Contacts of the helix formed by residues 74 - 78 (chain F) in PDB entry 6Q2J
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 GLY 74 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73F TYR* 1.3 75.9 - - - +
75F THR* 1.3 64.7 + - - -
76F TYR 3.6 0.3 + - - -
77F ARG 3.5 7.8 + - - -
78F THR 3.4 14.9 + - - -
80F LEU* 4.3 11.2 - - - -
113F ASN* 5.7 0.4 - - - -
118F LEU* 5.4 1.3 - - - -
120F THR* 4.2 15.7 - - - -
122F TYR* 3.3 24.2 - - - -
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Residues in contact with THR 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D LYS 5.1 3.8 + - - -
252D CYS* 3.3 26.7 + - - +
253D HIS* 3.5 29.9 + - + -
74F GLY* 1.3 68.1 - - - -
76F TYR* 1.3 83.6 + - + +
78F THR* 2.8 31.1 + - - -
113F ASN* 4.7 15.0 + - - -
116F PHE* 6.6 0.4 - - - -
118F LEU* 5.9 1.4 - - - +
120F THR* 4.9 9.7 + - - +
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Residues in contact with TYR 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ARG* 5.7 8.1 + - - -
238D ARG* 5.6 4.5 + - - +
253D HIS* 4.5 6.8 - - + +
254D GLU* 2.8 57.8 + - + +
255D ASP* 4.6 16.2 + - - +
74F GLY 3.6 0.4 + - - -
75F THR* 1.3 95.7 - - + +
77F ARG* 1.3 75.4 + - - +
78F THR* 3.1 7.7 + - - +
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Residues in contact with ARG 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ASP* 5.3 1.8 + - - -
257D ASN* 4.1 18.6 + - - +
73F TYR* 4.3 17.1 - - + -
74F GLY 3.5 8.0 + - - -
75F THR 3.2 1.4 - - - -
76F TYR* 1.3 85.3 - - - +
78F THR* 1.3 57.9 - - - +
79F ARG* 3.1 10.3 + - - +
122F TYR* 3.7 26.8 + - - +
124F LYS* 3.9 28.7 - - - +
135F GLY 4.8 1.8 + - - -
136F GLU* 3.9 28.6 + - - +
137F CYS 4.9 0.6 - - - +
144F ARG* 4.7 10.7 - - - +
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Residues in contact with THR 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F GLY 3.4 17.1 + - - -
75F THR 2.8 24.0 + - - -
76F TYR* 3.1 9.1 + - - +
77F ARG* 1.3 72.4 - - - +
79F ARG* 1.3 68.3 + - - +
80F LEU* 3.1 16.1 + - + +
112F ARG* 4.3 17.7 - - - +
113F ASN* 5.9 0.2 - - - -
114F HIS* 3.4 37.4 + - + +
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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