Contacts of the helix formed by residues 164 - 171 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E ASP* 2.7 33.0 + - - +
58E LYS 3.1 10.3 + - - -
59E ALA* 2.9 38.0 - - + +
120E PRO* 3.8 17.9 - - + +
163E ARG* 1.3 70.3 - - - +
165E VAL* 1.3 75.4 + - - +
166E SER* 3.1 14.0 + - - +
167E VAL* 3.0 22.6 + - + +
168E ASN* 2.5 46.3 + - - -
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Residues in contact with VAL 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 3.9 19.3 - - + -
55E LEU* 3.5 31.6 - - + -
57E ASP* 3.0 23.0 + - - +
164E ASN* 1.3 84.4 + - - +
166E SER* 1.3 57.4 + - - +
168E ASN* 3.2 11.0 + - + +
169E LEU* 2.8 33.5 + - + +
246E THR* 6.2 1.6 - - + -
251E THR 6.0 0.4 - - - +
255E ALA* 4.1 23.6 - - + -
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Residues in contact with SER 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ARG* 3.8 31.9 + - - +
51E VAL* 4.7 4.5 - - - +
52E GLU* 4.1 15.4 + - - +
59E ALA* 4.4 4.9 - - - +
118E TYR* 3.1 23.8 + - - -
164E ASN* 3.1 11.6 + - - -
165E VAL* 1.3 78.3 - - - +
167E VAL* 1.3 57.9 + - - +
169E LEU* 4.5 2.0 - - - -
170E PHE* 2.9 40.7 + - - +
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Residues in contact with VAL 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ALA* 4.7 2.9 - - + -
118E TYR* 3.4 33.4 - - + +
120E PRO* 5.1 1.3 - - + -
163E ARG* 4.3 13.2 - - + -
164E ASN* 3.0 31.3 + - + +
166E SER* 1.3 75.5 - - - +
168E ASN* 1.3 60.8 + - - +
171E GLY* 2.7 30.0 + - - +
172E ARG* 3.4 48.5 - - + +
182E VAL* 4.3 10.0 - - + +
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Residues in contact with ASN 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E ARG* 3.3 34.2 + - - +
164E ASN 2.5 38.8 + - - +
165E VAL* 3.6 11.7 - - + +
167E VAL* 1.3 73.0 - - - +
169E LEU* 1.3 61.0 + - - +
171E GLY 4.6 0.2 + - - -
182E VAL* 5.1 2.0 - - - -
183E ASP 4.7 0.3 - - - +
185E ALA* 4.0 3.6 + - - +
242E LEU* 3.3 16.2 - - + +
245E ASN* 3.4 37.3 + - + +
246E THR* 3.6 30.4 - - + +
255E ALA* 6.2 0.9 - - + -
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Residues in contact with LEU 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 4.9 9.2 - - + -
165E VAL* 2.8 26.4 + - + +
166E SER* 4.0 1.8 - - - +
168E ASN* 1.3 79.8 - - + +
170E PHE* 1.3 73.6 + - + +
185E ALA* 3.0 20.5 + - - -
186E VAL* 3.2 36.7 + - + +
237E VAL* 5.1 1.6 - - + -
242E LEU* 3.7 31.6 - - + -
255E ALA* 4.5 14.6 - - + +
256E VAL* 5.3 0.7 - - + -
259E PHE* 3.5 40.2 - - + -
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Residues in contact with PHE 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LYS* 3.4 48.8 + - + +
47E VAL* 4.1 11.7 - - + -
48E ARG* 3.7 32.1 - - + -
51E VAL* 5.9 1.3 - - + -
61E ARG* 6.1 1.1 - - - +
118E TYR* 4.8 5.2 - - + +
166E SER* 2.9 22.7 + - - +
169E LEU* 1.3 94.0 - - + +
171E GLY* 1.3 66.3 + - - +
184E GLY* 3.4 13.2 + - - -
186E VAL* 4.0 28.0 - - + +
188E PHE* 5.7 1.1 - - + -
259E PHE* 4.0 20.9 - + - -
273F ASN* 5.8 2.3 - - - +
30K U 5.0 5.4 + - - +
31K G 4.0 14.0 + - - +
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Residues in contact with GLY 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ARG* 4.6 3.8 + - - -
118E TYR* 3.8 14.4 - - - -
166E SER 3.9 0.2 + - - -
167E VAL* 2.7 29.3 + - - -
170E PHE* 1.3 79.1 - - - +
172E ARG* 1.3 60.9 + - - +
182E VAL* 3.2 15.7 - - - -
183E ASP 4.1 1.1 - - - -
184E GLY* 3.6 11.4 - - - -
30K U 5.4 4.1 - - - +
31K G 4.7 5.4 + - - -
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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