Contacts of the helix formed by residues 85 - 99 (chain p) in PDB entry 5M32
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 85 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54p LEU* 2.4 44.4 + - - +
55p ALA 3.6 15.7 + - - +
56p ASN* 5.4 2.5 - - - -
84p ILE* 1.3 68.1 - - - -
86p PHE* 1.3 65.0 + - - +
87p CYS 5.1 0.4 - - - -
88p THR* 4.5 15.3 - - - -
89p GLY 3.8 5.7 + - - -
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Residues in contact with PHE 86 (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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54p LEU* 4.6 8.4 - - - +
84p ILE* 4.3 0.8 - - - +
85p THR* 1.3 71.3 - - - +
87p CYS* 1.3 63.4 + - + +
89p GLY* 3.1 6.2 + - - -
90p ILE* 3.0 24.9 + - - +
117p VAL* 4.7 20.2 - - + +
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Residues in contact with CYS 87 (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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85p THR* 3.7 0.6 - - - -
86p PHE* 1.3 78.6 - - + +
88p THR* 1.3 58.3 + - - +
90p ILE* 3.3 11.8 + - - +
91p ARG* 3.0 24.6 + - - +
127p LEU* 5.3 13.9 - - + -
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Residues in contact with THR 88 (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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66n SER* 5.1 10.5 - - - -
67n VAL* 5.0 3.3 - - - +
55p ALA 5.2 3.8 - - - -
56p ASN 5.6 3.4 - - - -
58p CYS* 6.2 4.7 - - - -
85p THR* 4.3 18.2 + - - -
86p PHE 3.3 0.6 - - - -
87p CYS* 1.3 79.6 - - - +
89p GLY* 1.3 56.6 + - - +
91p ARG* 3.0 11.5 + - - +
92p VAL* 2.9 23.4 + - - +
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Residues in contact with GLY 89 (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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52p ILE* 5.7 1.4 - - - +
53p THR 3.9 20.5 - - - +
54p LEU* 4.8 2.5 - - - -
55p ALA 5.7 0.8 + - - -
58p CYS* 6.3 1.3 - - - -
85p THR 3.8 7.5 + - - -
86p PHE 3.1 8.8 + - - -
88p THR* 1.3 74.5 - - - +
90p ILE* 1.3 60.8 + - - +
92p VAL* 3.0 9.7 + - - +
93p ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 90 (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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86p PHE 3.0 12.7 + - - +
87p CYS* 3.3 14.6 - - - +
88p THR 3.2 0.2 - - - -
89p GLY* 1.3 75.9 - - - +
91p ARG* 1.3 57.5 + - - +
93p ALA* 3.9 3.8 - - - +
94p HIS* 2.9 30.0 + - - +
109p ILE* 6.0 4.0 - - - -
127p LEU* 6.5 0.7 - - + -
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Residues in contact with ARG 91 (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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60n GLU 5.4 7.0 - - - +
67n VAL* 4.4 17.5 - - + +
87p CYS 3.0 13.5 + - - +
88p THR* 3.0 14.1 + - - +
90p ILE* 1.3 75.0 - - - +
92p VAL* 1.3 57.3 + - - +
94p HIS* 3.4 8.0 - - - +
95p LEU* 3.0 28.8 + - - +
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Residues in contact with VAL 92 (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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67n VAL* 5.0 6.9 - - + +
68n TRP 5.9 5.2 - - - +
52p ILE* 4.9 14.8 - - + -
53p THR 5.4 0.9 - - - +
58p CYS* 5.0 15.7 - - + -
59p GLU 6.0 0.7 - - - +
60p VAL* 6.2 4.0 - - + -
88p THR 2.9 11.8 + - - +
89p GLY* 3.0 14.1 + - - +
91p ARG* 1.3 77.4 - - - +
93p ALA* 1.3 59.4 + - - +
95p LEU* 3.3 3.9 + - - +
96p ALA* 2.9 32.4 + - - +
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Residues in contact with ALA 93 (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 MET* 3.9 29.6 - - + +
52p ILE* 5.6 4.1 - - + +
89p GLY 3.0 14.4 + - - +
90p ILE* 4.4 3.1 - - - +
92p VAL* 1.3 73.4 - - - +
94p HIS* 1.3 60.4 + - - +
96p ALA* 4.5 3.1 - - - +
97p LEU* 2.9 36.8 + - + +
108p ARG 5.5 0.7 - - - +
109p ILE* 4.7 19.7 - - + -
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Residues in contact with HIS 94 (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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90p ILE 2.9 22.2 + - - +
91p ARG* 3.4 11.0 - - - +
92p VAL 3.2 0.2 - - - -
93p ALA* 1.3 76.7 - - - +
95p LEU* 1.3 49.8 + - - +
98p LYS* 2.5 39.7 + - - +
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Residues in contact with LEU 95 (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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59n ASP* 4.9 12.6 - - + +
67n VAL* 6.1 2.9 - - + -
68n TRP 4.7 14.1 - - - +
91p ARG 3.0 16.4 + - - +
92p VAL* 3.9 3.6 - - - +
94p HIS* 1.3 75.3 - - - +
96p ALA* 1.3 62.0 + - + +
98p LYS* 2.8 19.8 + - - +
99p HIS* 3.1 18.5 + - - +
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Residues in contact with ALA 96 (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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60p VAL* 6.1 4.7 - - + -
63p THR* 6.0 8.3 - - - -
64p LEU* 5.6 8.1 + - - +
92p VAL 2.9 17.9 + - - +
93p ALA* 4.8 2.5 - - - +
95p LEU* 1.3 76.5 - - - +
97p LEU* 1.3 57.9 + - - +
99p HIS* 4.6 4.6 + - - -
100p ARG* 4.8 6.9 + - - +
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Residues in contact with LEU 97 (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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6p THR* 5.9 3.8 - - - +
7p MET* 5.4 7.2 - - + -
93p ALA* 2.9 23.1 + - + +
96p ALA* 1.3 76.0 - - - +
98p LYS* 1.3 63.4 + - - +
99p HIS 3.4 0.7 - - - -
100p ARG* 3.5 18.6 - - - +
107p MET* 4.3 27.9 - - + +
108p ARG 5.5 4.3 - - - +
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Residues in contact with LYS 98 (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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94p HIS 2.5 25.0 + - - +
95p LEU* 2.8 8.4 + - - +
97p LEU* 1.3 79.2 - - - +
99p HIS* 1.3 56.1 + - + +
100p ARG* 3.3 4.8 + - - +
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Residues in contact with HIS 99 (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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57n PRO* 5.2 18.6 - - + +
95p LEU 3.1 13.1 + - - +
96p ALA* 4.9 4.0 - - - +
97p LEU 3.4 0.6 - - - -
98p LYS* 1.3 75.1 - - + +
100p ARG* 1.3 65.5 + - - +
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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