Contacts of the helix formed by residues 16 - 25 (chain C) in PDB entry 1MKG
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 LYS 16 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL 3.4 7.5 + - - +
15C VAL* 1.3 76.6 - - - +
17C PHE* 1.3 67.7 + - - +
18C MET* 3.3 4.9 - - + +
19C ASP* 3.0 36.3 + - - +
20C VAL* 3.3 11.4 + - - +
79D GLN* 3.4 12.3 - - - +
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Residues in contact with PHE 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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16C LYS* 1.3 72.1 - - - +
18C MET* 1.3 71.6 + - + +
19C ASP 3.2 0.3 + - - -
20C VAL* 3.3 3.0 + - - +
21C TYR* 3.0 48.0 + + + +
48D LYS* 3.2 31.4 - - + -
49D PRO* 4.2 5.8 - - + -
79D GLN* 2.8 44.7 + - + +
81D MET* 3.6 28.9 - - + -
91D ILE* 3.4 29.2 - - + -
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Residues in contact with MET 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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16C LYS* 3.3 3.4 - - + +
17C PHE* 1.3 87.9 - - + +
19C ASP* 1.3 64.3 + - - +
21C TYR* 3.4 30.7 - - + -
22C GLN* 3.1 68.5 + - + +
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Residues in contact with ASP 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 VAL* 4.0 14.8 - - + -
16C LYS* 3.0 41.5 + - - +
18C MET* 1.3 78.3 - - - +
20C VAL* 1.3 59.0 + - - +
22C GLN* 3.4 8.6 + - - +
23C ARG* 2.8 46.2 + - + +
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Residues in contact with VAL 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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15C VAL* 3.7 25.1 - - + +
16C LYS 3.4 14.6 - - - +
17C PHE 3.3 3.7 + - - +
19C ASP* 1.3 75.3 - - - +
21C TYR* 1.3 55.6 + - - +
23C ARG* 4.0 5.1 - - - +
24C SER* 2.8 39.6 + - - -
49D PRO* 3.8 13.0 - - + -
52D VAL* 3.6 31.4 - - + -
53D PRO* 4.0 13.9 - - + -
78D MET* 4.0 15.3 - - + -
79D GLN 4.1 12.1 - - - +
80D ILE* 4.0 3.4 - - + -
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Residues in contact with TYR 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 PHE* 3.0 34.4 + + + +
18C MET* 3.4 31.2 - - + +
20C VAL* 1.3 80.0 - - - +
22C GLN* 1.3 62.2 + - + +
24C SER* 3.4 11.9 + - - -
25C TYR* 3.5 14.0 + + - +
62C ASN* 3.8 19.2 + - - +
48D LYS* 3.8 31.8 + - + +
49D PRO* 4.2 21.0 - - + +
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Residues in contact with GLN 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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18C MET* 3.1 49.8 + - + +
19C ASP* 4.0 9.1 + - - +
21C TYR* 1.3 80.9 - - + +
23C ARG* 1.3 64.6 + - + +
24C SER 3.4 1.0 + - - -
25C TYR* 3.5 15.8 + - - +
27C HIS* 5.7 0.7 - - - -
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Residues in contact with ARG 23 (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 VAL* 3.7 30.5 - - - +
19C ASP* 2.8 33.6 + - + +
20C VAL* 4.0 2.4 - - - +
22C GLN* 1.3 80.2 - - + +
24C SER* 1.3 57.9 + - - +
27C HIS* 3.5 21.1 + - - -
30D GLU* 3.0 35.9 + - - +
32D LEU* 4.2 6.8 - - - +
53D PRO* 3.6 33.0 + - + +
76D ILE* 5.7 2.0 - - - +
78D MET* 4.6 3.2 - - - +
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Residues in contact with SER 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 VAL 2.8 23.1 + - - -
21C TYR 3.4 3.3 + - - -
23C ARG* 1.3 72.7 - - - +
25C TYR* 1.3 70.3 + - - +
27C HIS* 4.9 0.4 - - - -
59C GLY* 3.2 8.2 - - - -
60C CYS* 3.1 21.5 + - - -
62C ASN* 5.4 0.5 + - - -
32D LEU* 4.0 11.2 - - - -
49D PRO* 3.0 21.8 - - - +
51D CYS* 3.1 31.9 - - - -
53D PRO* 4.6 4.3 - - - -
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Residues in contact with TYR 25 (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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21C TYR* 3.5 12.5 + + - +
22C GLN* 3.7 14.4 - - - +
23C ARG 3.4 1.4 - - - -
24C SER* 1.3 80.2 + - - +
26C CYS* 1.3 80.8 + - + +
27C HIS* 2.6 36.7 - - - -
60C CYS* 3.7 11.7 - - - -
61C CYS* 4.7 6.5 - - - -
62C ASN* 4.8 10.5 - - - +
103C GLU* 5.9 3.0 - - + +
104C CYS* 3.7 34.8 + - - +
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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