Contacts of the helix formed by residues 13 - 36 (chain B) in PDB entry 6XWQ
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 PRO 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP 3.5 4.9 - - - +
12B TYR* 1.3 100.3 - - + +
14B VAL* 1.3 61.3 + - - +
15B LEU* 4.6 2.0 - - + +
16B TRP* 3.7 32.1 - - + +
17B LYS* 2.8 32.1 + - - +
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR 3.3 5.3 + - - +
13B PRO* 1.3 71.7 - - - +
15B LEU* 1.3 63.2 + - + +
17B LYS* 4.0 11.0 + - - +
18B ILE* 2.9 35.6 + - + +
201B GLY 5.9 0.2 - - - +
204B MET* 3.3 44.6 - - + +
205B GLN* 5.0 12.6 - - - +
273B THR* 6.0 2.9 - - + +
286B VAL* 5.9 6.1 - - + -
289B ARG* 6.3 1.6 - - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.2 2.4 - - + +
14B VAL* 1.3 83.1 - - + +
16B TRP* 1.3 74.5 + - + +
18B ILE* 3.0 9.7 - - + +
19B LEU* 3.0 24.9 + - + +
268B LYS* 5.7 1.6 - - - +
269B ASP* 4.1 36.3 - - + +
272B ILE* 3.7 38.1 - - + -
273B THR* 3.4 24.2 - - - +
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Residues in contact with TRP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 4.5 10.7 - - + +
13B PRO* 3.4 27.6 + - + +
15B LEU* 1.3 87.1 - - + +
17B LYS* 1.3 57.5 + - - +
19B LEU* 3.4 26.4 + - + -
20B TRP* 2.9 51.7 + + + +
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 3.2 47.6 - - + +
10B LEU 4.6 1.1 - - - -
12B TYR* 3.5 39.0 - - + -
13B PRO 2.8 14.1 + - - +
14B VAL* 4.0 12.1 - - - +
16B TRP* 1.3 76.2 - - - +
18B ILE* 1.3 59.6 + - - +
20B TRP* 3.8 3.4 - - + +
21B GLY* 2.9 27.7 + - - -
204B MET 4.1 3.2 + - - -
205B GLN* 3.7 20.6 + - - +
208B PRO* 3.3 31.6 - - + +
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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
----------------------------------------------------------
14B VAL* 2.9 21.2 + - + +
15B LEU* 3.0 26.7 - - + +
17B LYS* 1.3 75.8 - - - +
19B LEU* 1.3 60.3 + - + +
21B GLY 4.2 0.4 - - - -
22B LEU 3.7 8.5 + - - -
204B MET* 4.9 6.5 - - - +
207B ALA* 3.4 24.0 - - + +
208B PRO* 3.3 35.6 - - + +
211B VAL* 3.6 10.5 - - + +
273B THR* 4.2 18.2 - - + +
276B VAL* 3.1 46.0 - - + +
277B THR* 5.0 7.0 - - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 3.0 18.4 + - + +
16B TRP* 3.8 29.4 - - + +
18B ILE* 1.3 77.3 - - - +
20B TRP* 1.3 60.2 + - - +
21B GLY 3.3 0.4 - - - -
22B LEU* 3.3 10.4 + - + +
23B VAL* 2.9 43.5 + - + +
272B ILE* 3.8 28.3 - - + -
275B PHE* 5.8 2.2 - - + -
276B VAL* 3.7 22.4 - - + -
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Residues in contact with TRP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 5.2 15.5 + + + -
16B TRP* 2.9 38.3 + + + +
17B LYS* 3.2 6.9 + - + +
19B LEU* 1.3 73.6 - - - +
21B GLY* 1.3 61.1 + - - +
23B VAL* 3.3 23.0 + - + +
24B LEU* 2.9 55.9 + - + +
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Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS 2.9 16.2 + - - -
18B ILE 4.6 1.1 - - - -
20B TRP* 1.3 77.6 - - - +
22B LEU* 1.3 56.5 + - - +
24B LEU* 3.4 5.3 + - - -
25B GLY* 2.9 26.0 + - - -
208B PRO* 4.5 15.9 - - - -
212B PHE* 3.8 19.2 - - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE 3.7 14.5 + - - +
19B LEU* 3.3 14.8 + - + +
21B GLY* 1.3 76.4 - - - +
23B VAL* 1.3 63.9 + - + +
25B GLY* 3.5 7.3 + - - +
26B ALA* 3.6 11.6 + - - +
211B VAL* 4.4 12.1 - - + +
215B ILE* 3.7 36.3 - - + +
275B PHE* 4.4 10.8 - - + -
276B VAL* 3.6 29.8 - - + -
399B MET* 3.9 30.3 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 2.9 34.6 + - + +
20B TRP* 3.3 28.2 + - + +
22B LEU* 1.3 78.1 - - + +
24B LEU* 1.3 65.0 + - + +
26B ALA* 3.8 10.1 + - - +
27B VAL* 3.9 14.9 + - + +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TRP* 2.9 48.7 + - + +
21B GLY* 3.9 6.5 - - - +
23B VAL* 1.3 79.3 - - + +
25B GLY* 1.3 59.5 + - - +
26B ALA 3.3 0.2 - - - -
27B VAL* 3.3 17.9 + - + +
28B PHE* 3.0 29.5 + - - +
212B PHE* 4.0 9.8 - - + -
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 2.9 11.1 + - - -
22B LEU 3.5 0.8 + - - -
23B VAL 3.4 0.4 - - - -
24B LEU* 1.3 77.4 - - - +
26B ALA* 1.3 56.4 + - - +
28B PHE* 3.4 0.5 + - - -
29B GLY* 2.9 27.0 + - - -
212B PHE* 3.4 24.0 - - - -
215B ILE* 3.6 24.2 - - - -
216B ALA* 3.7 8.3 - - - +
219B MET* 4.4 0.3 - - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU 3.6 11.0 + - - +
23B VAL* 4.1 9.0 - - - +
24B LEU 3.3 0.4 - - - -
25B GLY* 1.3 77.3 - - - +
27B VAL* 1.3 63.7 + - + +
29B GLY* 3.3 1.0 + - - -
30B LEU* 2.9 33.7 + - + +
215B ILE* 4.3 4.7 - - + +
219B MET* 4.0 20.9 - - + -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 3.9 12.5 + - + +
24B LEU* 3.3 22.6 + - + +
26B ALA* 1.3 77.1 - - + +
28B PHE* 1.3 60.8 + - - +
30B LEU* 3.3 7.3 + - - +
31B ILE* 2.9 32.6 + - + +
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Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU 3.0 17.2 + - - +
25B GLY 4.0 0.7 - - - +
27B VAL* 1.3 76.9 - - + +
29B GLY* 1.3 60.3 + - - +
31B ILE* 3.1 18.6 - - + +
32B ALA* 2.9 31.3 + - + +
41B VAL* 3.9 24.0 - - + -
45B ILE* 3.4 34.1 - - + -
212B PHE* 3.6 20.6 - + + -
216B ALA* 3.5 25.4 - - + -
220B ALA* 6.3 0.2 - - + -
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Residues in contact with GLY 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 GLY 2.9 13.3 + - - -
26B ALA 3.8 0.2 - - - -
28B PHE* 1.3 78.7 - - - +
30B LEU* 1.3 56.7 + - - +
32B ALA* 3.3 2.8 + - - +
33B GLY* 2.9 24.1 + - - -
216B ALA* 3.8 13.5 - - - -
219B MET* 3.6 28.3 - - - -
220B ALA* 3.7 12.1 - - - -
223B GLY* 6.0 0.5 - - - -
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Residues in contact with LEU 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 ALA* 2.9 28.6 + - + +
27B VAL* 3.7 6.7 - - - +
29B GLY* 1.3 75.5 - - - +
31B ILE* 1.3 60.1 + - - +
33B GLY* 3.4 2.0 + - - +
34B HIS* 2.9 28.8 + - - +
219B MET* 3.7 25.6 - - + -
223B GLY* 5.6 9.0 - - - +
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Residues in contact with ILE 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 VAL* 2.9 15.9 + - + +
28B PHE* 3.1 41.5 - - + +
30B LEU* 1.3 75.7 - - - +
32B ALA* 1.3 60.1 + - - +
34B HIS* 3.5 13.7 - - + +
35B PHE* 3.3 34.4 + - + +
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Residues in contact with ALA 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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28B PHE* 2.9 25.4 + - + +
29B GLY* 3.6 4.7 - - - +
30B LEU 3.1 0.2 - - - -
31B ILE* 1.3 75.6 - - - +
33B GLY* 1.3 54.5 + - - +
34B HIS 3.1 1.3 - - - -
35B PHE* 3.1 4.9 + - - -
36B GLY 2.7 31.0 + - - -
37B TYR* 3.0 21.5 + - + +
41B VAL* 4.2 20.0 - - + -
220B ALA* 3.9 16.8 - - + -
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Residues in contact with GLY 33 (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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29B GLY 2.9 15.5 + - - -
30B LEU* 3.7 2.7 - - - -
32B ALA* 1.3 76.0 - - - +
34B HIS* 1.3 62.3 + - - +
36B GLY* 3.3 11.3 + - - -
37B TYR 5.0 0.2 - - - -
38B ALA 5.8 0.4 - - - -
220B ALA* 4.5 15.5 - - - +
223B GLY* 6.1 4.3 - - - -
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Residues in contact with HIS 34 (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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30B LEU 2.9 14.2 + - - +
31B ILE* 3.5 18.9 + - + +
32B ALA 3.1 0.2 - - - -
33B GLY* 1.3 78.4 - - - +
35B PHE* 1.3 101.1 + + - +
36B GLY* 3.2 1.4 + - - -
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Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.3 20.5 + - + +
32B ALA* 3.1 5.8 + - - +
34B HIS* 1.3 109.4 - + - +
36B GLY* 1.3 62.1 + - - +
37B TYR* 3.4 52.3 - + + -
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Residues in contact with GLY 36 (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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32B ALA 2.7 11.3 + - - -
33B GLY* 3.3 10.0 + - - -
34B HIS 3.1 6.4 + - - -
35B PHE* 1.3 76.1 - - - +
37B TYR* 1.3 58.6 + - - -
38B ALA* 3.3 9.5 + - - +
39B GLY 5.1 0.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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