Contacts of the helix formed by residues 82 - 96 (chain k) in PDB entry 5OOM
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 THR 82 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3183A U 5.2 14.2 - - + -
177K ARG* 6.2 0.7 - - - +
29k SER* 3.8 9.4 + - - -
81k LEU* 1.3 76.0 - - - +
83k ALA* 1.3 64.2 + - - +
84k LEU* 3.8 10.5 + - + +
85k GLU* 3.5 25.8 - - + +
86k MET* 3.0 29.8 + - - +
36r ARG* 3.5 25.8 - - - +
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Residues in contact with ALA 83 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29k SER* 4.0 26.9 - - - +
32k THR* 4.5 19.3 - - + -
33k PHE* 4.7 7.6 - - + +
82k THR* 1.3 79.2 + - - +
84k LEU* 1.3 61.7 + - + +
86k MET* 3.8 5.9 - - - +
87k LEU* 2.9 34.3 + - + +
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Residues in contact with LEU 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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3183A U 4.6 30.7 - - + +
3184A C 4.2 33.2 - - + +
82k THR* 3.3 9.2 + - + +
83k ALA* 1.3 79.1 - - + +
85k GLU* 1.3 54.6 + - - +
87k LEU* 4.4 11.0 - - + -
88k THR* 2.5 45.1 + - + +
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Residues in contact with GLU 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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177K ARG* 5.0 11.4 - - - +
81k LEU* 3.3 28.1 - - + +
82k THR* 3.5 22.4 - - + +
84k LEU* 1.3 77.5 - - - +
86k MET* 1.3 59.1 + - - +
88k THR* 3.7 4.4 + - - +
89k ALA* 2.8 46.8 + - - +
36r ARG* 5.5 0.7 - - - +
38r VAL* 3.4 38.4 - - + +
49r ILE* 4.1 5.7 - - - +
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Residues in contact with MET 86 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29k SER* 4.8 3.1 - - - +
30k THR* 4.3 19.1 - - - +
33k PHE* 3.9 37.0 - - + -
64k VAL* 4.4 13.0 - - + -
76k MET* 3.7 28.3 - - + +
78k GLY* 3.7 35.9 - - - +
81k LEU* 4.1 15.0 - - + -
82k THR 3.0 17.1 + - - +
83k ALA* 3.9 4.0 - - - +
85k GLU* 1.3 82.0 + - - +
87k LEU* 1.3 56.9 + - - +
89k ALA* 4.2 2.8 - - - +
90k PHE* 2.9 29.5 + - - +
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Residues in contact with LEU 87 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33k PHE* 4.1 13.4 - - + -
36k THR* 4.3 11.4 - - + -
37k VAL* 3.7 41.3 - - + -
83k ALA* 2.9 22.2 + - + +
84k LEU* 4.1 11.7 - - + +
86k MET* 1.3 75.5 - - - +
88k THR* 1.3 70.1 + - + +
90k PHE* 3.3 5.4 + - + +
91k ALA* 2.9 33.2 + - + +
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Residues in contact with THR 88 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3184A C 4.2 36.1 - - - +
3185A A 5.7 0.4 - - - +
84k LEU* 2.5 31.0 + - + +
85k GLU* 3.7 6.2 + - - +
87k LEU* 1.3 83.0 - - + +
89k ALA* 1.3 61.5 + - - +
91k ALA* 3.7 5.6 - - - +
92k SER* 2.7 31.8 + - - -
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Residues in contact with ALA 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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74k LEU* 5.5 0.4 - - - -
76k MET* 5.1 1.8 - - - -
85k GLU* 2.8 37.2 + - - +
86k MET* 4.2 3.4 - - - +
88k THR* 1.3 75.8 + - - +
90k PHE* 1.3 64.1 + - - +
92k SER* 3.1 7.9 + - - -
93k HIS* 3.0 32.8 + - + +
49r ILE* 4.3 19.7 - - + -
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Residues in contact with PHE 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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13k VAL* 4.1 14.4 - - + -
16k VAL* 5.3 11.4 - - + -
33k PHE* 4.2 28.3 - + + -
37k VAL* 6.2 2.0 - - + -
64k VAL* 6.0 0.2 - - + -
66k VAL* 3.7 39.0 - - + -
68k PHE* 5.9 0.4 - + - -
74k LEU* 4.7 10.8 - - + -
76k MET* 4.6 8.6 - - + -
86k MET 2.9 22.2 + - - +
87k LEU* 3.3 8.9 + - + +
89k ALA* 1.3 75.9 - - - +
91k ALA* 1.3 59.9 + - + +
93k HIS* 3.0 6.9 + - - +
94k ILE* 2.9 53.5 + - + +
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Residues in contact with ALA 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 LEU* 2.9 21.8 + - + +
88k THR* 4.1 6.3 - - - +
90k PHE* 1.3 75.4 - - + +
92k SER* 1.3 61.1 + - - +
93k HIS 3.2 0.2 - - - -
94k ILE* 3.5 15.2 - - + +
95k ARG* 3.0 35.3 + - + +
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Residues in contact with SER 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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88k THR* 2.7 24.1 + - - -
89k ALA* 3.1 11.0 + - - -
91k ALA* 1.3 76.9 - - - +
93k HIS* 1.3 64.9 + - - +
95k ARG* 4.1 4.8 - - - +
96k ALA* 3.0 21.8 + - - -
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Residues in contact with HIS 93 (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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68k PHE* 3.2 38.5 - + + -
74k LEU* 3.6 31.2 - - + +
89k ALA* 3.0 29.9 + - - +
90k PHE 3.0 6.0 + - - +
92k SER* 1.3 79.4 + - - +
94k ILE* 1.3 61.7 + - - +
95k ARG 3.4 0.2 - - - -
96k ALA* 3.5 18.3 - - - +
40r GLU* 5.7 2.3 + - - -
47r THR* 4.3 21.2 - - + +
49r ILE* 4.4 10.7 - - + +
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Residues in contact with ILE 94 (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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13k VAL* 3.7 36.1 - - + +
46k ASN* 5.8 3.8 - - - +
68k PHE* 4.3 13.2 - - + -
90k PHE* 2.9 45.7 + - + +
91k ALA* 3.2 16.7 + - + +
93k HIS* 1.3 76.5 - - - +
95k ARG* 1.3 83.3 + - - +
96k ALA* 4.2 2.8 - - - +
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Residues in contact with ARG 95 (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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91k ALA* 3.0 22.8 + - + +
92k SER* 4.1 5.2 - - - +
94k ILE* 1.3 103.8 + - - +
96k ALA* 1.3 68.0 + - - +
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Residues in contact with ALA 96 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68k PHE* 5.8 0.9 - - + -
72k HIS* 5.8 7.9 - - + +
92k SER 3.0 18.6 + - - -
93k HIS* 3.5 20.2 - - - +
94k ILE 3.4 3.1 - - - +
95k ARG* 1.3 82.2 - - - +
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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