Contacts of the helix formed by residues 21 - 34 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ARG* 3.2 39.9 + - + +
20B ILE* 1.3 75.7 - - - +
22B PRO* 1.3 73.7 - - + +
23B GLN* 3.7 7.3 + - - +
24B ARG* 3.1 37.1 + - - +
25B HIS* 3.0 22.6 + - - +
62B ASN* 5.2 0.2 + - - -
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Residues in contact with PRO 22 (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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20B ILE 4.3 2.2 - - - +
21B THR* 1.3 86.0 - - + +
23B GLN* 1.3 62.6 + - - +
25B HIS* 3.3 7.5 + - + +
26B ALA* 2.9 25.8 + - - +
51B PHE* 3.6 20.9 - - + -
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Residues in contact with GLN 23 (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 THR* 3.2 8.0 + - - +
22B PRO* 1.3 78.9 - - - +
24B ARG* 1.3 56.4 + - - +
26B ALA* 3.3 2.3 + - - +
27B ILE* 3.0 46.2 + - + +
51B PHE* 3.7 21.9 - - + +
53B ASN* 4.7 2.4 - - - +
54B MET* 3.4 32.3 + - + +
58B THR* 2.8 43.0 + - - +
59B VAL* 3.6 2.2 - - - +
62B ASN* 3.2 23.3 + - - +
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Residues in contact with ARG 24 (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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13B LEU* 4.8 6.5 - - + -
18B VAL* 3.4 24.2 - - - +
19B ARG* 2.9 42.5 + - - +
20B ILE* 5.0 0.7 - - + -
21B THR* 3.1 30.0 + - - +
23B GLN* 1.3 77.6 - - - +
25B HIS* 1.3 61.7 + - - +
27B ILE* 3.3 2.3 + - - -
28B LEU* 3.0 24.7 + - - +
62B ASN* 2.9 36.9 - - - +
65B VAL* 4.1 19.4 - - - +
66B PHE* 3.5 28.2 - - + -
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Residues in contact with HIS 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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6B LEU* 3.9 28.0 - - + +
10B LEU* 3.8 37.0 - - + +
20B ILE* 4.7 10.7 - - + +
21B THR 3.0 13.2 + - - +
22B PRO* 3.5 10.8 - - + +
24B ARG* 1.3 75.1 - - - +
26B ALA* 1.3 59.7 + - - +
28B LEU* 3.3 6.0 + - - +
29B GLU* 2.9 42.9 + - - +
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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 PRO 2.9 16.8 + - - +
23B GLN 3.7 2.7 - - - +
25B HIS* 1.3 82.2 + - - +
27B ILE* 1.3 55.8 + - - +
29B GLU* 3.8 10.1 - - - +
30B TYR* 3.0 28.2 + - - +
47B LEU* 3.7 18.1 - - + +
50B LYS* 5.7 2.7 - - + -
51B PHE* 3.5 28.3 - - + -
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Residues in contact with ILE 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 GLN* 3.0 42.9 + - + +
24B ARG* 3.8 3.8 - - - +
26B ALA* 1.3 72.8 - - - +
28B LEU* 1.3 66.9 + - - +
30B TYR* 3.2 4.4 + - - +
31B LEU* 2.9 35.9 + - + +
43B ILE* 4.0 16.6 - - + -
47B LEU* 3.9 20.6 - - + -
54B MET* 5.5 0.2 - - - -
59B VAL* 4.3 14.8 - - + +
62B ASN* 3.6 29.8 - - + +
63B LEU* 4.2 11.4 - - + -
66B PHE* 3.7 16.2 - - + -
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Residues in contact with LEU 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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6B LEU* 3.8 13.2 - - + -
9B ALA* 4.1 16.4 - - + -
10B LEU* 4.2 13.0 - - + -
13B LEU* 3.7 32.3 - - + -
24B ARG 3.0 19.3 + - - +
25B HIS 3.7 4.5 - - - +
27B ILE* 1.3 77.0 - - - +
29B GLU* 1.3 56.7 + - - +
31B LEU* 3.2 8.5 + - + +
32B VAL* 2.9 34.3 + - + +
66B PHE* 3.7 31.9 - - + -
71B LEU* 4.1 13.7 - - + -
72B VAL* 4.9 0.2 - - + -
86B PHE* 4.2 20.9 - - + -
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Residues in contact with GLU 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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6B LEU* 4.0 28.1 - - + +
25B HIS* 2.9 32.1 + - - +
26B ALA* 3.8 8.7 - - - +
28B LEU* 1.3 74.3 - - - +
30B TYR* 1.3 63.4 + - - +
32B VAL* 3.4 4.3 + - - +
33B ASN* 3.1 44.3 + - - +
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Residues in contact with TYR 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 18.6 + - - +
27B ILE* 3.2 7.2 + - - +
29B GLU* 1.3 76.9 - - - +
31B LEU* 1.3 62.3 + - - +
33B ASN* 3.2 6.1 + - + +
34B SER* 3.0 31.2 + - - -
38B PRO* 3.8 21.4 - - + +
42B ASP* 3.9 19.3 + - - +
43B ILE* 3.7 33.4 - - + -
46B ALA* 3.3 31.6 - - + +
47B LEU* 4.5 12.1 - - + -
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Residues in contact with LEU 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 ILE* 2.9 36.6 + - + +
28B LEU* 3.6 9.4 - - + +
30B TYR* 1.3 76.1 - - + +
32B VAL* 1.3 63.8 + - - +
34B SER* 3.3 18.7 + - - +
38B PRO* 3.6 31.6 - - + +
43B ILE* 4.0 12.3 - - + -
63B LEU* 4.1 7.4 - - + -
66B PHE* 4.5 5.2 - - + -
72B VAL* 3.6 29.2 - - + -
84B PHE* 4.2 15.9 - - + +
86B PHE* 4.2 24.3 - - + +
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Residues in contact with VAL 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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3B ALA* 4.8 9.9 - - + -
5B GLU* 3.4 33.3 - - + +
6B LEU* 4.3 21.1 - - + +
28B LEU 2.9 21.9 + - - +
29B GLU* 3.9 6.1 - - - +
31B LEU* 1.3 76.4 - - - +
33B ASN* 1.3 70.7 + - - +
34B SER 3.5 3.6 + - - +
86B PHE* 3.6 41.5 - - + -
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Residues in contact with ASN 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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3B ALA* 5.8 4.2 - - - +
29B GLU* 3.1 35.4 + - - +
30B TYR* 3.7 5.4 - - + +
32B VAL* 1.3 88.2 + - - +
34B SER* 1.3 61.8 + - - +
35B MET* 3.7 6.9 + - - +
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Residues in contact with SER 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 TYR* 3.0 24.2 + - - -
31B LEU* 3.3 14.5 + - - +
32B VAL 4.3 3.3 - - - +
33B ASN* 1.3 79.7 - - - +
35B MET* 1.3 62.4 + - - +
36B ALA 2.4 28.8 + - - -
38B PRO* 3.7 19.6 - - - +
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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