Contacts of the helix formed by residues 81 - 92 (chain K) in PDB entry 5A15
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 LEU 81 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78K ASP* 3.0 23.2 + - + +
79K GLY 3.3 0.2 - - - -
80K PHE* 1.3 73.5 - - - +
82K PHE* 1.3 63.9 + - - +
83K ARG 3.1 3.6 + - - -
84K TYR* 3.3 17.8 + - + -
85K ILE* 3.5 8.9 + - - +
100K PHE* 4.0 22.9 - - + -
102K GLU* 3.4 24.7 - - + +
105K ARG* 3.6 43.7 - - + +
106K LEU* 3.8 17.5 - - + +
109K GLU* 3.8 29.6 - - + +
83L ARG* 3.8 4.0 - - - +
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Residues in contact with PHE 82 (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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29K LEU* 3.9 30.1 - - + -
31K VAL* 3.7 36.3 - - + -
36K TYR* 3.7 16.6 - + + -
51K LEU* 4.4 17.5 - - + -
75K ILE* 5.2 2.9 - - + -
77K ARG* 6.0 0.2 - - + -
78K ASP 3.5 4.3 + - - +
79K GLY 3.5 12.5 + - - +
80K PHE 3.3 1.0 - - - -
81K LEU* 1.3 76.2 - - - +
83K ARG* 1.3 58.8 - - - +
84K TYR 3.2 0.2 - - - -
85K ILE* 3.6 15.9 - - + +
86K LEU* 2.8 54.5 + - + +
113K PHE* 3.6 42.4 - + - -
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Residues in contact with ARG 83 (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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36K TYR* 3.5 31.5 + - + +
80K PHE 3.6 10.5 - - - +
81K LEU 3.1 0.2 - - - -
82K PHE* 1.3 78.7 - - - +
84K TYR* 1.3 96.8 + - + +
86K LEU* 3.9 3.9 - - - +
87K ASP* 2.9 46.7 + - - +
95K VAL 5.5 2.2 + - - -
97K PRO* 5.4 2.4 - - - +
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Residues in contact with TYR 84 (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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80K PHE 4.1 14.8 - - - -
81K LEU* 3.3 18.2 + - + -
82K PHE 3.2 0.4 - - - -
83K ARG* 1.3 109.8 + - + +
85K ILE* 1.3 64.6 + - - +
86K LEU 3.3 0.2 - - - -
87K ASP* 3.9 7.4 - - + +
88K TYR* 3.3 15.6 + - - +
94K VAL* 3.3 19.4 - - + +
95K VAL 4.8 9.6 - - - -
96K LEU* 4.9 7.2 - - + -
97K PRO* 3.5 35.1 - - + +
100K PHE* 3.6 34.8 - + - -
106K LEU* 3.8 26.2 - - + -
118K LEU* 5.0 0.9 - - - +
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Residues in contact with ILE 85 (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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51K LEU* 4.9 1.3 - - + -
81K LEU 3.5 12.2 + - - +
82K PHE* 3.2 21.4 + - + +
84K TYR* 1.3 77.8 - - - +
86K LEU* 1.3 62.5 + - - +
88K TYR* 3.3 15.2 + - - +
89K LEU* 3.3 21.1 + - + +
106K LEU* 4.0 12.1 - - + -
109K GLU* 4.2 4.9 - - + -
110K ALA* 3.9 24.9 - - - +
113K PHE* 3.9 33.4 - - + -
115K LEU* 4.2 14.1 - - + -
118K LEU* 3.6 24.9 - - + -
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Residues in contact with LEU 86 (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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36K TYR* 4.3 21.8 - - + -
37K PHE 4.2 9.4 - - - +
38K THR* 3.5 42.4 - - + +
42K THR* 4.4 5.1 - - + +
43K LEU* 4.6 2.9 - - + -
82K PHE* 2.8 39.4 + - + +
83K ARG* 3.9 5.4 - - - +
85K ILE* 1.3 76.9 - - - +
87K ASP* 1.3 64.2 + - - +
89K LEU* 3.3 22.8 + - + +
90K ARG* 3.3 20.1 + - - +
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Residues in contact with ASP 87 (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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83K ARG* 2.9 48.0 + - - +
84K TYR* 4.0 9.7 - - + +
86K LEU* 1.3 76.4 - - - +
88K TYR* 1.3 59.8 + - - +
90K ARG* 3.3 8.4 + - - +
91K ASP* 2.9 38.0 + - - +
93K GLN 3.7 4.1 - - - +
94K VAL* 4.9 5.6 - - + -
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Residues in contact with TYR 88 (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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46K ILE* 3.4 29.8 - - + +
84K TYR 3.3 12.6 + - - +
85K ILE 3.4 8.7 - - - +
86K LEU 3.2 0.4 - - - -
87K ASP* 1.3 77.2 - - - +
89K LEU* 1.3 61.4 + - - +
92K ARG* 2.5 53.1 + - - +
93K GLN* 3.7 21.8 - - - -
94K VAL* 3.6 6.7 - - + +
115K LEU* 3.7 30.2 - - + +
117K ASP* 3.3 28.4 + - - +
118K LEU* 3.7 38.3 + - + -
121K LEU* 4.5 9.0 - - + -
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Residues in contact with LEU 89 (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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42K THR* 3.5 34.1 - - + +
43K LEU* 4.5 8.5 - - + +
45K SER* 4.0 17.0 + - - -
46K ILE* 3.7 32.9 - - + +
49K SER* 5.6 2.0 - - - +
51K LEU* 3.4 33.2 - - + -
82K PHE* 5.5 0.2 - - + -
85K ILE* 3.3 16.7 + - + +
86K LEU* 3.3 21.5 + - + +
88K TYR* 1.3 78.5 - - - +
90K ARG* 1.3 61.6 + - - +
92K ARG* 4.5 7.3 + - - +
115K LEU* 4.2 20.4 - - + -
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Residues in contact with ARG 90 (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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42K THR* 3.9 12.5 - - + +
86K LEU 3.3 9.8 + - - +
87K ASP* 3.6 12.3 - - - +
88K TYR 3.1 0.4 - - - -
89K LEU* 1.3 82.6 - - - +
91K ASP* 1.3 72.5 + - - +
92K ARG* 3.6 11.0 + - - -
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Residues in contact with ASP 91 (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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87K ASP* 2.9 21.5 + - - +
90K ARG* 1.3 86.9 - - - +
92K ARG* 1.3 74.5 + - - +
93K GLN* 3.1 35.5 + - + +
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Residues in contact with ARG 92 (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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45K SER* 3.0 32.2 + - - -
46K ILE* 5.5 11.7 - - + +
88K TYR* 2.5 46.0 + - + +
89K LEU* 4.6 5.3 + - - +
90K ARG 4.2 12.1 + - - -
91K ASP* 1.3 75.4 - - - +
93K GLN* 1.3 58.7 + - - +
121K LEU* 5.0 4.2 - - - +
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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