Contacts of the helix formed by residues 30 - 35 (chain L) in PDB entry 6AHU
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 ARG 30 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L SER 4.9 2.0 + - - +
28L ARG* 3.3 0.6 - - - +
29L HIS* 1.3 103.4 + - + +
31L HIS* 1.3 58.9 + - - +
32L LEU 3.3 0.7 - - - -
33L VAL* 3.4 3.1 + - - +
34L GLN* 3.1 64.1 + - - +
291L CYS* 4.3 22.3 - - - +
294L LEU* 4.8 6.3 - - - -
295L GLU* 3.5 39.1 + - - +
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Residues in contact with HIS 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L SER 5.6 0.2 + - - -
28L ARG* 3.8 28.3 + - + +
30L ARG* 1.3 79.1 - - - +
32L LEU* 1.3 54.7 + - - +
34L GLN* 4.8 6.7 - - - -
35L THR* 2.5 59.3 + - + +
325L GLU* 4.3 13.9 + - - -
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Residues in contact with LEU 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L ARG* 3.3 18.4 + - + +
29L HIS* 4.9 3.1 - - - +
30L ARG 3.3 0.2 - - - -
31L HIS* 1.3 81.4 + - - +
33L VAL* 1.3 64.8 + - + +
35L THR* 4.0 5.4 + - - -
36L HIS* 3.5 19.2 + - - +
324L TRP* 4.3 18.8 - - + +
339L TYR* 4.8 13.6 - - + -
341L PHE* 5.4 1.1 - - + -
351L LEU* 3.7 31.0 - - + -
353L MET* 3.7 34.1 - - + -
362L PRO* 5.0 4.9 - - + +
363L PRO 4.1 22.4 - - - +
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Residues in contact with VAL 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L HIS 3.3 20.9 - - - +
30L ARG 3.4 4.1 + - - +
31L HIS 3.3 0.2 - - - -
32L LEU* 1.3 80.2 - - + +
34L GLN* 1.3 64.1 + - - +
35L THR 3.2 1.3 - - - -
36L HIS* 3.3 15.2 + - - +
287L PRO* 3.4 23.2 - - + +
290L ILE* 4.2 13.9 - - + -
291L CYS* 3.7 23.1 - - - +
294L LEU* 4.5 7.6 - - + -
339L TYR* 4.0 21.7 + - + +
341L PHE* 3.7 29.4 - - + -
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Residues in contact with GLN 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ARG* 3.1 55.8 + - - +
31L HIS* 4.6 5.6 - - - +
33L VAL* 1.3 76.5 - - - +
35L THR* 1.3 63.5 + - + +
36L HIS 3.3 4.6 + - - +
37L TYR* 4.4 6.2 - - - -
93L TYR* 4.8 3.1 + - - -
111L PRO* 5.4 2.1 - - - +
287L PRO* 4.4 11.8 - - - +
288L GLU* 5.0 12.4 - - + +
291L CYS* 3.6 18.6 - - - +
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Residues in contact with THR 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L HIS* 2.5 46.9 + - + +
32L LEU* 4.0 5.7 - - - -
33L VAL 3.2 0.2 - - - -
34L GLN* 1.3 81.4 - - + +
36L HIS* 1.3 58.2 + - - +
37L TYR* 3.4 24.2 + - - +
324L TRP* 4.0 14.9 + - - -
325L GLU* 3.3 37.0 - - - +
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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