Contacts of the helix formed by residues 19 - 34 (chain A) in PDB entry 3W8I
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 19 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 1.3 78.9 - - - +
20A MET* 1.3 64.8 + - - +
21A PRO* 3.4 13.2 - - - -
22A LEU* 3.1 15.5 + - - +
23A TYR* 3.2 11.5 + - - -
52A GLU* 2.5 42.4 + - - +
56A PRO* 4.8 5.2 - - - +
57A GLY* 4.6 1.5 + - - -
199A HIS* 5.1 2.0 - - - -
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Residues in contact with MET 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL 3.7 1.4 + - - -
19A SER* 1.3 72.2 - - - +
21A PRO* 1.4 71.8 - - + +
23A TYR* 3.5 26.6 - - + +
24A ALA* 2.9 31.6 + - + +
80A LEU* 4.2 15.5 - - + -
84A ALA* 3.6 31.4 - - + -
195A ASN* 3.3 50.0 - - - +
198A ILE* 3.7 14.4 - - + -
199A HIS* 3.9 21.8 - - + +
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Residues in contact with PRO 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 3.6 12.1 - - - -
20A MET* 1.4 92.3 - - + +
22A LEU* 1.3 56.7 + - - +
25A VAL* 2.9 40.7 + - + +
26A MET 3.4 1.4 + - - -
57A GLY* 6.5 0.2 - - - -
59A THR* 4.2 16.8 - - + -
60A GLN* 4.1 31.9 - - + +
63A ILE* 4.1 4.4 - - + +
76A PHE* 4.1 21.5 - - + -
80A LEU* 4.7 8.5 - - + -
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.7 28.9 - - + -
19A SER* 3.1 15.9 + - - +
21A PRO* 1.3 78.8 - - - +
23A TYR* 1.3 58.6 + - - +
26A MET* 2.9 29.0 + - + +
27A TYR* 2.8 42.4 + - + -
30A PHE* 3.9 8.5 - - + -
48A PHE* 4.1 13.9 - - + +
49A ILE* 3.9 28.3 - - + +
52A GLU* 4.3 8.5 - - + -
59A THR* 3.9 23.1 - - + +
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.8 9.2 - - - -
18A VAL* 3.5 29.4 - - + -
19A SER 3.2 15.4 + - - -
20A MET* 3.5 25.6 - - + +
22A LEU* 1.3 80.0 - - - +
24A ALA* 1.3 75.8 + - + +
27A TYR* 3.3 41.0 - - + +
28A PRO* 3.5 5.4 - - - +
88A VAL* 3.7 32.2 - - + +
91A TYR* 3.9 9.9 - + - +
199A HIS* 2.8 33.1 + + - -
202A ASN* 3.1 32.9 + - + +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 2.9 23.2 + - + +
23A TYR* 1.3 91.5 - - + +
25A VAL* 1.3 60.7 + - - +
28A PRO* 3.7 5.2 - - - +
80A LEU* 4.0 21.3 - - + -
83A MET* 4.2 10.7 - - + +
84A ALA* 5.0 13.0 - - + -
88A VAL* 5.9 0.9 - - - -
406B LYS* 3.4 18.5 + - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 2.9 25.2 + - + +
24A ALA* 1.3 82.4 - - - +
26A MET* 1.3 63.2 + - - +
27A TYR 3.6 0.7 - - - -
28A PRO* 3.3 9.3 - - - +
29A VAL* 3.4 14.7 - - - +
63A ILE* 3.9 13.7 - - + -
76A PHE* 4.9 1.8 - - + -
80A LEU* 4.3 14.8 - - + -
83A MET* 3.8 20.2 - - - -
403B LEU* 3.7 17.7 - - + -
406B LYS* 3.7 11.7 - - + +
407B PHE* 3.6 34.5 - - + -
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Residues in contact with MET 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO 4.2 0.7 - - - +
22A LEU* 2.9 26.2 + - + +
25A VAL* 1.3 71.2 - - - +
27A TYR* 1.3 66.9 + - - +
29A VAL* 3.0 10.4 + - + +
30A PHE* 2.9 52.6 + - + -
48A PHE* 4.0 21.8 - - + -
59A THR* 3.8 28.0 - - + -
62A ILE* 6.3 0.2 - - - -
63A ILE* 3.9 24.7 - - + -
399B MET* 4.3 16.6 - - + -
403B LEU* 4.0 24.7 - - + -
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.4 27.1 - - + +
22A LEU* 2.8 40.7 + - + -
23A TYR* 3.3 38.6 - - + +
26A MET* 1.3 72.0 - - - +
28A PRO* 1.4 63.1 - - + +
30A PHE* 3.1 14.1 + + - +
31A ASN* 3.0 31.2 + - - +
45A ARG* 3.8 18.3 + - + +
49A ILE* 3.3 30.1 - - + +
88A VAL* 4.8 4.0 - - + -
90A GLU* 3.5 38.9 + - - +
91A TYR* 4.5 3.3 + - - -
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Residues in contact with PRO 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR 3.5 11.0 - - - +
24A ALA 3.7 5.8 - - - +
25A VAL 3.3 13.2 - - - +
27A TYR* 1.4 94.7 - - + +
29A VAL* 1.3 60.0 + - - +
31A ASN* 3.5 12.9 + - + +
32A GLU* 3.2 32.4 + - - +
406B LYS* 3.4 32.1 - - - +
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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 VAL 3.4 17.3 - - - +
26A MET* 3.0 14.5 + - + +
28A PRO* 1.3 75.6 - - - +
30A PHE* 1.3 65.4 + - + +
32A GLU* 3.3 10.5 + - - +
33A LEU* 3.1 38.2 + - + +
399B MET* 3.8 29.6 - - + +
402B LYS* 4.2 12.6 - - + -
403B LEU* 4.2 22.9 - - + +
406B LYS* 4.1 16.2 - - + -
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.9 13.9 - - + -
26A MET* 2.9 55.1 + - + -
27A TYR* 3.5 11.9 - + - +
29A VAL* 1.3 78.6 - - - +
31A ASN* 1.3 61.2 + - - +
33A LEU* 3.1 22.9 + - + +
34A GLU* 3.3 15.2 + - - +
41A ALA* 3.9 6.5 - - - +
44A LEU* 3.9 26.5 - - + -
45A ARG* 3.5 49.3 + - + +
48A PHE* 3.6 30.1 - + + -
399B MET* 4.4 6.5 - - + -
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Residues in contact with ASN 31 (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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27A TYR* 3.0 20.9 + - - +
28A PRO* 3.7 14.4 - - - +
29A VAL 3.3 0.2 - - - -
30A PHE* 1.3 77.8 - - - +
32A GLU* 1.3 62.2 + - + +
34A GLU* 3.3 29.8 + - - +
35A ARG* 4.4 1.7 + - - +
45A ARG* 2.5 33.1 + - - +
90A GLU* 5.5 3.3 + - - +
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Residues in contact with GLU 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 PRO* 3.2 20.2 + - - +
29A VAL* 3.7 8.7 - - - +
30A PHE 3.3 0.2 - - - -
31A ASN* 1.3 77.5 - - + +
33A LEU* 1.3 60.5 + - - +
34A GLU 3.2 0.2 - - - -
35A ARG* 3.2 37.0 + - - +
36A VAL* 4.3 3.1 - - - +
402B LYS* 3.2 41.6 + - + +
406B LYS* 5.5 5.4 - - - +
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Residues in contact with LEU 33 (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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29A VAL* 3.1 36.5 + - + +
30A PHE* 3.1 18.3 + - + +
32A GLU* 1.3 77.5 - - - +
34A GLU* 1.3 62.0 + - - +
35A ARG 3.3 0.9 - - - -
36A VAL* 3.2 20.5 + - + +
37A ASN 3.2 14.9 + - - +
41A ALA* 3.7 12.7 - - + +
44A LEU* 4.9 5.6 - - + -
395B ILE* 3.9 21.2 - - + +
398B LYS* 3.9 27.4 - - + -
399B MET* 3.8 22.2 - - + +
402B LYS* 4.0 17.3 - - + -
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Residues in contact with GLU 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 PHE 3.4 13.2 - - - +
31A ASN* 3.4 17.9 - - - +
32A GLU 3.2 1.0 - - - -
33A LEU* 1.3 78.9 - - - +
35A ARG* 1.3 61.9 + - - +
36A VAL 3.3 0.7 + - - -
37A ASN* 3.5 2.3 + - - -
38A LEU* 3.3 49.9 + - + +
41A ALA* 3.9 12.6 - - + -
42A GLN* 5.0 4.7 + - - +
45A ARG* 3.5 23.2 + - - +
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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