Contacts of the helix formed by residues 16 - 29 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B GLY 4.0 4.2 + - - +
14B ALA 3.4 1.4 - - - -
15B SER* 1.3 88.2 - - - +
17B GLY* 1.3 69.9 + - - +
18B ILE 3.3 1.9 + - - -
19B GLY* 3.4 5.2 + - - -
20B ALA* 3.3 17.2 + - - -
240B NAP 2.9 64.3 + - - +
241B SO4 4.0 15.5 + - - +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 1.3 75.5 - - - +
18B ILE* 1.3 57.6 + - - -
20B ALA* 3.6 3.2 - - - +
21B ALA* 2.9 30.1 + - - +
24B ARG* 5.2 0.7 + - - +
209B PRO* 3.8 18.2 - - - +
241B SO4 3.4 13.7 + - - -
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY* 1.3 70.3 - - - -
19B GLY* 1.3 51.7 + - - +
21B ALA* 3.3 2.1 + - - +
22B ILE* 2.7 50.1 + - + +
90B ASN* 3.5 14.1 - - - +
141B ILE* 4.4 11.2 - - + -
207B ILE 5.5 4.5 - - - +
209B PRO* 4.1 27.1 - - + +
212B ILE* 3.5 43.5 - - + -
241B SO4 2.4 41.1 + - - +
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.7 8.6 - - - +
13B GLY 3.5 9.4 - - - -
14B ALA* 3.9 9.4 - - - -
16B ARG 3.4 3.2 + - - -
17B GLY 3.3 0.4 - - - -
18B ILE* 1.3 77.8 - - - +
20B ALA* 1.4 51.6 + - - +
22B ILE* 3.1 5.1 + - - +
23B ALA* 2.8 36.4 + - - +
90B ASN* 3.4 27.7 + - - -
241B SO4 4.4 1.0 + - - -
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 3.3 20.2 + - - +
15B SER 4.2 0.2 - - - +
16B ARG* 3.3 30.5 + - - +
17B GLY 3.6 2.2 - - - +
19B GLY* 1.4 71.1 - - - +
21B ALA* 1.3 57.8 - - - +
23B ALA* 3.2 4.9 + - - +
24B ARG* 2.9 56.5 + - - +
46B VAL* 4.0 12.9 - - + +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY 2.9 16.9 + - - +
18B ILE 3.7 3.4 - - - +
20B ALA* 1.3 75.0 - - - +
22B ILE* 1.3 63.2 + - - +
24B ARG* 3.4 17.2 + - - +
25B LYS* 2.9 25.6 + - - +
209B PRO* 3.8 22.9 - - + +
210B ASP* 3.6 23.8 - - - +
213B ALA* 3.5 4.7 - - + +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.1 13.0 - - + -
18B ILE* 2.7 47.0 + - + +
19B GLY* 3.6 5.8 - - - +
21B ALA* 1.3 73.1 - - - +
23B ALA* 1.3 58.2 + - - +
25B LYS* 3.1 2.5 + - - +
26B LEU* 2.8 50.7 + - + +
88B VAL* 4.2 11.0 - - + -
90B ASN* 4.3 3.6 - - + +
141B ILE* 4.1 15.5 - - + -
212B ILE* 4.2 0.7 - - + -
213B ALA* 3.8 26.0 - - - +
216B VAL* 4.0 31.0 - - + -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.4 7.2 - - + +
14B ALA* 4.6 0.4 - - + -
19B GLY 2.8 16.5 + - - +
20B ALA* 3.5 8.5 - - - +
22B ILE* 1.3 74.2 - - - +
24B ARG* 1.3 57.8 + - - +
26B LEU* 4.9 0.2 - - - -
27B GLY* 2.8 29.5 + - - -
33B VAL* 3.7 17.0 - - + +
35B LEU* 3.2 35.2 - - + -
46B VAL* 4.3 3.4 - - + -
50B ILE* 3.8 8.7 - - + +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY 5.2 1.0 + - - +
20B ALA* 2.9 42.1 + - - +
21B ALA* 3.5 30.8 - - - +
23B ALA* 1.3 70.2 - - - +
25B LYS* 1.3 59.2 + - - +
27B GLY* 3.4 0.5 + - - -
28B SER* 2.9 31.4 + - - -
46B VAL* 4.5 7.9 - - + +
49B GLU* 2.7 38.4 + - + +
50B ILE* 4.0 20.2 - - + +
210B ASP* 4.9 4.2 + - - -
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA 2.9 18.0 + - - +
22B ILE 3.6 3.4 - - - +
24B ARG* 1.3 77.7 - - - +
26B LEU* 1.3 62.7 + - + +
28B SER* 2.9 30.4 + - - +
29B LEU* 3.3 19.9 + - - +
213B ALA* 3.7 29.4 - - + +
214B ASP* 3.3 24.9 + - - +
217B ALA* 3.8 22.0 - - + -
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.0 19.7 - - + -
9B ALA* 3.8 21.1 - - + -
11B VAL* 4.4 4.7 - - + -
22B ILE* 2.8 41.2 + - + +
23B ALA* 4.1 2.0 - - - +
25B LYS* 1.3 73.8 - - + +
27B GLY* 1.3 62.9 + - - +
29B LEU* 3.1 14.2 + - + +
30B GLY 3.5 0.2 + - - -
31B ALA* 3.2 26.0 + - + +
33B VAL* 4.1 9.9 - - + -
86B VAL* 4.4 6.1 - - + -
88B VAL* 4.3 14.4 - - + -
213B ALA 5.5 0.2 - - - +
216B VAL* 4.3 7.4 - - + -
217B ALA* 4.2 27.6 - - + -
220B ALA* 4.3 8.7 - - + -
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Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA 2.8 14.3 + - - -
24B ARG 3.8 1.1 - - - -
26B LEU* 1.3 77.2 - - - +
28B SER* 1.3 56.5 + - - +
29B LEU 3.0 0.2 - - - -
30B GLY* 2.9 22.9 + - - -
31B ALA 3.9 6.6 + - - +
33B VAL* 3.5 18.7 - - - +
50B ILE* 4.1 20.0 - - - -
55B GLY* 4.4 11.9 - - - -
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 4.5 4.9 + - - -
24B ARG 2.9 16.0 + - - -
25B LYS* 2.9 24.5 + - - +
27B GLY* 1.3 74.8 - - - +
29B LEU* 1.3 64.9 + - - +
30B GLY 3.3 1.7 + - - -
50B ILE* 5.3 0.2 - - - +
53B ALA* 6.0 7.4 - - - -
55B GLY* 6.2 0.2 - - - -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 3.0 17.9 - - - -
3B SER* 3.5 13.6 + - - +
4B LEU* 2.8 53.0 + - + +
25B LYS* 3.3 24.0 + - - +
26B LEU* 3.1 8.4 + - - +
27B GLY 3.0 1.4 - - - -
28B SER* 1.3 84.5 + - - +
30B GLY* 1.3 56.6 + - - +
31B ALA 3.6 1.3 - - - -
217B ALA* 3.8 29.6 - - + -
221B THR* 4.2 11.2 - - + -
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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