Contacts of the helix formed by residues 22 - 32 (chain B) in PDB entry 3E5X
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 ILE 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.7 8.3 - - + +
21B PRO* 1.3 77.5 - - - +
23B GLU* 1.3 65.4 - - - +
24B LYS* 3.1 7.0 + - + +
25B LEU* 3.2 27.3 + - + +
55B PHE* 3.3 15.2 - - - -
81B ASN* 2.9 12.7 + - - +
83B LEU* 4.0 22.7 - - + -
122B MET* 4.2 15.3 - - + -
125B GLU* 3.6 55.2 - - + +
126B ILE* 4.1 5.6 - - + +
129B ASN* 3.9 18.2 - - + +
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Residues in contact with GLU 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 PRO* 3.8 2.6 - - - +
22B ILE* 1.3 73.8 - - - +
24B LYS* 1.3 76.4 + - + +
26B ARG* 3.0 53.3 + - - +
27B ASN* 5.0 5.5 + - - +
81B ASN* 3.5 29.6 - - + +
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Residues in contact with LYS 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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22B ILE* 3.1 5.1 - - + +
23B GLU* 1.3 90.1 + - + +
25B LEU* 1.3 55.9 + - - +
26B ARG 3.1 1.3 - - - -
27B ASN* 3.0 43.8 + - - +
28B TYR* 3.4 6.7 - - + -
122B MET* 3.7 30.3 - - + -
125B GLU* 6.0 1.6 - - + -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.2 38.6 + - + +
23B GLU 3.2 0.8 + - - -
24B LYS* 1.3 70.0 - - - +
26B ARG* 1.3 63.0 + - - +
27B ASN 3.0 2.2 - - - -
28B TYR* 2.9 29.8 + - + +
29B THR* 3.5 12.5 + - - +
55B PHE* 3.7 28.0 - - + -
83B LEU* 4.1 21.8 - - + -
107B PHE* 4.3 17.6 - - + -
112B LEU* 5.6 2.9 - - + -
115B VAL* 4.4 11.9 - - + -
122B MET* 4.0 24.8 - - + -
126B ILE* 4.6 13.0 - - + -
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Residues in contact with ARG 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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23B GLU* 3.0 36.5 + - - +
25B LEU* 1.3 79.4 - - - +
27B ASN* 1.3 61.4 + - - +
28B TYR 3.2 1.4 + - - -
29B THR* 3.5 22.4 + - + -
30B GLN* 4.9 0.9 + - - -
55B PHE* 3.8 12.9 - - + -
57B VAL* 2.5 47.4 + - + +
58B GLU* 5.0 2.6 - - - +
80B GLY* 4.8 1.8 - - - -
81B ASN* 2.8 29.9 + - - +
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Residues in contact with ASN 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 GLU* 5.0 5.2 + - - +
24B LYS* 3.0 37.9 + - - +
25B LEU 3.0 1.8 - - - -
26B ARG* 1.3 80.7 - - - +
28B TYR* 1.3 81.1 + - + +
30B GLN* 3.0 16.5 + - - -
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Residues in contact with TYR 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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24B LYS* 3.4 23.6 - - + -
25B LEU* 2.9 15.8 + - + +
27B ASN* 1.3 94.4 + - + +
29B THR* 1.3 60.7 + - - +
30B GLN* 3.1 7.2 - - - +
31B MET* 3.0 46.8 + - + +
107B PHE* 3.4 10.3 - - + -
115B VAL* 3.9 24.7 - - + -
118B THR* 4.0 23.6 - - + +
119B ASP* 3.0 33.4 + - + +
122B MET* 3.7 23.8 - - + -
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Residues in contact with THR 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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25B LEU 3.6 14.1 - - - +
26B ARG* 3.5 17.3 + - + -
28B TYR* 1.3 78.3 - - - +
30B GLN* 1.3 64.2 + - - +
32B GLY 3.1 16.6 + - - +
34B ILE* 4.0 17.2 - - - +
55B PHE* 4.0 14.4 - - + -
57B VAL* 4.1 10.8 - - + -
105B CYS* 3.4 37.9 - - + -
107B PHE* 4.0 1.3 - - + -
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Residues in contact with GLN 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 ARG 4.9 0.8 + - - -
27B ASN 3.0 33.5 + - - -
28B TYR* 3.5 4.2 - - - +
29B THR* 1.3 82.4 + - - +
31B MET* 1.3 70.5 + - + +
32B GLY 3.4 6.1 - - - +
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Residues in contact with MET 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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28B TYR* 3.0 30.7 + - + +
30B GLN* 1.3 88.9 - - + +
32B GLY* 1.3 56.3 + - - +
107B PHE* 4.4 0.9 - - + -
111B SER* 3.1 26.7 - - - +
114B THR* 4.1 18.4 - - + -
115B VAL* 4.0 39.7 - - + -
118B THR* 3.6 26.0 - - + +
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Residues in contact with GLY 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 TYR 3.9 1.8 + - - -
29B THR 3.1 17.2 + - - +
30B GLN* 3.8 6.6 - - - +
31B MET* 1.3 81.2 - - - +
33B LEU* 1.3 72.7 + - - +
34B ILE* 4.2 0.9 + - - +
105B CYS* 3.7 10.5 - - - -
106B TRP 3.4 12.8 - - - -
107B PHE* 3.9 8.0 - - - -
111B SER* 4.5 2.5 - - - -
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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
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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