Contacts of the helix formed by residues 22 - 32 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.7 10.1 - - + +
21D PRO* 1.3 77.8 - - - +
23D GLU* 1.3 63.8 + - - +
24D LYS* 3.1 4.9 + - + +
25D LEU* 3.2 32.1 + - + +
55D PHE* 3.2 15.1 - - + -
81D ASN 3.0 12.8 + - - +
83D LEU* 3.9 28.7 - - + -
122D MET* 4.2 12.6 - - - -
125D GLU* 3.6 55.2 - - + +
126D ILE* 3.8 8.3 - - + +
129D ASN* 3.9 8.5 - - + +
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Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 3.7 2.8 + - - +
22D ILE* 1.3 74.0 - - - +
24D LYS* 1.3 77.1 + - + +
26D ARG* 2.7 57.3 + - - +
27D ASN* 5.0 5.4 + - - +
81D ASN* 3.5 31.6 - - + +
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Residues in contact with LYS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.1 4.0 - - + +
23D GLU* 1.3 92.1 + - + +
25D LEU* 1.4 56.5 + - - +
26D ARG 3.1 0.2 - - - -
27D ASN* 2.9 48.5 + - - +
28D TYR* 3.5 6.1 - - + -
119D ASP* 5.5 2.0 - - - +
121D ASP* 6.4 0.2 - - + -
122D MET* 3.6 31.2 - - + -
125D GLU* 5.9 1.6 - - + -
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.2 35.6 + - + +
24D LYS* 1.4 76.3 - - - +
26D ARG* 1.3 56.8 + - - +
27D ASN 3.1 0.2 - - - -
28D TYR* 3.0 27.7 + - + +
29D THR* 3.6 11.1 + - - +
55D PHE* 3.6 31.6 - - + -
83D LEU* 4.0 22.7 - - + -
107D PHE* 4.3 19.8 - - + -
112D LEU* 5.8 2.7 - - + -
115D VAL* 4.5 10.1 - - + -
122D MET* 3.9 27.6 - - + -
126D ILE* 4.8 12.3 - - + -
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Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLU* 2.7 42.6 + - - +
24D LYS 3.1 0.8 - - - -
25D LEU* 1.3 77.1 - - - +
27D ASN* 1.3 64.6 + - - +
28D TYR 3.4 0.9 + - - -
29D THR* 3.5 26.2 + - + -
55D PHE* 3.7 8.7 - - + -
57D VAL* 2.8 49.6 + - + +
80D GLY* 5.0 0.6 - - - -
81D ASN* 2.9 34.2 + - - +
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Residues in contact with ASN 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLU* 5.0 4.3 + - - +
24D LYS* 2.9 46.2 + - - +
26D ARG* 1.3 83.8 - - - +
28D TYR* 1.3 79.9 + - + +
29D THR 3.7 0.4 - - - -
30D GLN* 5.0 8.1 - - - +
31D MET* 5.7 0.3 - - - +
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Residues in contact with TYR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LYS* 3.5 22.0 - - + -
25D LEU* 3.0 15.8 + - + +
27D ASN* 1.3 95.4 + - + +
29D THR* 1.3 59.4 + - - +
30D GLN* 3.3 3.1 - - - -
31D MET* 3.0 50.1 + - + +
107D PHE* 3.3 10.5 - - + -
115D VAL* 3.9 26.0 - - + -
118D THR* 3.8 24.1 - - + +
119D ASP* 3.1 32.9 + - + +
122D MET* 3.8 25.1 - - + -
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Residues in contact with THR 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU 3.6 14.1 - - - +
26D ARG* 3.5 23.3 + - + -
27D ASN 3.7 0.6 - - - -
28D TYR* 1.3 72.4 - - - +
30D GLN* 1.3 63.8 + - - +
31D MET 3.1 4.9 - - - -
32D GLY 3.0 20.1 + - - +
34D ILE* 4.3 16.8 - - - +
55D PHE* 4.2 10.8 - - + -
57D VAL* 4.4 10.3 - - + -
105D CYS* 3.4 36.0 - - + -
107D PHE* 4.1 0.9 - - + -
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Residues in contact with GLN 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASN 5.0 8.0 - - - +
28D TYR 3.3 1.1 - - - -
29D THR* 1.3 81.2 + - - +
31D MET* 1.3 61.2 + - + +
32D GLY 3.3 5.3 + - - +
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Residues in contact with MET 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASN 5.7 0.4 - - - +
28D TYR* 3.0 32.5 + - + +
30D GLN* 1.3 79.8 - - + +
32D GLY* 1.3 56.8 + - - +
107D PHE* 4.4 0.2 - - - -
111D SER* 3.1 25.2 - - - +
114D THR* 3.7 27.4 - - + -
115D VAL* 3.9 31.6 - - + -
118D THR* 3.5 27.4 - - + +
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Residues in contact with GLY 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D TYR 3.9 1.4 + - - -
29D THR 3.0 18.7 + - - +
30D GLN 4.0 5.0 - - - +
31D MET* 1.3 80.5 - - - +
33D LEU* 1.3 72.2 + - - +
34D ILE* 4.1 1.4 + - - +
105D CYS* 3.7 8.3 - - - -
106D TRP 3.4 11.4 - - - -
107D PHE* 3.9 9.1 - - - -
111D SER* 4.5 2.9 - - - -
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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