Contacts of the helix formed by residues 20 - 37 (chain A) in PDB entry 4R8A
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.2 10.5 - - - +
19A PRO* 1.3 83.7 - - + +
21A TYR* 1.3 62.8 + - - +
22A TYR* 3.2 16.2 - + - -
23A LEU* 3.2 15.3 + - + -
24A HIS* 3.1 43.6 + - + +
57A GLU* 4.4 24.2 - - + +
58A ALA* 4.8 4.5 - - + -
61A ALA* 3.5 33.2 - - + -
83A GLU* 3.1 40.8 - - + -
84A ILE* 4.4 1.3 - - + -
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Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 5.0 12.6 - - - +
18A GLU* 3.1 22.7 + - + +
19A PRO* 3.8 9.0 - - + -
20A PHE* 1.3 77.9 - - - +
22A TYR* 1.3 89.5 + + + +
24A HIS* 3.4 10.7 + - - +
25A ASN* 3.0 44.6 + - - +
65A ARG* 4.5 2.6 + - - -
191A VAL* 3.5 31.6 - - + -
194A ASP* 6.1 1.3 - - - +
9C T 4.3 0.3 - - - +
10C G 2.7 70.9 + + - -
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Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO 3.4 22.9 - - - -
20A PHE* 4.1 8.3 - + - -
21A TYR* 1.3 105.1 - + + +
23A LEU* 1.3 69.2 + - + +
25A ASN* 3.5 6.0 + - - +
26A PHE* 3.1 22.5 + - - +
61A ALA* 3.3 48.1 + - + +
64A VAL* 3.6 15.7 - - + +
65A ARG* 3.2 46.9 + - - +
68A MET* 3.5 31.7 - - + +
83A GLU* 2.8 18.3 + - - -
84A ILE* 3.7 4.0 - - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.2 23.4 + - + +
22A TYR* 1.3 91.4 - - + +
24A HIS* 1.3 56.5 + - - +
26A PHE* 3.2 3.5 + - + +
27A ARG* 2.8 59.5 + - - +
52A PHE* 3.8 16.8 - - + -
57A GLU* 3.7 30.3 - - - +
60A GLN* 3.6 38.1 - - + +
61A ALA* 4.0 3.8 - - - +
64A VAL* 3.8 11.9 - - + -
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Residues in contact with HIS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.4 39.4 + - + +
20A PHE* 3.1 25.5 + - + +
21A TYR* 3.4 9.4 + - - +
23A LEU* 1.3 77.2 - - + +
25A ASN* 1.3 60.1 + - - +
27A ARG* 3.4 34.2 + - - +
28A ALA* 2.9 28.9 + - - +
57A GLU* 4.3 5.8 - - - -
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 3.0 36.8 + - - +
22A TYR* 3.7 7.9 - - - +
23A LEU 3.2 0.2 - - - -
24A HIS* 1.3 78.6 - - - +
26A PHE* 1.3 60.8 + - - +
28A ALA* 3.3 8.2 + - - +
29A VAL* 3.1 27.8 + - - +
68A MET* 5.2 5.5 - - + +
187A TRP* 4.8 3.9 + - + +
190A PHE* 3.4 47.5 - - + +
191A VAL* 4.3 8.3 - - - +
194A ASP* 4.4 10.6 + - - +
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR 3.1 15.0 + - - +
23A LEU 3.2 6.7 + - - +
25A ASN* 1.3 74.0 - - - +
27A ARG* 1.3 64.0 + - - +
29A VAL* 3.3 10.8 + - + +
30A LEU* 3.1 48.3 + - + +
48A PHE* 4.7 8.1 - + - -
52A PHE* 3.5 43.3 - + - -
63A LEU* 5.7 1.8 - - + -
64A VAL* 3.6 25.4 - - + -
67A VAL* 4.8 14.6 - - + -
68A MET* 4.9 2.2 - - + +
172A CYS* 4.6 16.8 - - + -
175A LEU* 5.1 5.2 - - + -
187A TRP* 3.9 35.0 - + - -
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 2.8 32.7 + - + +
24A HIS* 3.6 30.1 + - - +
25A ASN 3.3 0.2 - - - -
26A PHE* 1.3 73.5 - - - +
28A ALA* 1.3 60.3 + - - +
30A LEU* 3.2 9.7 + - + +
31A ALA* 2.9 30.5 + - - +
52A PHE* 4.4 10.1 - - + -
57A GLU* 3.0 40.2 + - - +
60A GLN* 2.6 33.7 + - - +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS 2.9 18.5 + - - +
25A ASN* 3.4 10.1 - - - +
27A ARG* 1.3 76.7 - - - +
29A VAL* 1.3 56.1 + - - +
31A ALA* 3.9 5.1 - - - +
32A TRP* 3.0 29.9 + - - +
179A TYR* 4.9 2.6 - - - +
190A PHE* 4.7 11.9 - - + -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN 3.1 15.2 + - - +
26A PHE* 3.6 10.8 - - + +
27A ARG 3.3 0.2 - - - -
28A ALA* 1.3 72.1 - - - +
30A LEU* 1.3 62.4 + - + +
32A TRP* 3.3 2.1 + - - +
33A ILE* 2.9 41.2 + - + +
175A LEU* 4.3 14.1 - - + +
176A ARG* 5.2 1.8 - - - -
179A TYR* 3.9 37.5 - - + -
180A PHE* 5.8 0.9 - - + -
187A TRP* 4.5 19.5 - - + +
190A PHE* 3.6 28.7 - - + -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.1 34.5 + - + +
27A ARG* 3.2 12.1 + - + +
29A VAL* 1.3 80.0 - - + +
31A ALA* 1.3 57.2 + - - +
33A ILE* 3.3 5.4 + - + +
34A GLY* 2.9 23.9 + - - -
48A PHE* 5.0 3.1 - - + -
49A ILE* 4.0 44.4 - - + +
52A PHE* 3.5 36.3 - - + -
175A LEU* 3.6 33.7 - - + -
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG 2.9 16.1 + - - +
28A ALA* 3.9 5.6 - - - +
30A LEU* 1.3 73.2 - - - +
32A TRP* 1.3 66.8 + - - +
34A GLY* 3.1 4.1 + - - +
35A GLU* 3.0 38.6 + - - +
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Residues in contact with TRP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA 3.0 19.1 + - - +
29A VAL 3.3 4.9 + - - +
31A ALA* 1.3 75.7 - - - +
33A ILE* 1.3 62.7 + - + +
35A GLU* 3.4 11.2 + - - +
36A ARG* 3.2 73.6 + - - +
37A TYR* 3.7 19.4 + + - -
179A TYR* 3.5 38.4 + + + -
205A PHE* 3.8 17.7 - + - -
411A PHE 3.1 29.4 + - - -
412A HIS* 3.9 8.0 - - - +
413A PRO* 4.5 10.5 - - + -
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 2.9 27.5 + - + +
30A LEU* 3.5 6.7 - - - +
32A TRP* 1.3 74.8 - - + +
34A GLY* 1.3 66.6 + - - +
37A TYR* 3.0 47.1 + - + -
38A ALA* 4.2 0.3 - - - -
41A LEU* 4.4 19.9 - - + +
49A ILE* 4.4 17.0 - - + -
175A LEU* 3.7 26.9 - - + +
178A MET* 3.6 31.6 - - + -
179A TYR* 3.9 11.4 - - + +
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU 2.9 13.9 + - - -
31A ALA* 3.1 5.8 + - - -
33A ILE* 1.3 79.1 - - - +
35A GLU* 1.3 59.5 + - - +
38A ALA* 3.3 22.6 - - - +
41A LEU* 5.7 3.1 - - - -
49A ILE* 5.1 6.7 - - - +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.0 28.5 + - - +
32A TRP* 3.8 7.1 + - - +
33A ILE 3.2 0.2 - - - -
34A GLY* 1.3 81.7 - - - +
36A ARG* 1.3 88.4 + - + +
37A TYR 3.7 0.3 + - - -
38A ALA* 4.1 7.3 + - - +
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 3.2 69.0 + - - +
35A GLU* 1.3 98.9 + - + +
37A TYR* 1.3 78.0 + - + +
38A ALA 3.5 1.2 + - - -
39A ASP* 4.2 7.7 - - - +
40A LEU* 4.8 2.6 - - - +
205A PHE* 4.3 5.7 + - - -
206A SER 4.0 7.5 + - - -
207A ALA* 3.1 43.2 + - - +
208A ASP* 4.9 2.7 - - - +
209A SER 3.5 22.8 + - - +
210A ARG* 5.8 3.5 - - - +
411A PHE 4.9 0.4 - - - -
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 3.7 26.9 - + - -
33A ILE* 3.0 39.2 + - + +
36A ARG* 1.3 90.2 - - + +
38A ALA* 1.3 63.4 + - - +
39A ASP 3.3 2.9 - - - -
40A LEU* 3.3 33.0 + - + +
41A LEU* 3.5 13.2 + - - +
178A MET* 3.2 37.0 + - + -
179A TYR 4.2 1.6 + - - -
209A SER 4.4 0.5 + - - -
210A ARG* 3.7 8.1 - - + -
211A GLY* 2.8 34.3 + - - -
212A PHE* 3.6 23.3 - - + -
411A PHE* 3.9 13.5 + - - +
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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
------------------------------------------------------------
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