Contacts of the helix formed by residues 16 - 29 (chain C) in PDB entry 3RKR
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 ARG 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C GLY 4.2 4.1 + - - +
14C ALA 3.3 1.0 - - - -
15C SER* 1.3 92.3 + - - +
17C GLY* 1.3 70.7 + - - +
18C ILE 3.4 0.2 + - - -
19C GLY* 3.2 7.3 + - - -
20C ALA* 3.2 17.6 + - - -
42C LYS* 5.6 5.8 - - - +
240C SO4 4.0 14.2 + - - +
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Residues in contact with GLY 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 ARG* 1.3 75.9 - - - +
18C ILE* 1.3 62.6 + - - -
20C ALA* 3.8 2.2 - - - +
21C ALA* 3.1 22.9 + - - +
24C ARG* 5.4 0.7 + - - -
209C PRO* 3.9 16.1 - - - +
240C SO4 3.3 15.9 - - - -
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Residues in contact with ILE 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 ARG 3.4 0.4 + - - -
17C GLY* 1.3 71.9 - - - -
19C GLY* 1.3 56.1 + - - +
21C ALA* 3.2 2.3 + - - +
22C ILE* 2.8 45.2 + - + +
90C ASN* 3.4 18.8 - - - +
141C ILE* 4.4 5.2 - - + -
203C ALA* 3.9 21.8 - - + +
204C LEU* 4.0 13.2 - - + -
207C ILE 5.5 2.2 - - - +
209C PRO* 4.1 23.3 - - + +
212C ILE* 3.6 38.6 - - + -
240C SO4 2.8 34.5 + - - +
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Residues in contact with GLY 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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11C VAL* 3.7 8.5 - - - +
13C GLY 3.4 11.6 + - - -
14C ALA* 3.8 8.3 - - - -
16C ARG 3.2 4.0 + - - -
18C ILE* 1.3 78.6 - - - +
20C ALA* 1.3 55.0 + - - +
22C ILE* 3.2 5.5 + - - +
23C ALA* 3.0 28.6 + - - +
90C ASN* 3.3 26.9 + - - -
240C SO4 4.4 1.2 + - - -
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Residues in contact with ALA 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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14C ALA 3.2 19.8 + - - +
15C SER 4.0 2.5 - - - +
16C ARG* 3.2 28.3 + - - -
17C GLY 3.8 2.0 - - - +
19C GLY* 1.3 75.6 - - - +
21C ALA* 1.3 58.4 + - - +
23C ALA* 3.3 3.1 + - - +
24C ARG* 2.9 56.7 + - - +
46C VAL* 3.7 11.3 - - + +
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Residues in contact with ALA 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 GLY 3.1 16.6 + - - +
18C ILE 3.7 3.4 - - - +
20C ALA* 1.3 76.5 - - - +
22C ILE* 1.3 66.1 + - - +
24C ARG* 3.8 16.7 - - - +
25C LYS* 2.9 24.8 + - - +
209C PRO* 3.8 30.1 - - + +
210C ASP* 3.8 14.8 - - - +
213C ALA* 3.4 5.9 - - + +
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 4.0 14.4 - - + -
18C ILE* 2.8 41.6 + - + +
19C GLY 3.6 3.4 - - - +
21C ALA* 1.3 77.2 - - - +
23C ALA* 1.3 57.3 + - - +
25C LYS* 3.2 3.0 + - - +
26C LEU* 2.9 42.6 + - + +
88C VAL* 4.1 10.5 - - + -
90C ASN* 4.2 7.6 - - + +
141C ILE* 4.0 16.2 - - + -
212C ILE* 4.3 0.7 - - + -
213C ALA* 3.9 24.2 - - - +
216C VAL* 3.9 37.7 - - + -
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Residues in contact with ALA 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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11C VAL* 4.3 6.7 - - + -
14C ALA* 4.4 3.1 - - + -
19C GLY 3.0 16.2 + - - +
20C ALA* 3.6 8.5 - - - +
22C ILE* 1.3 73.3 - - - +
24C ARG* 1.3 60.7 + - - +
26C LEU* 3.2 2.1 + - - -
27C GLY* 2.9 26.3 + - - -
33C VAL* 3.7 19.5 - - + +
35C LEU* 3.4 32.3 - - + -
46C VAL* 4.5 1.6 - - + -
50C ILE* 3.9 7.9 - - + +
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Residues in contact with ARG 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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17C GLY 5.4 0.4 + - - -
20C ALA* 2.9 42.8 + - - +
21C ALA* 3.8 26.7 - - - +
23C ALA* 1.3 71.5 - - - +
25C LYS* 1.3 58.4 + - - +
27C GLY* 3.2 1.9 + - - -
28C SER* 2.8 31.2 + - - -
46C VAL* 4.4 6.5 - - + +
49C GLU* 2.8 41.5 + - + +
50C ILE* 4.0 20.9 - - + +
210C ASP* 5.0 4.8 + - - -
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Residues in contact with LYS 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 ALA 2.9 19.1 + - - +
22C ILE 3.6 4.3 - - - +
24C ARG* 1.3 77.0 - - - +
26C LEU* 1.3 63.7 + - + +
28C SER* 2.8 29.3 + - - +
29C LEU* 3.2 19.9 + - - +
213C ALA* 3.9 17.7 - - + +
214C ASP* 3.3 27.2 + - - +
217C ALA* 3.7 31.0 - - + -
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Residues in contact with LEU 26 (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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4C LEU* 4.0 19.2 - - + +
9C ALA* 3.7 27.1 - - + -
11C VAL* 4.2 6.1 - - + -
22C ILE* 2.9 39.5 + - + +
23C ALA* 4.0 3.4 - - - +
25C LYS* 1.3 74.3 - - + +
27C GLY* 1.3 62.5 + - - +
29C LEU* 3.1 13.7 + - + +
30C GLY 3.3 0.3 + - - -
31C ALA* 3.2 22.0 + - + +
33C VAL* 4.2 10.3 - - + -
86C VAL* 4.3 6.7 - - + -
88C VAL* 4.1 15.3 - - + -
213C ALA 5.5 0.2 - - - +
216C VAL* 4.3 10.3 - - + -
217C ALA* 4.2 25.1 - - + +
220C ALA* 4.3 6.1 - - + -
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Residues in contact with GLY 27 (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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23C ALA 2.9 12.7 + - - -
24C ARG 3.6 3.4 - - - -
26C LEU* 1.3 76.9 - - - +
28C SER* 1.3 57.0 + - - +
30C GLY* 2.9 21.3 + - - -
31C ALA 3.9 6.1 - - - -
33C VAL* 3.6 17.5 - - - +
50C ILE* 4.0 17.7 - - - -
55C GLY* 4.5 13.0 - - - -
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Residues in contact with SER 28 (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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2C SER* 4.4 5.4 + - - -
24C ARG 2.8 16.4 + - - -
25C LYS* 2.8 30.5 + - - +
27C GLY* 1.3 72.7 - - - +
29C LEU* 1.3 64.9 + - - +
30C GLY 3.2 1.0 + - - -
53C ALA* 5.8 9.6 - - - -
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Residues in contact with LEU 29 (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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2C SER* 3.2 16.5 - - - +
3C SER* 4.5 12.8 - - - +
4C LEU* 2.9 45.1 + - + +
25C LYS* 3.5 22.7 - - + +
26C LEU* 3.1 8.6 + - - +
27C GLY 3.1 0.8 - - - -
28C SER* 1.3 83.4 + - - +
30C GLY* 1.3 58.1 + - - +
31C ALA 3.7 0.9 - - - -
217C ALA* 3.6 31.2 - - + -
221C THR* 3.9 20.2 - - + -
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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