Contacts of the helix formed by residues 74 - 79 (chain H) in PDB entry 1ZUM
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 74 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68H ALA 4.3 4.7 - - - -
69H ALA* 2.8 30.1 + - - -
71H GLN* 2.9 21.5 + - - +
72H LEU 3.3 1.0 + - - -
73H GLY* 1.3 80.9 - - - +
75H PRO* 1.3 76.6 - - - +
76H TRP 3.4 0.7 + - - -
77H ARG* 3.0 16.3 + - - +
78H ARG* 3.0 21.6 + - - +
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Residues in contact with PRO 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H ALA* 5.5 0.7 - - - +
73H GLY 4.7 0.2 - - - +
74H SER* 1.3 87.8 - - - +
76H TRP* 1.3 56.6 + - - +
78H ARG* 3.9 3.3 - - + -
79H MET* 3.0 34.8 + - + +
214H PRO* 4.1 24.5 - - + -
215H PRO* 6.4 0.4 - - + -
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Residues in contact with TRP 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500E SER* 4.6 4.0 + - - -
69H ALA* 3.8 13.9 - - + +
70H PHE* 4.9 3.4 - + - -
74H SER* 3.3 1.2 + - - -
75H PRO* 1.3 81.4 - - - +
77H ARG* 1.3 63.8 + - - +
79H MET* 3.8 39.5 + - - +
84H ARG* 3.8 25.6 + - + -
87H LEU* 4.0 5.4 - - + -
183H LEU* 3.5 26.5 - - + -
186H GLY* 3.1 22.1 + - - -
187H ASN 2.8 23.8 + - - -
188H VAL* 3.7 19.5 - - + -
213H PHE* 3.8 33.7 - + - -
214H PRO* 3.9 18.7 - - + +
217H VAL* 3.5 29.6 - - + +
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Residues in contact with ARG 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498E LYS* 5.8 0.2 - - - -
499E ASN* 3.3 20.2 - - - +
500E SER* 2.7 73.2 + - - +
444G GLN* 5.9 1.0 + - - +
70H PHE* 2.9 79.4 + - - +
71H GLN 3.4 6.7 - - - +
72H LEU* 3.7 31.5 - - - +
74H SER* 3.0 20.0 + - - +
76H TRP* 1.3 78.9 - - - +
78H ARG* 1.3 62.3 + - - +
79H MET 3.7 2.6 + - - +
155H ARG* 5.6 0.4 - - - +
157H GLU* 5.7 3.8 - - - +
158H PRO* 5.1 1.6 - - - +
186H GLY 4.7 2.5 - - - -
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Residues in contact with ARG 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E ASP* 4.3 16.6 + - - -
497E GLN* 3.5 38.3 - - - +
498E LYS* 3.6 29.2 + - - +
499E ASN* 3.7 15.9 - - - +
73H GLY* 3.4 20.9 + - - +
74H SER 3.0 15.9 + - - +
75H PRO* 4.3 3.4 - - + +
77H ARG* 1.3 74.0 - - - +
79H MET* 1.3 66.6 + - - +
80H ASP* 3.4 3.3 + - - +
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Residues in contact with MET 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498E LYS* 4.7 3.3 - - - -
500E SER* 5.6 0.5 - - - -
75H PRO* 3.0 19.3 + - + +
76H TRP* 3.8 25.0 - - + +
77H ARG 3.4 4.8 - - - +
78H ARG* 1.3 78.4 - - - +
80H ASP* 1.3 76.8 + - - +
81H ALA 3.4 1.6 + - - -
83H HIS* 3.5 32.3 - - + +
84H ARG* 3.9 23.3 + - + -
87H LEU* 3.7 28.0 - - + -
212H GLY 5.5 0.7 - - - +
214H PRO* 4.0 24.2 - - + -
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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