Contacts of the helix formed by residues 21 - 34 (chain A) in PDB entry 2FE3
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 THR 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ARG* 3.1 37.4 + - + +
20A ILE* 1.3 75.9 - - - +
22A PRO* 1.3 75.0 - - + +
23A GLN* 3.7 6.9 + - - +
24A ARG* 3.1 38.7 + - - +
25A HIS* 3.0 22.3 + - - +
62A ASN* 5.1 0.2 + - - -
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Residues in contact with PRO 22 (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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20A ILE 4.4 1.8 - - - +
21A THR* 1.3 87.0 - - + +
23A GLN* 1.3 62.3 + - - +
25A HIS* 3.3 7.0 + - + +
26A ALA* 3.0 24.3 + - - +
51A PHE* 3.6 19.6 - - + -
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Residues in contact with GLN 23 (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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21A THR* 3.2 7.4 + - - +
22A PRO* 1.3 79.8 - - - +
24A ARG* 1.3 57.4 + - - +
26A ALA* 3.2 2.6 + - - +
27A ILE* 2.9 34.8 + - + +
51A PHE* 3.7 19.2 - - + +
53A ASN 4.7 1.7 - - - +
54A MET* 3.4 38.5 + - + +
58A THR* 2.5 46.3 + - - +
59A VAL 3.7 1.6 - - - +
62A ASN* 3.1 22.4 + - - +
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Residues in contact with ARG 24 (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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13A LEU* 4.8 6.3 - - + -
18A VAL* 3.4 24.5 - - - +
19A ARG* 2.9 41.5 + - - +
20A ILE* 4.9 0.9 - - + -
21A THR* 3.1 28.1 + - - +
23A GLN* 1.3 74.5 - - - +
25A HIS* 1.3 65.5 + - - +
27A ILE* 3.3 2.6 + - - -
28A LEU* 3.0 24.9 + - - +
62A ASN* 2.8 35.9 - - - +
65A VAL* 4.0 20.9 - - - +
66A PHE* 3.5 29.1 - - + -
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Residues in contact with HIS 25 (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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6A LEU* 4.0 22.5 - - + +
10A LEU* 3.8 40.0 - - + +
20A ILE* 4.6 10.9 - - + +
21A THR 3.0 17.2 + - - +
22A PRO* 3.6 7.2 - - + +
24A ARG* 1.3 73.7 - - - +
26A ALA* 1.3 58.8 + - - +
28A LEU* 3.3 5.9 + - - +
29A GLU* 2.9 41.1 + - - +
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Residues in contact with ALA 26 (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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22A PRO 3.0 16.4 + - - +
23A GLN 3.6 2.9 - - - +
25A HIS* 1.3 77.2 + - - +
27A ILE* 1.3 60.2 + - - +
29A GLU* 3.5 11.5 + - - +
30A TYR* 3.0 28.6 + - - +
47A LEU* 3.8 14.3 - - + +
50A LYS* 3.8 15.5 - - - +
51A PHE* 3.5 28.5 - - + -
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Residues in contact with ILE 27 (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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23A GLN* 2.9 34.8 + - + +
24A ARG* 3.9 3.8 - - - +
26A ALA* 1.3 75.5 - - - +
28A LEU* 1.3 63.7 + - - +
30A TYR* 3.3 4.1 + - - +
31A LEU* 3.0 36.1 + - + +
43A ILE* 4.0 15.5 - - + -
47A LEU* 3.9 19.1 - - + -
54A MET* 4.6 0.7 - - + -
59A VAL* 4.2 15.5 - - + +
62A ASN* 3.6 37.0 - - + +
63A LEU* 4.2 11.7 - - + -
66A PHE* 3.7 17.0 - - + -
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Residues in contact with LEU 28 (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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6A LEU* 3.7 11.2 - - + -
9A ALA* 4.0 17.7 - - + -
10A LEU* 4.0 16.4 - - + -
13A LEU* 3.7 31.2 - - + -
24A ARG 3.0 17.8 + - - +
25A HIS 3.7 3.8 - - - +
27A ILE* 1.3 77.0 - - - +
29A GLU* 1.3 56.0 + - - +
31A LEU* 3.2 7.0 + - + +
32A VAL* 2.8 34.7 + - + +
66A PHE* 3.7 26.0 - - + -
71A LEU* 4.3 12.3 - - + -
72A VAL* 5.2 0.2 - - + -
86A PHE* 4.2 27.6 - - + -
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Residues in contact with GLU 29 (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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6A LEU* 3.9 25.7 - - + +
25A HIS* 2.9 30.3 + - - +
26A ALA* 3.6 9.9 - - - +
28A LEU* 1.3 77.0 - - - +
30A TYR* 1.3 61.9 + - - +
32A VAL* 3.4 3.1 + - - -
33A ASN* 3.1 44.3 + - - +
50A LYS* 4.5 11.3 + - - -
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Residues in contact with TYR 30 (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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26A ALA 3.0 14.3 + - - +
27A ILE* 3.3 11.6 + - - +
29A GLU* 1.3 76.6 - - - +
31A LEU* 1.3 60.8 + - + +
33A ASN* 3.4 3.6 + - - +
34A SER* 3.0 46.8 + - - -
38A PRO* 3.8 26.9 - - + +
42A ASP* 4.1 19.2 + - - +
43A ILE* 3.8 23.1 - - + -
46A ALA* 3.4 31.9 - - + +
47A LEU* 4.6 13.0 - - + -
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Residues in contact with LEU 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 ILE* 3.0 35.6 + - + +
28A LEU* 3.2 11.2 + - + +
30A TYR* 1.3 78.6 - - + +
32A VAL* 1.3 64.0 + - - +
33A ASN 3.4 0.2 + - - -
34A SER* 3.6 16.9 - - - +
36A ALA 5.6 0.2 - - - +
38A PRO* 3.6 34.3 - - + -
43A ILE* 4.3 9.0 - - + -
63A LEU* 4.0 7.9 - - + -
66A PHE* 4.4 5.4 - - + -
72A VAL* 3.8 28.3 - - + -
84A PHE* 4.0 15.7 - - + +
86A PHE* 4.1 25.9 - - + +
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Residues in contact with VAL 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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4A HIS* 6.1 1.6 - - - +
5A GLU* 3.7 30.9 - - + +
6A LEU* 4.2 25.1 - - + +
9A ALA* 5.3 0.2 - - + -
28A LEU* 2.8 26.0 + - + +
29A GLU* 3.9 5.2 - - - +
30A TYR 3.3 0.2 - - - -
31A LEU* 1.3 74.7 - - - +
33A ASN* 1.3 70.7 + - - +
34A SER 4.4 2.4 - - - +
86A PHE* 3.8 38.6 - - + -
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Residues in contact with ASN 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 GLU* 3.1 36.0 + - - +
30A TYR* 4.1 3.1 - - - +
32A VAL* 1.3 91.6 + - - +
34A SER* 1.3 59.7 + - - +
35A MET* 3.8 14.9 + - - +
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Residues in contact with SER 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 TYR* 3.0 39.1 + - - -
31A LEU* 3.6 14.5 + - - +
32A VAL 3.5 3.2 - - - +
33A ASN* 1.3 78.0 - - - +
35A MET* 1.3 65.0 + - - +
36A ALA* 3.0 28.1 + - - +
38A PRO* 4.4 5.7 - - - +
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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
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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