Contacts of the helix formed by residues 14 - 35 (chain B) in PDB entry 5JNO
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 SER 14 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PHE* 3.8 1.1 - - - -
338A ARG* 5.3 1.6 - - - -
12B ALA 3.2 3.4 + - - -
13B LEU* 1.3 74.0 - - - +
15B PRO* 1.3 72.3 - - - +
16B GLU* 3.4 19.1 + - - +
17B GLN* 2.9 40.8 + - - +
18B ALA* 3.0 22.0 + - - +
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Residues in contact with PRO 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PHE* 3.8 31.6 - - + +
338A ARG* 3.6 45.5 - - + +
339A PHE* 3.8 27.4 - - + +
342A GLN* 3.8 15.0 - - - +
13B LEU 4.4 0.4 - - - +
14B SER* 1.3 84.4 - - - +
16B GLU* 1.3 66.5 + - - +
18B ALA* 3.7 1.8 - - + +
19B ALA* 3.0 28.2 + - - +
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 3.9 8.3 + - - -
342A GLN* 3.5 30.4 + - - +
14B SER* 3.5 12.9 + - - +
15B PRO* 1.3 91.7 - - - +
17B GLN* 1.3 66.5 + - + +
19B ALA* 3.3 6.3 + - - +
20B HIS* 3.2 36.9 + - + -
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.4 23.1 + - - +
12B ALA 3.4 10.9 - - - +
13B LEU* 3.5 20.1 - - + +
14B SER* 2.9 37.8 + - - +
16B GLU* 1.3 76.9 - - + +
18B ALA* 1.3 62.1 + - - +
20B HIS* 3.1 8.7 + - - +
21B TYR* 2.8 23.9 + - - +
50B ILE* 3.7 24.1 + - + +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL* 3.9 18.4 - - + -
335A PHE* 3.5 33.2 - - + -
339A PHE* 4.9 3.4 - - + -
13B LEU* 4.0 9.6 - - + +
14B SER 3.0 9.0 + - - +
15B PRO 3.7 3.8 - - - +
17B GLN* 1.3 75.5 - - - +
19B ALA* 1.3 54.3 + - - +
21B TYR* 3.3 6.7 + - - +
22B LEU* 2.8 45.3 + - + +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 3.5 27.1 - - + -
342A GLN* 5.7 1.3 - - - +
343A ARG* 5.3 4.9 - - + -
346A GLU* 5.7 1.3 - - - +
15B PRO 3.0 17.9 + - - +
16B GLU* 3.7 7.2 - - - +
17B GLN 3.2 0.2 - - - -
18B ALA* 1.3 78.3 - - - +
20B HIS* 1.3 56.4 + - + +
22B LEU* 3.4 3.5 + - - +
23B ARG* 3.0 45.5 + - - +
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Residues in contact with HIS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 3.2 25.3 + - + +
17B GLN* 3.1 8.6 + - - +
19B ALA* 1.3 75.1 - - + +
21B TYR* 1.3 65.3 - - - +
23B ARG* 3.3 23.1 + - - +
24B TYR* 2.9 53.6 + + + -
50B ILE* 3.7 14.8 - - + -
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Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL* 4.0 24.0 - - + -
273A GLN* 3.1 23.2 + - - -
13B LEU* 5.8 0.4 - - + -
17B GLN 2.8 20.1 + - - +
18B ALA* 3.5 5.6 - - - +
20B HIS* 1.3 72.1 - - - +
22B LEU* 1.3 69.6 + - + +
24B TYR* 3.3 5.3 + - - +
25B VAL* 3.0 44.5 + - + +
47B ALA* 3.4 36.1 - - + -
50B ILE* 3.7 17.1 - - + +
51B PHE* 3.4 31.4 - + + -
53B ASN* 2.8 21.7 + - - -
56B VAL* 3.6 11.2 - - + +
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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
----------------------------------------------------------
272A VAL* 4.0 23.1 - - + +
276A PRO* 3.5 33.0 - - + +
279A PHE* 3.6 45.1 - - + -
339A PHE* 4.6 4.5 - - + -
18B ALA* 2.8 28.4 + - + +
19B ALA* 3.9 3.8 - - - +
21B TYR* 1.3 85.0 - - + +
23B ARG* 1.3 64.5 + - - +
25B VAL* 3.6 4.8 + - + +
26B LYS* 3.0 23.6 + - - +
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 4.5 11.5 - - - +
346A GLU* 3.6 26.5 + - - -
19B ALA* 3.0 34.7 + - - +
20B HIS* 3.3 33.3 + - - +
22B LEU* 1.3 75.4 - - - +
24B TYR* 1.3 64.4 + - + +
26B LYS* 3.2 9.5 + - + +
27B GLU* 2.9 55.7 + - + +
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Residues in contact with TYR 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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20B HIS* 2.9 46.1 + - + +
21B TYR 3.5 4.0 - - - +
23B ARG* 1.3 84.1 - - + +
25B VAL* 1.3 57.3 + - - +
27B GLU* 3.4 8.1 + - - -
28B ALA* 2.8 31.9 + - - +
43B LEU* 3.8 38.2 - - + +
46B LEU* 3.8 41.5 - - + +
47B ALA* 3.9 11.9 - - + -
50B ILE* 3.9 18.2 - - + -
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 3.0 48.6 + - + +
22B LEU* 4.1 7.0 - - + +
24B TYR* 1.3 72.2 - - - +
26B LYS* 1.3 68.0 + - - +
28B ALA* 3.3 5.8 + - - +
29B LYS* 3.0 51.6 + - + +
44B PHE* 4.5 9.9 - - + -
47B ALA* 4.0 13.9 - - + -
56B VAL* 4.1 11.0 - - + -
59B ARG* 6.0 0.4 - - - +
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Residues in contact with LYS 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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280A SER* 4.4 20.2 - - - -
22B LEU 3.0 17.6 + - - +
23B ARG* 3.5 9.6 - - + +
25B VAL* 1.3 78.7 - - - +
27B GLU* 1.3 62.0 + - + +
29B LYS* 3.4 8.9 + - - +
30B GLU* 3.2 49.8 + - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 2.9 44.6 + - + +
24B TYR* 3.9 4.7 - - - +
26B LYS* 1.3 77.6 - - + +
28B ALA* 1.3 61.2 + - - +
30B GLU* 3.3 15.3 + - - +
31B ALA* 2.8 31.0 + - - +
43B LEU* 3.6 28.8 - - + +
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR 2.8 19.1 + - - +
25B VAL 3.8 0.2 - - - +
27B GLU* 1.3 76.8 - - - +
29B LYS* 1.3 56.4 + - - +
31B ALA 3.6 0.2 + - - -
32B THR* 2.9 31.9 + - - -
40B ALA* 3.6 9.3 - - - +
43B LEU* 3.6 20.5 - - + +
44B PHE* 3.5 43.3 - - + +
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Residues in contact with LYS 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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276A PRO* 6.2 1.4 - - - +
25B VAL* 3.0 39.9 + - + +
26B LYS* 3.6 7.6 - - - +
28B ALA* 1.3 74.4 - - - +
30B GLU* 1.3 60.6 + - + +
32B THR* 3.2 6.4 + - - -
33B LYS* 2.9 51.4 + - + +
44B PHE* 4.3 10.5 - - + -
59B ARG* 4.1 21.8 - - - +
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Residues in contact with GLU 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 LYS* 3.2 46.6 + - - +
27B GLU* 3.3 20.2 + - - +
29B LYS* 1.3 74.9 - - + +
31B ALA* 1.3 60.9 - - - +
33B LYS* 3.2 12.5 + - + +
34B ASN* 2.9 39.4 + - - +
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Residues in contact with ALA 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 GLU 2.8 17.5 + - - +
28B ALA* 3.7 5.2 - - - +
30B GLU* 1.3 76.9 - - - +
32B THR* 1.3 56.0 + - - +
34B ASN* 3.3 8.2 + - - +
35B GLY 3.0 8.1 + - - -
36B ASP* 2.9 47.7 + - + +
39B GLU* 4.1 14.8 - - + -
40B ALA* 3.8 14.8 - - - +
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Residues in contact with THR 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 ALA 2.9 18.5 + - - -
29B LYS* 3.5 10.5 - - - -
30B GLU 3.2 0.2 - - - -
31B ALA* 1.3 72.4 - - - +
33B LYS* 1.3 69.0 + - + +
35B GLY* 3.0 15.2 + - - -
37B LEU* 4.2 20.4 - - + +
40B ALA* 3.4 13.6 - - - +
44B PHE* 3.9 11.1 - - - -
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Residues in contact with LYS 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 LYS* 2.9 45.7 + - - +
30B GLU* 3.3 12.8 - - + +
32B THR* 1.3 79.8 - - + +
34B ASN* 1.3 64.5 + - - +
35B GLY* 4.6 0.2 - - - -
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Residues in contact with ASN 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 GLU* 2.9 27.3 + - - +
31B ALA* 3.7 8.3 - - - +
32B THR 3.2 0.2 - - - -
33B LYS* 1.3 80.1 - - - +
35B GLY* 1.3 58.1 + - - +
36B ASP* 3.5 5.4 - - + +
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Residues in contact with GLY 35 (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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31B ALA 3.0 3.2 + - - -
32B THR 3.0 12.1 + - - -
33B LYS 4.6 0.2 - - - -
34B ASN* 1.3 78.5 - - - +
36B ASP* 1.3 59.6 + - - +
37B LEU* 3.0 21.7 + - - +
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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