Contacts of the helix formed by residues 28 - 32 (chain X) in PDB entry 1MHP
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 THR 28 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27X PHE* 1.3 67.2 - - - +
29X PHE* 1.3 64.8 + - - +
30X SER* 3.4 20.4 - - - +
31X ARG* 3.1 35.6 + - + +
32X TYR* 3.1 18.9 + - - -
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Residues in contact with PHE 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X CYS* 6.6 0.2 - - - -
24X ALA* 3.8 20.0 - - + -
27X PHE* 2.7 19.4 + + + +
28X THR* 1.3 69.8 - - - +
30X SER* 1.3 55.0 + - - +
31X ARG 2.7 12.3 + - - -
32X TYR* 3.1 15.2 + - - +
34X MET* 3.3 48.0 - - + -
71X ARG* 3.1 22.3 + - + -
73X ASN* 3.5 28.9 - - - -
76X ASN* 3.5 39.3 + - + +
77X THR 3.7 35.2 - - - -
78X LEU* 3.9 10.3 - - + -
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Residues in contact with SER 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B TYR* 3.6 30.5 + - - -
28X THR* 3.4 18.0 - - - +
29X PHE* 1.3 77.7 - - - +
31X ARG* 1.3 60.1 + - - +
53X GLY* 3.7 10.2 - - - +
71X ARG* 3.5 16.3 + - - +
73X ASN* 3.9 25.0 + - - -
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Residues in contact with ARG 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ASN 5.5 0.9 - - - +
158B SER* 5.2 3.3 - - - +
160B TYR* 4.2 45.4 + - + +
161B PRO* 5.3 2.2 - - - +
288B HIS* 5.1 13.0 + - + +
291B ARG* 3.1 58.5 - - - +
320B ASP* 5.9 0.8 - - - +
322B LEU* 6.1 2.4 - - - +
28X THR* 3.1 31.7 + - + +
29X PHE 2.7 6.3 + - - -
30X SER* 1.3 77.8 + - - +
32X TYR* 1.3 73.7 + - + +
33X THR* 4.0 2.9 + - - +
53X GLY* 4.2 9.2 + - - -
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Residues in contact with TYR 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B ARG* 5.0 15.0 - - + +
292B GLY* 6.0 2.9 - - - -
27X PHE* 3.1 27.5 - + + +
28X THR* 3.1 30.2 + - - -
29X PHE 3.1 3.2 + - - +
31X ARG* 1.3 91.1 - - + +
33X THR* 1.3 54.3 + - - +
34X MET* 3.6 7.1 + - - +
53X GLY 4.2 1.8 + - - -
71X ARG* 2.3 34.5 + - - -
97X ARG* 3.4 57.5 + - + -
98X GLY 4.0 12.8 - - - +
99X PHE* 5.7 1.3 - + - -
106X ASP* 4.8 1.6 - - - -
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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