Contacts of the helix formed by residues 15 - 32 (chain B) in PDB entry 6P59
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 ASP 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 1.3 77.7 - - - +
16B ARG* 1.3 85.6 + - - +
17B ARG* 3.6 17.6 + - + +
18B LYS* 3.1 34.7 + - + +
19B ILE 3.7 2.9 + - - -
218B THR* 6.3 0.6 - - - +
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Residues in contact with ARG 16 (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 VAL 3.6 2.7 + - - -
15B ASP* 1.3 80.6 + - - +
17B ARG* 1.3 69.0 + - - +
19B ILE* 2.9 18.8 + - + +
20B GLU* 2.9 41.0 + - + +
83B LEU* 5.4 12.1 - - - +
86B TYR* 4.0 53.4 + - + -
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 3.1 14.9 + - + +
16B ARG* 1.3 86.9 - - - +
18B LYS* 1.3 58.8 + - + +
20B GLU* 3.2 36.6 + - - +
21B GLN* 3.1 65.0 + - - +
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.9 0.7 - - + -
15B ASP* 3.1 28.1 + - + +
17B ARG* 1.3 79.4 - - + +
19B ILE* 1.3 53.5 + - - +
21B GLN* 3.3 10.5 + - - +
22B TRP* 2.7 35.9 + - - +
214B TYR* 3.2 51.8 - - + +
215B LEU* 3.8 22.2 - - + +
217B GLY 3.4 24.9 + - - +
218B THR* 4.6 8.3 - - - +
219B LEU* 4.4 12.1 - - - +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 3.6 23.8 - - + -
15B ASP 4.2 2.7 - - - +
16B ARG* 2.9 10.4 + - + +
18B LYS* 1.3 75.2 - - - +
20B GLU* 1.3 61.9 + - + +
22B TRP* 3.8 1.5 - - + +
23B HIS* 2.9 59.9 + - + +
55B HIS* 4.9 12.3 - - + +
72B THR* 4.3 17.3 - - + -
73B TYR 4.6 0.7 - - - +
86B TYR* 3.7 37.2 - - + -
87B GLY 4.3 11.9 - - - +
88B ALA* 5.8 0.7 - - + -
215B LEU* 4.1 11.4 - - + -
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 2.9 50.2 + - + +
17B ARG* 3.2 35.7 + - - +
19B ILE* 1.3 74.4 - - + +
21B GLN* 1.3 64.1 + - - +
23B HIS* 3.5 4.9 + - - +
24B SER* 3.0 26.4 + - - -
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 3.1 56.9 + - - +
18B LYS* 3.6 8.9 - - - +
19B ILE 3.2 0.2 - - - -
20B GLU* 1.3 78.2 - - - +
22B TRP* 1.3 61.4 + - - +
24B SER* 3.6 5.5 + - - -
25B LEU* 3.3 30.3 + - + +
214B TYR* 2.4 40.1 + - + -
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Residues in contact with TRP 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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18B LYS 2.7 20.7 + - - +
19B ILE* 3.8 3.1 - - + +
20B GLU 3.2 0.2 - - - -
21B GLN* 1.3 71.8 - - - +
23B HIS* 1.3 92.2 + + - +
25B LEU* 3.1 16.8 + - + +
26B VAL* 3.1 27.7 + - + +
40B TRP* 4.6 6.9 - + - -
56B SER* 5.7 0.2 - - - -
58B VAL* 3.5 40.6 - - + -
60B ILE* 5.2 0.9 - - + -
70B VAL* 3.6 26.9 - - + -
72B THR* 4.7 4.9 - - + -
210B PRO* 3.5 27.0 - - + +
211B SER 4.0 18.4 - - - -
212B LEU* 3.6 27.1 - - + +
214B TYR* 5.7 4.9 - + + -
215B LEU* 4.0 27.6 - - + -
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Residues in contact with HIS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 2.9 44.7 + - + +
20B GLU* 4.1 4.3 - - - +
22B TRP* 1.3 93.7 - + - +
24B SER* 1.3 58.0 + - - +
26B VAL* 3.2 5.6 + - + +
27B LYS* 2.9 39.3 + - + +
42B TYR* 3.2 34.4 - + - -
55B HIS* 4.7 8.1 - + - -
56B SER* 2.7 29.8 + - - -
58B VAL* 4.6 2.9 - - + +
72B THR* 3.7 14.6 - - + -
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Residues in contact with SER 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU 3.0 19.0 + - - -
21B GLN* 3.8 7.6 - - - -
22B TRP 3.2 0.2 - - - -
23B HIS* 1.3 75.8 - - - +
25B LEU* 1.3 61.9 + - - +
27B LYS* 3.7 4.8 + - - +
28B TYR* 3.1 28.6 + - - +
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Residues in contact with LEU 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 GLN* 3.3 16.4 + - + +
22B TRP* 3.1 11.0 + - + +
24B SER* 1.3 80.8 - - - +
26B VAL* 1.3 60.0 + - - +
28B TYR* 3.4 2.9 + - + +
29B HIS* 3.0 36.6 + - + +
207B VAL* 4.2 16.6 - - + -
208B HIS* 3.6 31.6 - - + +
209B PHE 3.7 23.1 - - - +
210B PRO* 4.0 18.6 - - + -
211B SER 5.2 0.2 - - - +
214B TYR* 6.1 3.8 - - + -
302B GOL 4.5 6.3 - - - +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 3.1 39.2 + - + +
23B HIS* 3.2 8.0 + - + +
25B LEU* 1.3 73.9 - - - +
27B LYS* 1.3 61.2 + - + +
29B HIS* 3.2 2.7 + - - +
30B MET* 2.8 50.1 + - + +
37B ALA* 5.0 0.2 - - - +
40B TRP* 3.6 39.7 - - + -
42B TYR* 5.2 4.9 - - + -
58B VAL* 4.7 13.7 - - + -
210B PRO* 3.9 8.3 - - + -
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Residues in contact with LYS 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 HIS* 2.9 26.6 + - + +
24B SER* 4.1 5.6 - - - +
26B VAL* 1.3 78.4 - - + +
28B TYR* 1.3 62.3 + - - +
30B MET* 4.6 3.1 - - - -
31B TYR* 3.3 49.4 + - + +
42B TYR* 4.4 37.8 - - + -
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Residues in contact with TYR 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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24B SER* 3.1 20.1 + - - +
25B LEU* 3.7 5.2 - - + +
26B VAL 3.2 0.2 - - - -
27B LYS* 1.3 78.3 - - - +
29B HIS* 1.3 82.3 + + - +
31B TYR 3.3 0.5 + - - -
32B LYS* 2.8 68.3 + - + +
33B GLY* 3.8 21.9 - - - -
207B VAL* 3.4 45.4 - - + +
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Residues in contact with HIS 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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25B LEU* 3.0 26.7 + - + +
26B VAL* 3.6 1.8 - - - +
28B TYR* 1.3 101.8 - + - +
30B MET* 1.3 56.4 + - - +
32B LYS 4.6 3.2 + - - -
33B GLY* 6.0 1.0 - - - -
34B LYS 6.1 0.4 + - - -
35B LYS* 3.5 2.8 + - - -
36B GLU* 3.3 19.9 + - + +
37B ALA* 2.6 47.1 + - + +
119B PHE* 5.2 0.7 - + + -
207B VAL* 4.0 6.2 - - + +
208B HIS 2.8 25.2 + - - -
209B PHE* 3.6 28.8 - + - -
210B PRO* 3.5 25.6 - - + -
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Residues in contact with MET 30 (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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26B VAL* 2.8 40.9 + - + +
27B LYS* 4.6 3.6 - - - -
28B TYR 3.3 0.4 - - - -
29B HIS* 1.3 79.9 - - - +
31B TYR* 1.3 102.1 + - + +
35B LYS* 4.3 7.6 - - - +
37B ALA* 3.4 23.1 - - + +
38B ARG* 3.7 22.2 - - - +
40B TRP* 3.7 25.4 - - + +
41B GLU* 4.5 0.4 - - - -
42B TYR* 4.1 28.3 - - + +
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Residues in contact with TYR 31 (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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27B LYS* 3.3 41.0 + - + +
28B TYR 3.3 2.2 + - - -
30B MET* 1.3 119.3 - - + +
32B LYS* 1.3 70.5 + - + +
33B GLY 5.0 0.2 - - - +
35B LYS* 2.9 33.5 + - - +
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Residues in contact with LYS 32 (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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27B LYS 5.7 0.2 - - - +
28B TYR* 2.8 48.2 + - + +
29B HIS* 4.6 1.9 + - - -
31B TYR* 1.3 81.6 - - + +
33B GLY* 1.3 70.3 + - - +
35B LYS* 3.1 15.9 + - - -
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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