78.7 - - - +
19H ILE* 1.3 60.4 + - - +
21H ASN* 3.3 16.7 + - - +
22H MET* 3.3 24.5 + - + +
72H ILE* 5.9 2.7 - - + -
74H LEU* 3.6 26.2 - - + -
128H VAL* 4.5 13.9 - - + -
135H ALA* 3.2 22.2 - - + +
139H PRO* 3.8 25.4 - - + -
141H LEU* 5.5 4.3 - - + -
160H ILE* 4.7 5.2 - - + -
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Residues in contact with ILE 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LEU* 3.7 35.0 - - + +
11H LEU* 4.5 5.8 - - + -
15H GLY 3.4 11.2 + - - +
16H GLN* 3.2 9.3 + - - +
17H ASN 3.2 0.4 - - - -
18H LEU* 1.3 77.4 - - - +
20H LEU* 1.3 62.3 + - - +
21H ASN 3.1 0.2 - - - -
22H MET* 3.2 9.1 + - - +
23H ASN* 3.2 22.3 + - - +
29H VAL* 3.8 27.4 - - + +
31H ALA* 3.7 28.7 - - + -
42H PHE* 4.0 14.6 - - + -
52H VAL* 3.9 25.4 - - + -
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H GLN* 3.0 24.9 + - + +
17H ASN* 3.0 15.3 + - - +
19H ILE* 1.3 76.3 - - + +
21H ASN* 1.3 59.2 + - - +
23H ASN* 2.7 30.6 - - - +
24H ASP* 3.5 1.0 - - - +
42H PHE* 3.5 28.7 - - + -
46H GLU* 3.9 27.4 - - + +
47H ALA* 4.0 11.2 - - + -
50H THR* 6.1 0.2 - - + -
136H ARG* 2.9 46.6 + - - +
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Residues in contact with ASN 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ASN 2.3 32.9 + - - -
18H LEU* 3.3 10.0 - - - +
19H ILE 3.1 0.2 - - - -
20H LEU* 1.3 78.1 - - - +
22H MET* 1.3 58.7 + - - +
24H ASP* 3.5 2.1 + - - +
25H HIS* 3.0 39.4 + - + -
135H ALA 2.2 30.0 + - - +
136H ARG* 2.8 29.4 + - - +
137H TYR 2.9 21.3 - - - +
139H PRO* 4.3 0.3 - - - +
160H ILE* 3.4 28.6 - - + +
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Residues in contact with MET 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ILE* 3.6 31.6 - - + -
8H LEU* 4.3 14.6 - - + -
18H LEU* 3.3 21.7 + - + +
19H ILE* 3.2 5.8 + - - -
21H ASN* 1.3 73.9 - - - +
23H ASN* 1.3 60.8 + - - +
25H HIS 3.7 0.4 - - - +
26H GLY 3.1 8.8 + - - -
27H PHE* 2.7 40.1 + - + -
29H VAL* 3.6 28.5 - - + -
72H ILE* 4.4 12.6 - - + -
156H ILE* 3.7 18.2 - - + -
160H ILE* 3.5 22.9 - - + -
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Residues in contact with ASN 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ILE 3.2 9.1 + - - +
20H LEU* 2.7 36.9 - - - +
22H MET* 1.3 75.5 - - - +
24H ASP* 1.3 87.8 + - - +
26H GLY* 3.2 12.1 + - - -
27H PHE 3.4 15.7 + - - +
29H VAL* 4.5 0.9 - - + +
50H THR* 3.0 34.4 + - - +
51H LYS* 4.5 15.6 - - + +
52H VAL* 3.2 23.8 - - + +
136H ARG* 4.8 0.2 + - - -
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Residues in contact with ASP 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LEU 3.5 15.7 - - - +
21H ASN 3.5 4.0 + - - +
22H MET 3.4 0.4 - - - -
23H ASN* 1.3 87.8 + - - +
25H HIS* 1.3 71.9 + - + +
26H GLY 3.4 1.4 + - - -
136H ARG* 3.7 16.4 + - - +
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Residues in contact with HIS 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ASN* 3.0 24.9 + - - +
22H MET* 3.4 4.7 + - - +
23H ASN 3.1 0.2 - - - -
24H ASP* 1.3 94.1 + - + +
26H GLY* 1.3 58.7 + - - +
27H PHE* 3.3 25.6 - - + -
136H ARG* 5.8 1.3 + - - -
137H TYR 4.3 12.0 + - - -
159H GLY* 3.9 10.4 + - - +
160H ILE* 3.2 42.5 - - + +
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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