Contacts of the helix formed by residues 164 - 171 (chain F) in PDB entry 5U07
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 ASN 164 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F GLU* 3.9 2.7 + - - +
57F ASP* 2.6 47.7 + - - +
58F LYS 2.9 3.2 + - - -
59F ALA* 2.9 41.3 - - + +
120F PRO* 3.7 17.9 - - + +
163F ARG* 1.3 69.5 - - - +
165F VAL* 1.3 85.9 + - - +
166F SER* 3.2 9.6 + - - +
167F VAL* 3.1 10.7 + - + +
168F ASN* 2.4 41.2 + - - -
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Residues in contact with VAL 165 (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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51F VAL* 3.9 25.8 - - + -
55F LEU* 3.5 27.4 - - + -
57F ASP* 4.0 10.0 + - + +
164F ASN* 1.3 90.8 + - - +
166F SER* 1.3 55.9 + - - +
168F ASN* 3.2 10.6 + - + +
169F LEU* 2.9 34.6 + - + +
246F THR* 5.9 0.7 - - - -
255F ALA* 4.1 22.4 - - + -
258F GLU* 3.9 7.9 - - - +
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Residues in contact with SER 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ARG* 4.1 10.7 + - - +
51F VAL* 4.7 6.3 - - - +
52F GLU* 2.4 42.8 + - - +
59F ALA* 4.3 3.1 - - - -
118F TYR* 3.1 19.8 + - - -
164F ASN* 3.2 2.6 + - - -
165F VAL* 1.3 78.4 - - - +
167F VAL* 1.3 58.6 + - - +
169F LEU* 4.5 1.3 - - - -
170F PHE* 2.8 45.3 + - - +
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Residues in contact with VAL 167 (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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59F ALA* 4.8 2.9 - - + -
118F TYR* 3.6 32.3 - - + +
120F PRO* 5.0 2.0 - - + -
163F ARG* 4.2 11.9 - - + -
164F ASN* 3.1 28.9 + - + +
166F SER* 1.3 73.6 - - - +
168F ASN* 1.3 63.1 + - - +
171F GLY* 2.8 30.8 + - - +
172F ARG* 3.4 47.6 - - + +
182F VAL* 4.1 12.8 - - + +
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Residues in contact with ASN 168 (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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163F ARG* 3.3 28.1 + - - +
164F ASN 2.4 34.6 + - - +
165F VAL* 3.6 9.7 - - + +
167F VAL* 1.3 76.0 - - - +
169F LEU* 1.3 60.5 + - - +
185F ALA* 3.9 2.4 + - - +
242F LEU* 3.4 9.9 - - + +
245F ASN* 3.0 56.4 + - + +
246F THR* 3.6 30.4 - - + +
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Residues in contact with LEU 169 (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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51F VAL* 5.0 7.2 - - + -
165F VAL* 2.9 26.2 + - + +
166F SER 4.0 1.8 - - - +
168F ASN* 1.3 78.3 - - - +
170F PHE* 1.3 74.8 + - + +
185F ALA* 2.9 21.4 + - + -
186F VAL* 3.2 38.0 + - + +
237F VAL* 4.9 2.5 - - + -
242F LEU* 3.5 32.8 - - + -
255F ALA* 4.5 11.9 - - + +
256F VAL* 5.3 0.9 - - + -
259F PHE* 3.7 38.6 - - + -
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Residues in contact with PHE 170 (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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44F LYS* 3.6 47.5 + - + +
47F VAL* 4.3 11.7 - - + -
48F ARG* 3.6 31.9 - - + -
51F VAL* 5.9 1.8 - - + -
61F ARG* 6.2 0.9 - - - +
118F TYR* 5.2 3.4 - - + +
166F SER* 2.8 35.0 + - - +
169F LEU* 1.3 86.4 - - + +
171F GLY* 1.3 66.9 + - - +
184F GLY* 3.3 15.4 + - - -
186F VAL* 4.1 28.8 - - + +
188F PHE* 5.7 2.2 - + + -
259F PHE* 4.0 22.0 - + - -
273G ASN* 5.6 2.1 - - - +
24K A 4.6 10.7 + - - +
25K U 5.1 6.0 + - - +
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Residues in contact with GLY 171 (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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61F ARG* 4.7 4.3 + - - -
118F TYR* 4.0 14.4 - - - -
167F VAL* 2.8 23.9 + - - -
170F PHE* 1.3 86.2 - - - +
172F ARG* 1.3 60.9 + - - +
182F VAL* 3.2 16.6 - - - -
183F ASP 4.1 1.3 - - - -
184F GLY* 3.5 10.7 - - - -
24K A 4.9 8.1 - - - +
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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