Contacts of the helix formed by residues 20 - 38 (chain B) in PDB entry 4N6N
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 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.7 13.3 - - + +
17B SER* 3.0 27.6 + - - +
19B ASP* 1.3 77.9 - - - +
21B PRO* 1.4 76.8 - - - +
22B GLN* 3.2 32.0 + - - +
23B VAL* 3.0 17.5 + - + +
24B GLN* 2.9 20.1 + - - +
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Residues in contact with PRO 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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19B ASP 3.3 6.3 - - - +
20B ASP* 1.4 93.9 - - - +
22B GLN* 1.3 65.3 + - - +
24B GLN* 3.4 11.9 + - - +
25B LYS* 3.0 34.0 + - + +
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASP* 3.2 15.0 + - - +
21B PRO* 1.3 85.3 - - - +
23B VAL* 1.3 58.6 + - - +
25B LYS* 3.4 29.1 + - - +
26B ALA* 3.0 28.2 + - - +
60B ILE* 5.8 3.1 - - + -
62B TYR* 3.4 27.3 - - + +
107B VAL* 6.5 0.9 - - + -
109B PRO* 6.3 4.3 - - + +
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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
----------------------------------------------------------
16B LEU* 3.7 31.0 - - + -
17B SER 3.8 14.8 - - - +
18B PRO* 3.8 17.7 - - + +
20B ASP* 3.0 15.5 + - + +
22B GLN* 1.3 76.4 - - - +
24B GLN* 1.3 59.2 + - - +
26B ALA* 3.3 7.2 + - - +
27B ALA* 2.8 27.7 + - - +
49B ILE* 4.2 9.4 - - + -
52B ALA* 3.6 27.6 - - + -
62B TYR* 4.2 7.9 - - + -
64B LEU* 3.9 11.5 - - + +
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PRO 3.8 14.9 + - - +
19B ASP* 3.8 21.4 + - - +
20B ASP 2.9 14.9 + - - +
21B PRO* 3.7 13.2 - - + +
23B VAL* 1.3 75.9 - - - +
25B LYS* 1.3 60.8 + - + +
27B ALA* 3.4 7.7 + - - +
28B GLN* 3.1 31.3 + - + +
49B ILE* 4.3 8.7 - - + +
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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 PRO* 3.0 16.4 + - + +
22B GLN* 3.6 33.9 - - - +
23B VAL 3.3 0.2 - - - -
24B GLN* 1.3 74.1 - - - +
26B ALA* 1.3 63.8 - - - +
28B GLN* 3.3 7.7 + - - +
29B ALA* 3.0 22.4 + - - +
107B VAL* 6.3 3.4 - - - -
112B ASN* 5.6 9.0 - - - +
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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
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22B GLN 3.0 17.6 + - - +
23B VAL* 3.6 5.4 - - - +
25B LYS* 1.3 75.8 - - - +
27B ALA* 1.3 58.7 + - - +
29B ALA* 3.3 8.1 + - - +
30B ALA* 3.0 28.2 + - - +
62B TYR* 3.7 38.8 - - + -
64B LEU* 4.0 6.1 - - + -
105B VAL* 3.9 7.9 - - + +
107B VAL* 4.2 13.0 - - + +
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Residues in contact with ALA 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 VAL 2.8 17.2 + - - +
24B GLN 3.6 4.9 - - - +
26B ALA* 1.3 77.8 - - - +
28B GLN* 1.3 61.6 + - + +
30B ALA* 3.2 3.6 + - - +
31B VAL* 2.9 34.8 + - - +
46B ASP* 5.9 0.7 - - - +
49B ILE* 3.5 26.5 - - + -
64B LEU* 3.6 13.2 - - + +
66B MET* 3.9 19.0 - - + +
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Residues in contact with GLN 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 GLN* 3.1 21.3 + - + +
25B LYS* 3.3 9.6 + - - +
27B ALA* 1.3 76.6 - - - +
29B ALA* 1.3 61.6 + - - +
31B VAL* 3.5 6.4 + - - +
32B ALA* 3.1 25.1 + - - +
46B ASP* 3.1 39.2 + - - +
85B LEU* 5.1 7.8 - - - +
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Residues in contact with ALA 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 LYS 3.0 13.4 + - - +
26B ALA* 3.5 11.4 - - - +
27B ALA 3.3 0.2 - - - -
28B GLN* 1.3 73.4 - - - +
30B ALA* 1.3 64.4 + - - +
32B ALA* 3.4 5.3 + - - +
33B SER* 3.0 25.3 + - - -
105B VAL* 4.6 4.0 - - + -
114B SER* 3.4 34.9 + - - +
116B LEU* 5.8 0.4 - - - -
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Residues in contact with ALA 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 3.0 13.8 + - - +
27B ALA* 3.5 10.3 - - - +
29B ALA* 1.3 75.3 - - - +
31B VAL* 1.3 52.1 + - - +
33B SER* 3.3 1.4 + - - -
34B TYR* 2.7 37.5 + - - +
64B LEU* 4.9 0.9 - - + -
103B PHE* 3.8 28.0 - - + -
105B VAL* 3.6 23.0 - - + +
116B LEU* 3.7 13.8 - - + +
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Residues in contact with VAL 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 ALA 2.9 21.7 + - - +
28B GLN* 3.8 8.1 - - - +
30B ALA* 1.3 76.1 - - - +
32B ALA* 1.3 64.3 + - - +
34B TYR* 3.4 4.0 + - - +
35B ASN* 3.1 28.2 + - - +
44B PHE 3.8 1.1 - - - +
46B ASP* 3.9 17.3 - - + +
66B MET* 3.4 26.7 - - + -
68B MET* 3.5 31.2 - - + -
85B LEU* 3.7 29.6 - - + -
103B PHE* 4.9 1.3 - - + -
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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 GLN 3.1 18.1 + - - +
29B ALA* 3.7 6.1 - - - +
31B VAL* 1.3 79.0 - - - +
33B SER* 1.3 61.1 + - - +
35B ASN* 3.6 5.2 + - - +
36B MET* 3.2 30.2 + - + +
83B VAL* 6.5 1.3 - - + -
85B LEU* 5.9 2.5 - - + -
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Residues in contact with SER 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 4.6 10.6 + - - -
29B ALA 3.0 17.0 + - - -
30B ALA 3.8 0.7 - - - -
32B ALA* 1.3 74.4 - - - +
34B TYR* 1.3 66.9 + - - +
36B MET* 3.4 5.3 + - - +
37B GLY* 3.1 20.3 + - - -
116B LEU* 3.4 35.1 + - - +
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Residues in contact with TYR 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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189A SCH 5.6 0.2 - - - +
215A SER* 4.4 7.6 - - - -
217A TYR* 2.7 42.9 + + - -
30B ALA 2.7 21.8 + - - +
31B VAL* 3.6 4.5 - - - +
33B SER* 1.3 74.6 - - - +
35B ASN* 1.3 78.2 + - - +
37B GLY* 3.3 1.8 + - - -
38B SER* 3.2 28.2 + - - -
44B PHE* 4.6 13.2 - + + -
68B MET* 4.5 11.9 - - + -
99B LEU* 3.7 26.1 - - + +
103B PHE* 3.9 27.6 - + + -
116B LEU* 3.6 7.3 - - + +
119B HIS* 4.0 14.8 - + - -
121B CYS* 3.5 20.9 - - - +
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Residues in contact with ASN 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 VAL* 3.1 29.0 + - - +
32B ALA* 3.9 5.3 - - - +
34B TYR* 1.3 84.6 - - - +
36B MET* 1.3 59.1 + - + +
38B SER* 3.2 8.0 + - - -
42B TYR 4.5 1.0 - - - +
43B TYR* 3.8 31.2 - - + +
44B PHE* 2.8 54.4 + - - +
68B MET* 5.1 0.2 - - - -
75B LYS* 2.6 33.9 + - - +
83B VAL* 5.6 0.6 - - - +
85B LEU* 4.2 5.5 - - - +
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Residues in contact with MET 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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41A TYR* 3.9 27.1 - - + +
44A ARG* 3.9 17.8 + - - -
228A TYR* 3.8 14.6 - - + -
32B ALA* 3.2 18.3 + - + +
33B SER* 4.1 5.6 - - - +
34B TYR 3.3 0.4 - - - -
35B ASN* 1.3 79.4 - - + +
37B GLY* 1.3 59.2 + - - +
38B SER 3.7 0.3 + - - +
43B TYR* 4.6 16.2 - - + -
75B LYS* 4.7 7.2 + - - +
80B GLY 3.6 25.1 - - - +
81B ASP* 4.0 31.2 - - - +
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Residues in contact with GLY 37 (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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44A ARG* 4.5 0.2 - - - -
217A TYR* 3.5 11.2 - - - +
218A ALA* 2.8 33.6 + - - +
228A TYR* 3.7 24.0 - - - -
33B SER 3.1 13.7 + - - -
34B TYR 3.8 4.0 - - - -
35B ASN 3.3 0.4 - - - -
36B MET* 1.3 75.7 - - - +
38B SER* 1.3 58.3 + - - +
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 3.3 12.1 + - - -
148A HIS* 3.6 0.3 - - - -
215A SER* 2.7 29.1 + - - -
217A TYR* 3.9 14.9 - - - -
34B TYR* 3.2 24.4 + - - -
35B ASN* 3.2 11.7 + - - -
37B GLY* 1.3 78.7 - - - +
39B ASN* 1.3 56.8 + - - +
40B SER* 3.2 15.3 + - - -
44B PHE* 5.9 0.6 - - - -
75B LYS* 2.7 24.9 + - - -
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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