Contacts of the helix formed by residues 25 - 33 (chain A) in PDB entry 3H0G
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 SER 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ILE 4.3 1.3 - - - -
24A LEU* 1.3 76.6 - - - +
26A PRO* 1.3 62.5 - - - -
27A GLU* 4.4 4.0 + - - +
28A GLU* 2.8 38.3 + - - +
29A ILE* 2.7 38.7 + - - +
239A TRP* 2.2 44.7 - - - -
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Residues in contact with PRO 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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24A LEU 4.7 0.2 - - - +
25A SER* 1.3 75.3 - - - +
27A GLU* 1.3 74.8 + - + +
29A ILE* 3.3 15.0 + - + +
30A ARG* 3.0 29.1 + - - +
214A HIS* 5.6 4.7 - - + +
238A ASP 4.9 6.1 - - - +
239A TRP* 2.6 39.0 - - + +
241A ILE 5.3 5.6 - - - +
243A THR* 4.4 18.4 - - - +
244A VAL* 3.7 19.8 - - + +
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Residues in contact with GLU 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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25A SER* 3.1 4.6 + - - +
26A PRO* 1.3 88.5 - - + +
28A GLU* 1.3 63.8 + - + +
30A ARG* 3.3 7.9 + - - +
31A SER* 3.1 21.9 + - - -
239A TRP* 5.5 8.2 - - - -
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Residues in contact with GLU 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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23A ILE 5.5 0.2 - - - +
24A LEU* 4.6 13.3 - - + +
25A SER* 2.8 36.3 + - - +
27A GLU* 1.3 75.3 - - + +
29A ILE* 1.3 65.9 + - - +
31A SER* 2.6 24.5 + - - +
32A MET* 2.8 21.2 + - + +
233A GLN 5.4 4.2 - - - +
239A TRP* 6.2 0.7 - - - -
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Residues in contact with ILE 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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24A LEU* 4.0 37.7 - - + +
25A SER* 2.7 32.8 + - - +
26A PRO* 3.5 10.8 - - + +
28A GLU* 1.3 72.2 - - - +
30A ARG* 1.3 61.3 + - - +
32A MET* 4.1 5.6 - - - +
33A SER* 3.3 23.6 + - - -
85A HIS* 4.2 1.3 - - + -
242A ILE* 6.3 1.8 - - + -
244A VAL* 3.4 31.6 - - + +
245A LEU 5.2 0.4 - - - +
246A PRO* 3.6 36.6 - - + -
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Residues in contact with ARG 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 PRO* 3.0 8.7 + - - +
27A GLU* 3.5 11.2 - - - +
28A GLU 3.1 0.2 - - - -
29A ILE* 1.3 75.1 - - - +
31A SER* 1.3 59.8 + - - +
33A SER* 2.8 32.9 + - - +
85A HIS* 3.3 17.1 + - + +
87A GLU* 5.4 4.6 - - - +
243A THR* 3.8 19.6 + - - +
244A VAL* 2.5 47.3 - - + +
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Residues in contact with SER 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 GLU 3.1 8.0 + - - -
28A GLU* 2.6 30.5 + - - +
30A ARG* 1.3 78.9 - - - +
32A MET* 1.3 71.0 + - - +
33A SER 3.0 9.0 - - - +
34A VAL* 4.7 4.3 - - - +
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Residues in contact with MET 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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24A LEU* 6.2 3.8 - - + -
28A GLU* 2.8 24.0 + - + +
29A ILE* 4.1 5.4 - - - +
31A SER* 1.3 85.0 + - - +
33A SER* 1.3 61.9 + - - +
34A VAL* 3.6 11.1 + - - +
83A PHE* 4.7 8.8 - - + +
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Residues in contact with SER 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 ILE 3.3 8.2 + - - -
30A ARG 2.8 28.9 + - - +
31A SER 3.0 7.8 - - - +
32A MET* 1.3 77.9 - - - +
34A VAL* 1.3 57.8 + - - +
35A ALA 4.2 1.8 + - - +
83A PHE* 3.6 11.4 - - - +
84A GLY* 2.9 13.5 - - - -
85A HIS* 2.7 51.7 + - - +
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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