Contacts of the helix formed by residues 22 - 32 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.7 10.5 - - + +
21A PRO* 1.3 77.4 - - - +
23A GLU* 1.3 64.8 + - - +
24A LYS* 3.2 5.8 + - + +
25A LEU* 3.2 34.5 + - + +
55A PHE* 3.2 14.4 - - - -
81A ASN* 2.9 13.5 + - - +
83A LEU* 3.7 33.7 - - + -
122A MET* 4.3 6.7 - - - -
125A GLU* 3.5 58.1 - - + +
126A ILE* 4.0 7.6 - - + +
129A ASN* 4.1 5.6 - - + +
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Residues in contact with GLU 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 PRO* 3.7 5.1 + - + -
22A ILE* 1.3 73.1 - - - +
24A LYS* 1.3 70.9 + - - +
26A ARG* 3.1 42.0 + - - +
27A ASN* 5.1 4.0 - - - +
81A ASN* 3.5 31.5 - - - +
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Residues in contact with LYS 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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22A ILE* 3.2 4.9 + - + -
23A GLU* 1.3 84.1 + - - +
25A LEU* 1.3 59.9 + - - +
26A ARG 3.0 5.2 - - - -
27A ASN* 3.0 35.6 + - - +
28A TYR* 3.6 8.9 - - + -
119A ASP* 3.7 12.9 + - - -
121A ASP* 5.7 2.2 + - + +
122A MET* 3.6 28.9 - - + -
125A GLU* 6.0 0.4 - - + -
161C CYS 4.7 1.6 + - - -
162C SER 4.3 7.5 + - - -
163C SER 3.7 24.4 + - - +
164C GLN* 4.7 0.7 - - - +
165C GLY* 3.0 30.3 + - - +
172C TYR* 5.6 3.6 - - - -
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Residues in contact with LEU 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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22A ILE* 3.2 30.8 + - + +
24A LYS* 1.3 76.4 - - - +
26A ARG* 1.3 56.0 + - - +
27A ASN 3.1 0.2 - - - -
28A TYR* 3.0 30.3 + - + +
29A THR* 3.5 13.0 + - - +
55A PHE* 3.6 41.3 - - + -
83A LEU* 3.9 23.1 - - + -
107A PHE* 4.4 21.0 - - + -
112A LEU* 5.7 2.9 - - + -
115A VAL* 4.6 9.0 - - + -
122A MET* 4.2 20.2 - - + -
126A ILE* 4.9 11.9 - - + -
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Residues in contact with ARG 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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23A GLU* 3.1 37.7 + - - +
25A LEU* 1.3 76.4 - - - +
27A ASN* 1.3 65.2 + - - +
28A TYR 3.3 1.0 + - - -
29A THR* 3.6 23.7 + - - -
30A GLN* 4.8 0.5 - - - +
55A PHE* 3.8 11.0 - - + -
57A VAL* 3.7 37.2 + - + +
58A GLU* 5.4 3.8 + - - +
81A ASN* 3.6 22.2 + - - +
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Residues in contact with ASN 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 GLU* 5.1 4.2 - - - +
24A LYS* 3.0 33.5 + - - +
26A ARG* 1.3 82.0 - - - +
28A TYR* 1.3 75.3 + - + +
29A THR 3.8 0.2 - - - -
30A GLN* 3.2 19.9 + - - +
163C SER 3.5 23.4 + - - -
164C GLN* 3.9 14.8 + - - +
166C LYS* 6.1 0.4 - - - -
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Residues in contact with TYR 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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24A LYS* 3.6 29.3 - - - -
25A LEU* 3.0 16.0 + - + +
27A ASN* 1.3 93.4 + - + +
29A THR* 1.3 60.6 + - - +
30A GLN* 3.2 9.6 - - - +
31A MET* 2.8 45.1 + - + +
107A PHE* 3.4 7.7 - - - -
115A VAL* 4.0 24.2 - - + -
118A THR* 4.0 20.6 - - + -
119A ASP* 2.6 32.4 + - + +
122A MET* 3.6 31.9 - - + -
164C GLN 5.0 0.7 + - - -
165C GLY 4.3 0.2 + - - -
166C LYS* 3.5 20.9 - - - +
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Residues in contact with THR 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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25A LEU 3.5 14.8 - - - +
26A ARG* 3.6 17.2 + - - +
28A TYR* 1.3 72.8 - - - +
30A GLN* 1.3 64.9 + - - +
31A MET 3.0 5.6 - - - -
32A GLY 3.1 14.9 + - - +
34A ILE* 4.2 17.3 - - - +
55A PHE* 4.0 15.7 - - + -
57A VAL* 4.3 9.4 - - + -
105A CYS* 3.4 37.3 - - + -
107A PHE* 3.9 1.8 - - + -
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Residues in contact with GLN 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 ARG 4.8 0.7 - - - +
27A ASN 3.2 28.1 + - - +
28A TYR* 3.8 9.9 - - - +
29A THR* 1.3 82.7 + - - +
31A MET* 1.3 81.3 + - + +
32A GLY 3.4 5.8 - - - +
34A ILE* 6.3 0.2 - - - -
166C LYS* 6.1 0.6 - - - +
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Residues in contact with MET 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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28A TYR* 2.8 24.8 + - + +
30A GLN* 1.3 100.2 - - + +
32A GLY* 1.3 58.3 + - - +
107A PHE* 4.3 0.9 - - - -
111A SER* 3.1 26.4 - - - +
114A THR* 3.9 24.9 - - + -
115A VAL* 3.8 35.2 - - + -
118A THR* 3.5 29.8 - - + +
166C LYS* 6.0 0.9 - - - +
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Residues in contact with GLY 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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29A THR 3.1 18.6 + - - +
30A GLN 3.9 5.9 - - - +
31A MET* 1.3 82.0 - - - +
33A LEU* 1.3 70.4 + - - +
34A ILE* 4.2 1.2 + - - +
105A CYS* 3.8 7.2 - - - -
106A TRP 3.4 12.6 - - - -
107A PHE* 3.8 10.0 - - - -
111A SER* 4.3 3.1 - - - -
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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