Contacts of the helix formed by residues 39 - 44 (chain P) in PDB entry 2X86
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 PHE 39 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P LEU* 4.4 9.9 - - + +
36P GLY 3.0 24.1 + - - +
37P THR 4.0 2.5 - - - -
38P LYS* 1.3 78.7 - - - +
40P VAL* 1.3 89.7 + - + +
42P LEU* 2.8 20.0 + - - +
43P VAL* 3.0 25.4 + - + -
84T TRP* 3.7 13.0 - + - -
136T PRO 3.5 19.5 - - - -
137T LEU* 3.4 9.0 - - - -
138T ASN* 3.4 36.3 - - - -
139T VAL* 3.9 15.3 - - + -
142T TYR* 3.8 39.0 - + + -
271T ARG* 4.0 3.4 - - - -
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Residues in contact with VAL 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P THR 3.2 16.2 - - - +
38P LYS* 3.1 1.4 - - - -
39P PHE* 1.3 108.1 - - + +
41P ASN* 1.3 79.1 + - - +
42P LEU 3.1 1.6 + - - -
43P VAL* 3.2 25.0 + - + +
44P ASP* 4.1 4.5 - - - +
174P ARG* 4.5 1.0 + - - -
177P HIS* 6.3 1.6 - - + -
271T ARG* 4.3 11.7 - - - +
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Residues in contact with ASN 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P ALA 2.9 27.8 + - - +
9P GLY 4.2 0.4 + - - -
13P SER* 3.6 17.1 - - - +
38P LYS* 3.0 13.6 + - - +
39P PHE 2.9 1.4 + - - -
40P VAL* 1.3 88.4 - - - +
42P LEU* 1.3 58.0 + - - +
45P LEU* 3.4 9.2 - - - +
174P ARG* 2.8 58.5 + - + +
176P GLY 5.3 0.9 + - - -
177P HIS* 3.1 32.6 + - - +
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Residues in contact with LEU 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P GLY 3.4 22.4 - - - +
8P ALA* 3.8 25.6 - - + -
16P VAL* 4.7 2.2 - - + -
29P VAL* 4.1 26.9 - - + -
33P LEU* 5.3 3.4 - - + -
38P LYS 5.3 0.9 - - - +
39P PHE* 2.8 10.3 + - - +
41P ASN* 1.3 84.1 - - - +
43P VAL* 1.3 54.7 + - - +
44P ASP 3.2 2.9 - - - -
45P LEU* 2.8 45.5 + - + +
47P ILE* 4.4 15.6 - - + +
50P TYR* 4.7 7.2 - - + -
142T TYR* 3.5 35.5 + - + +
145T PHE* 5.7 0.3 - - - -
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Residues in contact with VAL 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P PHE* 3.0 21.9 + - + +
40P VAL* 3.2 22.1 + - + +
42P LEU* 1.3 76.2 - - - +
44P ASP* 1.3 67.3 + - + +
45P LEU 4.2 0.2 - - - +
131T ARG* 3.3 19.9 + - - -
134T GLU 4.9 2.3 - - - +
135T LYS* 4.0 20.7 - - + +
136T PRO* 3.5 50.0 - - + +
142T TYR* 4.2 9.6 - - + -
145T PHE* 4.6 6.1 - - + -
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Residues in contact with ASP 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P ASN* 5.0 0.2 - - - +
40P VAL 4.1 5.1 - - - +
41P ASN 4.2 0.3 - - - +
43P VAL* 1.3 77.0 - - + +
45P LEU* 1.3 66.8 + - - +
46P ASN* 5.1 2.8 + - - -
174P ARG* 3.0 43.3 + - - -
131T ARG* 3.8 7.3 + - - +
135T LYS* 4.4 23.3 - - - +
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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