Contacts of the helix formed by residues 9 - 20 (chain C) in PDB entry 6D6U
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 MET 9 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ASP* 6.3 0.2 - - + -
30B LEU* 3.6 30.7 - - + -
31B ARG 4.7 2.5 - - - +
33B GLY* 4.6 7.9 - - - +
34B LEU* 4.1 31.2 - - - +
35B GLY 5.9 0.7 - - - +
36B GLU* 5.1 14.8 + - + +
74B ARG* 3.5 40.4 - - + +
8C ASN* 1.3 90.2 + - - +
10C SER* 1.3 61.7 + - - +
11C LEU 3.5 0.7 - - - -
12C VAL* 3.9 3.1 + - - +
13C LYS* 3.9 17.5 + - + +
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Residues in contact with SER 10 (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 ASN* 3.4 15.4 + - - -
9C MET* 1.3 77.4 - - - +
11C LEU* 1.3 67.6 + - - +
12C VAL 3.4 0.2 + - - -
13C LYS* 3.5 12.2 + - - +
14C GLU* 3.6 14.0 + - - +
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Residues in contact with LEU 11 (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 ASN* 4.5 25.9 - - + +
9C MET 3.5 1.2 - - - +
10C SER* 1.3 79.0 - - - +
12C VAL* 1.3 62.7 + - + +
14C GLU* 3.2 24.0 - - - +
15C THR* 2.8 28.8 + - - +
76C VAL* 3.9 26.9 - - + +
77C ILE* 4.2 18.8 - - + -
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Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.5 24.2 - - + -
34B LEU* 3.6 15.0 - - + -
8C ASN 3.5 21.5 - - - +
9C MET* 3.9 4.4 + - - +
10C SER 3.3 0.6 - - - -
11C LEU* 1.3 75.4 - - - +
13C LYS* 1.3 63.4 + - - +
15C THR* 3.7 6.1 - - - -
16C VAL* 2.9 33.6 + - + +
77C ILE* 4.2 24.7 - - + -
79C LEU* 6.3 1.6 - - + -
81C LEU* 3.6 29.6 - - + -
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Residues in contact with LYS 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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25B GLY* 3.5 34.0 - - - +
26B TYR 5.3 0.2 - - - -
27B ASP* 4.3 28.1 - - + +
30B LEU* 4.2 11.1 - - + +
9C MET* 3.9 12.0 + - + +
10C SER* 3.5 10.0 + - - +
11C LEU 3.3 0.6 - - - -
12C VAL* 1.3 79.0 - - - +
14C GLU* 1.3 59.1 + - - +
16C VAL* 3.8 2.8 - - - +
17C ASP* 2.9 50.2 + - - +
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Residues in contact with GLU 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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10C SER 3.6 10.2 + - - +
11C LEU* 3.2 36.7 - - - +
13C LYS* 1.3 79.3 - - - +
15C THR* 1.3 59.6 + - - +
17C ASP* 3.7 8.8 - - - +
18C ARG* 2.9 35.1 + - - +
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Residues in contact with THR 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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11C LEU* 2.8 25.2 + - - +
12C VAL* 3.7 7.6 - - - -
14C GLU* 1.3 81.7 + - - +
16C VAL* 1.3 58.6 + - - +
18C ARG* 3.3 22.9 + - - +
19C LEU* 2.9 41.3 + - + +
74C TYR* 3.9 31.6 - - + -
76C VAL* 4.6 8.1 - - + +
77C ILE* 3.8 15.8 - - + +
81C LEU* 5.3 5.4 - - + -
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Residues in contact with VAL 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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27B ASP* 4.8 4.3 - - - +
29B ARG* 3.9 32.8 - - - +
30B LEU* 4.6 4.7 - - + -
12C VAL* 2.9 32.9 + - + +
13C LYS* 3.9 4.0 - - - +
15C THR* 1.3 74.8 - - - +
17C ASP* 1.3 63.1 + - - +
19C LEU* 3.6 10.1 - - + +
20C LEU* 2.9 38.3 + - + +
81C LEU* 4.4 17.5 - - + -
83C LEU* 4.5 21.3 - - + -
118C LEU* 6.2 0.9 - - + -
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Residues in contact with ASP 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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27B ASP* 4.3 2.9 - - - +
29B ARG* 3.6 21.3 + - - +
13C LYS* 2.9 49.9 + - - +
14C GLU* 3.7 8.5 - - - +
16C VAL* 1.3 77.6 - - - +
18C ARG* 1.3 61.7 + - - +
20C LEU* 3.7 2.1 + - - -
21C LYS* 3.2 27.8 + - - +
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Residues in contact with ARG 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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14C GLU* 2.9 19.3 + - - +
15C THR* 3.3 31.9 + - - +
17C ASP* 1.3 73.5 - - - +
19C LEU* 1.3 78.7 + - - +
21C LYS* 3.5 25.1 - - - +
73C SER 5.1 3.6 + - - -
74C TYR* 4.7 10.9 - - - +
75C ASN 5.1 1.0 - - - +
76C VAL* 4.2 23.0 - - - +
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Residues in contact with LEU 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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15C THR* 2.9 36.6 + - + +
16C VAL* 3.2 11.4 + - + +
18C ARG* 1.3 92.9 - - + +
20C LEU* 1.3 68.1 + - + +
21C LYS 3.1 10.2 + - - +
22C GLY 5.2 0.2 - - - -
23C TYR* 3.8 14.7 - - - +
71C ARG 3.8 19.9 - - - +
72C LEU* 4.5 13.8 - - + +
73C SER 3.6 24.5 - - - +
74C TYR* 4.3 18.8 - - + -
81C LEU* 5.4 1.3 - - + -
118C LEU* 4.9 14.6 - - + -
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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
----------------------------------------------------------
29B ARG* 4.7 14.6 - - - +
16C VAL* 2.9 29.2 + - + +
17C ASP* 3.9 3.4 - - - +
19C LEU* 1.3 87.3 - - + +
21C LYS* 1.3 56.7 + - - +
22C GLY 4.2 0.5 + - - -
23C TYR* 4.2 17.1 + - + +
72C LEU* 4.5 7.0 - - + -
83C LEU* 5.4 5.8 - - + -
87C VAL* 3.5 25.8 - - + -
90C GLN* 3.2 32.7 - - + +
91C LEU* 4.4 21.1 - - + -
118C LEU* 5.9 1.8 - - + -
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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