Contacts of the helix formed by residues 12 - 24 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C GLY 3.2 7.0 + - - +
11C LEU* 1.3 76.9 - - - +
13C VAL* 1.3 62.6 + - + +
14C MET* 3.1 9.4 - - + +
15C GLY 3.7 3.3 - - - +
16C GLN* 2.7 38.3 + - - +
74C LEU 5.3 6.1 - - - +
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Residues in contact with VAL 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 1.3 77.9 - - + +
14C MET* 1.3 63.9 + - + +
16C GLN* 4.6 8.7 + - - +
17C ASN* 2.6 50.8 + - - +
132C GLU* 3.5 23.1 - - + +
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Residues in contact with MET 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 3.1 5.9 - - + +
13C VAL* 1.3 83.3 - - + +
15C GLY* 1.3 64.7 + - - +
17C ASN* 4.0 1.7 - - - +
18C LEU* 3.1 34.7 + - + +
74C LEU* 3.9 27.1 - - + -
128C VAL* 4.8 16.4 - - + +
130C GLY 4.7 5.6 - - - +
131C GLY* 3.8 7.9 - - - +
132C GLU* 3.2 20.9 - - - +
135C ALA* 3.7 25.8 - - - -
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Residues in contact with GLY 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.6 16.2 - - - +
10C GLY 3.5 22.3 + - - -
11C LEU* 5.2 0.4 - - - -
12C ALA* 3.1 6.3 + - - +
14C MET* 1.3 76.8 - - - +
16C GLN* 1.3 59.4 + - - +
18C LEU 3.4 0.2 + - - -
19C ILE* 2.9 37.1 + - - +
74C LEU* 3.7 10.3 - - - +
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Residues in contact with GLN 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.0 24.5 + - + +
12C ALA 2.7 27.0 + - - +
13C VAL* 4.5 8.5 - - - +
15C GLY* 1.3 70.2 - - - +
17C ASN* 1.3 66.3 + - - +
19C ILE* 3.2 3.5 + - - +
20C LEU* 3.1 29.4 + - + +
38C LYS 5.8 0.2 + - - -
42C PHE* 3.5 49.2 - - + +
46C GLU* 4.0 24.4 - - - +
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Residues in contact with ASN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C VAL* 2.6 29.6 + - - +
14C MET 4.1 2.0 - - - +
15C GLY 3.3 0.6 - - - -
16C GLN* 1.3 78.7 - - - +
18C LEU* 1.3 57.2 + - - +
20C LEU* 3.6 9.2 + - - +
21C ASN* 2.9 30.8 + - - +
132C GLU* 2.4 38.1 + - - +
135C ALA* 3.9 6.2 - - + +
136C ARG* 3.3 48.1 + - + +
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.0 13.7 - - + -
14C MET* 3.1 22.7 + - + +
17C ASN* 1.3 74.9 - - - +
19C ILE* 1.3 65.6 + - - +
21C ASN* 3.6 4.6 + - - +
22C MET* 3.4 30.4 + - + +
72C ILE* 5.7 4.7 - - + -
74C LEU* 3.6 26.9 - - + -
128C VAL* 4.5 22.9 - - + -
135C ALA* 3.2 22.9 - - - +
139C PRO* 3.9 23.8 - - + -
141C LEU* 5.5 2.9 - - + -
160C ILE* 4.8 13.0 - - + -
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.6 41.7 - - + +
11C LEU* 4.4 6.7 - - + -
15C GLY 2.9 19.7 + - - +
16C GLN 3.2 4.2 + - - +
18C LEU* 1.3 77.2 - - - +
20C LEU* 1.3 63.9 + - - +
22C MET* 3.2 16.7 + - - +
23C ASN 3.6 2.1 + - - -
29C VAL* 3.4 37.1 - - + +
31C ALA* 3.7 29.2 - - + -
42C PHE* 3.8 19.1 - - + -
52C VAL* 3.7 17.3 - - + -
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLN* 3.1 20.4 + - + +
17C ASN* 3.6 13.7 - - - +
19C ILE* 1.3 79.5 - - + +
21C ASN* 1.3 65.4 + - - +
23C ASN* 2.7 36.8 - - - +
24C ASP* 2.9 29.5 - - - +
42C PHE* 5.2 7.4 - - + -
46C GLU* 5.7 4.3 - - + +
47C ALA* 5.1 13.7 - - + -
50C THR* 6.0 0.4 - - + -
136C ARG* 3.2 51.8 - - + +
137C TYR* 5.6 2.2 - - + -
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Residues in contact with ASN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ASN 2.9 21.2 + - - +
18C LEU* 3.8 9.0 - - - +
19C ILE 3.2 0.2 - - - -
20C LEU* 1.3 77.3 - - - +
22C MET* 1.3 59.5 + - - +
24C ASP* 3.8 10.9 + - - +
25C HIS* 2.9 37.5 + - - -
135C ALA 4.3 3.4 - - - +
136C ARG* 2.6 33.6 + - - +
137C TYR* 3.3 18.1 + - - +
138C GLY 4.7 0.7 - - - -
139C PRO* 4.4 3.0 - - - +
160C ILE* 3.1 39.8 + - - +
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Residues in contact with MET 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.6 25.1 - - + -
8C LEU* 4.6 11.4 - - + -
18C LEU* 3.4 22.2 + - + +
19C ILE* 3.2 7.5 + - - +
20C LEU 3.2 0.8 - - - -
21C ASN* 1.3 77.4 - - - +
23C ASN* 1.3 60.4 + - - +
24C ASP 3.2 0.2 - - - -
25C HIS* 3.0 15.1 + - - -
26C GLY 3.2 1.6 + - - -
27C PHE* 3.1 32.7 + - + -
29C VAL* 3.7 31.9 - - + -
72C ILE* 4.4 13.7 - - + -
156C ILE* 3.7 17.7 - - + -
160C ILE* 3.8 32.1 - - + -
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Residues in contact with ASN 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE 3.6 2.9 + - - +
20C LEU* 2.7 25.1 - - - +
22C MET* 1.3 73.8 - - - +
24C ASP* 1.3 87.3 + - - +
25C HIS 3.0 1.8 - - - -
26C GLY* 2.7 21.5 + - - -
27C PHE 3.2 23.0 + - - +
29C VAL* 4.6 0.4 - - + -
50C THR* 2.5 38.7 + - - +
51C LYS* 4.6 11.8 - - + +
52C VAL* 3.2 21.1 - - + +
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Residues in contact with ASP 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU* 2.9 34.5 - - - +
21C ASN* 3.8 12.3 + - - +
22C MET 3.2 0.6 - - - -
23C ASN* 1.3 93.9 + - - +
25C HIS* 1.3 65.9 + - + +
26C GLY 3.4 0.4 + - - -
136C ARG 5.0 1.9 - - - +
137C TYR* 5.7 4.5 - - - -
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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