Contacts of the helix formed by residues 39 - 44 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K LEU* 4.4 10.3 - - + +
36K GLY 3.0 23.7 + - - +
37K THR 4.0 2.9 - - - -
38K LYS* 1.3 78.1 - - - +
40K VAL* 1.3 89.7 + - + +
42K LEU* 2.8 19.6 + - - +
43K VAL* 3.0 25.8 + - + -
84O TRP* 3.8 10.3 - + - -
136O PRO 3.4 20.2 - - - -
137O LEU* 3.4 26.7 - - - -
138O ASN* 3.4 17.7 - - - -
139O VAL* 3.9 15.7 - - + -
142O TYR* 3.9 38.3 - + + -
271O ARG* 4.0 4.7 - - - -
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Residues in contact with VAL 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K THR 3.2 16.4 - - - +
38K LYS* 3.1 1.2 - - - -
39K PHE* 1.3 107.2 - - + +
41K ASN* 1.3 79.5 + - - +
42K LEU 3.1 1.7 + - - -
43K VAL* 3.2 25.4 + - + +
44K ASP* 4.1 4.5 - - - +
174K ARG* 4.5 1.0 + - - -
177K HIS* 6.3 1.3 - - + -
271O ARG* 4.3 11.7 - - - +
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Residues in contact with ASN 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K ALA 2.9 27.2 + - - +
9K GLY 4.2 0.4 + - - -
13K SER* 3.6 16.8 - - - +
38K LYS* 3.0 13.8 + - - +
39K PHE 2.9 1.4 + - - -
40K VAL* 1.3 87.5 - - - +
42K LEU* 1.3 57.4 + - - +
45K LEU* 3.4 9.9 - - - +
174K ARG* 2.8 57.5 + - + +
176K GLY 5.3 1.0 + - - -
177K HIS* 3.1 32.6 + - - +
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Residues in contact with LEU 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K GLY 3.4 23.3 - - - +
8K ALA* 3.8 25.1 - - + -
16K VAL* 4.7 2.5 - - + -
29K VAL* 4.1 26.9 - - + -
33K LEU* 5.3 3.1 - - + -
38K LYS 5.4 0.9 - - - +
39K PHE* 2.8 10.7 + - - +
41K ASN* 1.3 84.4 - - - +
43K VAL* 1.3 55.1 + - - +
44K ASP 3.2 2.9 - - - -
45K LEU* 2.8 45.3 + - + +
47K ILE* 4.4 15.2 - - + +
50K TYR* 4.7 7.4 - - + -
142O TYR* 3.5 35.6 + - + +
145O PHE* 5.7 0.5 - - - -
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Residues in contact with VAL 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K PHE* 3.0 20.3 + - + +
40K VAL* 3.2 23.1 + - + +
42K LEU* 1.3 77.1 - - - +
44K ASP* 1.3 67.4 + - + +
45K LEU 4.2 0.2 - - - +
131O ARG* 3.2 20.3 + - - -
134O GLU 4.9 2.8 - - - +
135O LYS* 3.9 20.8 - - + +
136O PRO* 3.5 50.2 - - + +
142O TYR* 4.3 10.1 - - + -
145O PHE* 4.6 5.2 - - - -
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Residues in contact with ASP 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K VAL 4.1 5.3 - - - +
41K ASN 4.2 0.3 - - - +
43K VAL* 1.3 80.4 - - + +
45K LEU* 1.3 67.3 + - - +
46K ASN* 5.1 2.8 + - - -
174K ARG* 3.0 43.0 + - - -
131O ARG* 3.8 7.1 + - - +
135O LYS* 4.7 15.9 - - + +
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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