Contacts of the helix formed by residues 20 - 37 (chain B) in PDB entry 5Y7G
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 PHE 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B PRO* 1.3 89.5 - - + +
21B TYR* 1.3 54.0 + - - +
22B TYR* 2.6 27.7 + + - -
23B LEU* 2.6 42.4 + - + -
24B HIS* 3.2 25.8 + + + +
57B GLU* 3.9 37.5 - - + -
58B ALA* 5.8 0.9 - - - -
61B ALA* 3.9 15.9 - - + -
83B GLU* 3.5 48.5 - - + -
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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
----------------------------------------------------------
18B GLU* 3.8 51.2 - - + +
19B PRO 3.6 4.7 - - - -
20B PHE* 1.3 75.2 - - - +
22B TYR* 1.3 95.3 + + + +
24B HIS* 3.8 16.1 - - + -
25B ASN* 3.0 40.0 + - - +
65B ARG* 4.4 16.9 + - - -
191B VAL* 3.9 39.4 - - + +
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Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PRO 4.8 1.6 - - - -
20B PHE* 2.6 23.2 + + - -
21B TYR* 1.3 101.1 - + + +
23B LEU* 1.3 82.2 + - + -
25B ASN* 4.0 6.1 - - - +
26B PHE* 3.3 21.3 + - - +
61B ALA* 3.3 39.0 + - - +
64B VAL* 3.5 20.3 - - + +
65B ARG* 3.2 32.2 + - - +
68B MET* 4.0 24.0 - - + +
83B GLU* 3.1 42.9 + - + +
84B ILE* 3.8 4.7 - - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 2.6 28.4 + - + +
22B TYR* 1.3 86.7 - - + +
24B HIS* 1.3 66.0 + - + +
26B PHE* 3.0 3.5 + - + +
27B ARG* 2.9 33.0 + - + +
52B PHE* 3.8 17.7 - - + -
57B GLU* 4.1 12.6 - - + +
60B GLN* 3.7 34.8 - - + +
61B ALA* 3.7 25.6 - - + -
64B VAL* 3.6 25.1 - - + -
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Residues in contact with HIS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 6.1 1.1 - - + -
19B PRO* 4.5 12.9 - - + +
20B PHE* 3.2 33.8 + + + +
21B TYR* 3.4 22.4 + - + +
23B LEU* 1.3 77.6 - - + +
25B ASN* 1.3 60.9 + - - +
27B ARG* 3.4 5.9 + - - +
28B ALA* 2.9 28.4 + - - +
57B GLU* 5.4 4.5 - - - -
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Residues in contact with ASN 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 31.1 + - - +
22B TYR* 4.0 5.8 - - - +
24B HIS* 1.3 78.9 - - - +
26B PHE* 1.3 58.0 + - - +
28B ALA* 3.1 10.3 - - - +
29B VAL* 2.9 30.7 + - - +
187B TRP* 5.2 1.3 + - + -
190B PHE* 3.2 48.3 - - + +
191B VAL* 4.2 8.9 - - - +
194B ASP* 4.8 10.3 + - - +
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR 3.3 15.9 + - - +
23B LEU* 3.0 5.8 + - + +
25B ASN* 1.3 74.4 - - - +
27B ARG* 1.3 68.4 + - - +
28B ALA 3.1 1.1 - - - -
29B VAL* 2.8 17.3 + - + +
30B LEU* 2.9 34.6 + - + +
48B PHE* 4.9 11.7 - + - -
52B PHE* 3.7 35.0 - + - -
63B LEU* 6.5 0.4 - - + -
64B VAL* 3.7 31.6 - - + -
67B VAL* 5.4 11.4 - - + -
172B CYS* 5.2 9.9 - - - -
175B LEU* 5.7 3.4 - - + -
187B TRP* 4.3 40.4 - + - -
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Residues in contact with ARG 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 LEU* 2.9 21.2 + - + +
24B HIS* 3.9 4.5 - - - +
26B PHE* 1.3 74.8 - - - +
28B ALA* 1.3 63.8 + - - +
30B LEU* 3.1 14.6 + - - +
31B ALA* 3.0 22.7 + - - +
49B ILE 5.6 0.2 + - - -
52B PHE* 3.1 42.4 - - + -
53B ALA* 3.2 37.8 - - - +
60B GLN* 3.5 24.5 + - - +
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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 HIS 2.9 15.8 + - - +
25B ASN* 3.1 15.9 - - - +
27B ARG* 1.3 78.3 - - - +
29B VAL* 1.3 64.9 + - + +
31B ALA* 3.2 6.7 + - - +
32B TRP* 3.0 21.6 + - - +
190B PHE* 5.4 5.8 - - + -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASN 2.9 11.4 + - - +
26B PHE* 2.8 10.4 + - + +
28B ALA* 1.3 76.2 - - - +
30B LEU* 1.3 65.8 + - + +
32B TRP* 3.1 5.1 + - - +
33B ILE* 2.9 44.6 + - + +
175B LEU* 5.9 0.2 - - + -
179B TYR* 4.0 22.2 - - + -
187B TRP* 3.7 31.0 - - + -
190B PHE* 3.3 39.0 - - + -
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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
----------------------------------------------------------
26B PHE* 2.9 35.5 + - + +
27B ARG* 3.1 14.5 + - - +
29B VAL* 1.3 79.0 - - + +
31B ALA* 1.3 57.1 + - - +
33B ILE* 3.5 7.9 + - + +
34B GLY* 2.8 25.1 + - - -
48B PHE* 4.7 3.6 - - + -
49B ILE* 3.9 50.7 - - + +
52B PHE* 3.8 37.2 - - + -
175B LEU* 4.0 22.0 - - + -
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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
----------------------------------------------------------
27B ARG 3.0 11.7 + - - +
28B ALA* 3.6 9.9 - - - +
30B LEU* 1.3 76.3 - - - +
32B TRP* 1.3 54.1 + - - +
34B GLY* 2.7 22.2 + - - -
35B GLU* 3.0 14.8 + - - +
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Residues in contact with TRP 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 3.0 13.3 + - - +
29B VAL* 3.1 11.6 + - - +
31B ALA* 1.3 76.5 - - - +
33B ILE* 1.3 64.6 + - + +
35B GLU* 3.2 15.7 + - + +
36B ARG* 3.0 74.9 + - + +
37B TYR* 5.0 7.5 - + - -
179B TYR* 3.6 36.4 + + + -
205B PHE* 4.5 10.1 - + - -
411B PHE* 3.7 20.9 + - - +
412B HIS* 5.2 2.5 - - - -
413B PRO* 5.8 4.7 - - + -
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Residues in contact with ILE 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 VAL* 2.9 39.4 + - + +
30B LEU* 3.9 6.3 - - + +
32B TRP* 1.3 73.5 - - + +
34B GLY* 1.3 63.2 + - - +
37B TYR* 3.2 46.0 + - + +
38B ALA* 3.5 3.1 + - - -
41B LEU* 4.2 22.5 - - + +
49B ILE* 4.5 6.3 - - + -
175B LEU* 3.3 53.8 - - + +
178B MET* 4.7 5.4 - - + -
179B TYR* 4.3 12.3 - - + +
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Residues in contact with GLY 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 2.8 12.1 + - - -
31B ALA* 2.7 11.9 + - - -
33B ILE* 1.3 79.8 - - - +
35B GLU* 1.3 57.1 + - - -
38B ALA* 3.0 26.9 - - - +
41B LEU* 4.9 9.8 - - - +
49B ILE* 5.0 4.2 - - - +
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Residues in contact with GLU 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 12.8 + - - +
32B TRP* 3.8 19.6 - - + +
34B GLY* 1.3 76.4 - - - +
36B ARG* 1.3 85.4 + - + +
38B ALA* 3.5 11.8 + - - +
39B ASP* 5.5 0.2 - - - +
207B ALA* 5.7 1.9 - - - +
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Residues in contact with ARG 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 TRP* 3.0 62.8 + - - +
35B GLU* 1.3 92.2 + - + +
37B TYR* 1.3 64.4 + - + +
38B ALA 3.4 0.4 + - - -
39B ASP* 3.8 0.7 - - - +
205B PHE* 4.1 11.5 - - - -
206B SER 3.1 13.3 + - - -
207B ALA* 3.0 47.0 + - - +
208B ASP* 5.2 2.0 - - - -
209B SER 2.5 36.5 + - - +
210B ARG* 2.8 53.8 + - + +
411B PHE* 4.9 3.1 + - - -
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Residues in contact with TYR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TRP* 5.0 6.5 - + - -
33B ILE* 3.2 35.2 + - + +
36B ARG* 1.3 88.0 - - + +
38B ALA* 1.3 55.9 + - - +
39B ASP* 3.2 5.8 - - - -
40B LEU* 2.6 55.4 + - + +
41B LEU* 3.3 6.7 + - + +
178B MET* 2.7 47.0 + - + -
179B TYR* 4.8 6.1 + - - -
210B ARG* 3.8 15.5 - - + +
211B GLY* 2.6 33.6 + - - -
212B PHE* 3.2 26.6 + - + -
411B PHE* 5.1 1.8 - - + +
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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