Contacts of the helix formed by residues 164 - 171 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52I GLU* 5.7 0.2 - - - +
57I ASP* 2.8 47.6 + - - +
58I LYS 3.1 2.4 + - - -
59I ALA* 3.0 36.1 - - + +
120I PRO* 3.8 16.7 - - + +
163I ARG* 1.3 74.0 - - - +
165I VAL* 1.3 84.9 + - - +
166I SER* 3.2 10.8 + - - +
167I VAL* 3.1 20.3 + - + +
168I ASN* 2.6 39.0 + - - -
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Residues in contact with VAL 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I VAL* 4.1 13.5 - - + -
55I LEU* 3.7 23.6 - - + -
57I ASP* 4.2 9.1 + - + +
164I ASN* 1.3 88.5 + - - +
166I SER* 1.3 56.2 + - - +
168I ASN* 3.1 11.5 + - + +
169I LEU* 2.9 32.7 + - + +
246I THR* 6.0 2.5 - - + -
255I ALA* 4.1 21.1 - - + -
258I GLU* 3.6 20.9 - - + +
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Residues in contact with SER 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I ARG* 3.0 35.5 + - - +
51I VAL* 5.2 5.9 - - - +
52I GLU* 5.4 5.6 - - - -
59I ALA* 4.3 13.9 - - - -
118I TYR* 2.2 30.4 + - - -
164I ASN* 3.1 5.8 + - - -
165I VAL* 1.3 81.2 - - - +
167I VAL* 1.3 56.7 + - - +
169I LEU* 4.5 2.5 - - - -
170I PHE* 2.9 36.2 + - - +
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Residues in contact with VAL 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ALA* 4.8 2.9 - - + -
118I TYR* 3.3 33.0 - - + +
120I PRO* 5.1 2.5 - - + -
163I ARG* 4.3 5.2 - - + -
164I ASN* 3.1 30.6 + - + +
166I SER* 1.3 74.1 - - - +
168I ASN* 1.3 61.5 + - - +
171I GLY* 2.8 27.4 + - - +
172I ARG* 3.4 45.3 - - + +
182I VAL* 4.0 21.0 - - + +
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Residues in contact with ASN 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I ARG* 3.3 32.4 + - - +
164I ASN 2.6 32.3 + - - -
165I VAL* 3.1 11.6 + - + +
167I VAL* 1.3 77.0 - - - +
169I LEU* 1.3 61.3 + - - +
182I VAL* 4.8 2.0 - - - -
183I ASP 4.5 0.5 - - - +
185I ALA* 4.0 4.7 + - - +
242I LEU* 3.4 17.5 - - + +
245I ASN* 3.3 38.9 + - + +
246I THR* 3.4 31.9 - - + +
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Residues in contact with LEU 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I VAL* 4.7 15.3 - - + -
165I VAL* 2.9 20.5 + - + +
166I SER* 3.9 2.9 - - - +
168I ASN* 1.3 80.2 - - - +
170I PHE* 1.3 76.6 + - + +
185I ALA 3.2 19.3 + - - -
186I VAL* 3.3 37.8 + - + +
237I VAL* 5.2 1.1 - - + -
242I LEU* 3.6 30.7 - - + -
255I ALA* 4.5 12.8 - - + +
256I VAL* 5.4 0.4 - - - -
259I PHE* 3.6 40.4 - - + -
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Residues in contact with PHE 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E ASN* 5.7 2.1 - - - +
44I LYS* 3.4 51.5 + - + +
47I VAL* 4.0 12.8 - - + -
48I ARG* 3.6 28.9 - - + -
51I VAL* 5.6 0.4 - - + -
61I ARG* 6.1 1.1 - - - +
118I TYR* 5.0 2.9 - - - +
166I SER* 2.9 29.2 + - - +
169I LEU* 1.3 96.3 - - + +
171I GLY* 1.3 67.2 + - - +
184I GLY* 3.7 10.4 - - - -
186I VAL* 4.1 18.2 - - + +
188I PHE* 5.7 2.5 - + + -
259I PHE* 3.8 30.1 - + - -
36K C 4.6 7.6 + - - +
37K U 4.6 9.5 + - - +
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Residues in contact with GLY 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I ARG* 4.3 5.5 + - - -
118I TYR* 3.9 13.9 - - - -
166I SER 4.0 0.2 + - - -
167I VAL 2.8 26.4 + - - -
169I LEU 3.7 0.6 - - - -
170I PHE* 1.3 79.8 - - - +
172I ARG* 1.3 62.8 + - - +
182I VAL* 3.3 17.3 - - - -
184I GLY* 3.8 10.2 - - - -
36K C 5.2 6.1 - - - +
37K U 5.0 4.0 + - - -
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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