Contacts of the helix formed by residues 131 - 137 (chain C) in PDB entry 5IWM
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 ILE 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C TYR* 4.2 23.1 - - + +
102C PRO 3.6 13.2 - - - +
103C LEU* 4.1 13.7 - - + -
129C THR* 3.2 14.8 + - - +
130C LYS* 1.3 74.8 - - - +
132C THR* 1.3 62.9 + - - +
133C LEU 3.0 2.2 - - - -
134C GLU* 2.8 29.0 + - + +
164C PHE* 3.6 29.8 - - + -
188C LEU* 4.0 16.4 - - + -
480C PHE* 3.5 48.4 - - + -
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Residues in contact with THR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 4.0 28.0 - - + -
103C LEU* 2.7 44.5 + - - +
128C MET* 4.1 11.9 - - + -
129C THR* 3.4 12.1 + - - -
130C LYS 3.4 0.8 - - - -
131C ILE* 1.3 79.4 - - - +
133C LEU* 1.3 56.8 + - - +
135C LEU* 3.0 27.5 + - + +
136C LEU* 3.2 29.5 + - + +
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Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ASN* 6.0 1.3 - - - +
59C THR* 4.2 17.7 - - + -
60C PRO* 3.5 33.4 - - + -
61C ASP* 6.0 0.4 - - - +
128C MET* 4.1 18.8 - - + -
129C THR 3.8 1.9 + - - +
130C LYS* 3.3 18.8 + - + +
131C ILE 3.0 0.2 - - - -
132C THR* 1.3 77.8 - - - +
134C GLU* 1.3 63.7 + - - +
136C LEU* 3.6 6.0 - - + +
137C ARG* 2.9 30.1 + - - +
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LYS 4.6 0.4 - - - +
131C ILE 2.8 13.2 + - - +
133C LEU* 1.3 83.4 - - - +
135C LEU* 1.3 60.4 + - - +
137C ARG* 2.9 43.4 + - - +
163C ARG* 2.9 33.7 + - + +
164C PHE* 3.9 16.6 - - + -
476C ILE* 3.7 18.2 - - + +
479C ARG* 3.5 25.8 + - - -
480C PHE* 3.7 26.4 - - + -
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ASP* 4.6 4.0 - - + +
42C LEU* 5.1 2.0 - - + -
50C LEU* 4.0 21.5 - - + -
103C LEU* 3.7 32.5 - - + -
131C ILE 3.7 0.2 + - - -
132C THR* 3.0 14.5 + - + +
134C GLU* 1.3 78.6 - - - +
136C LEU* 1.3 60.1 + - + +
160C LEU* 3.6 20.0 - - + +
161C PRO* 3.2 13.3 - - - +
162C ALA* 3.0 47.1 + - + +
164C PHE* 3.6 22.0 - - + -
166C ASN* 3.9 22.9 - - + +
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 3.7 16.4 - - + +
51C TYR* 4.5 5.6 - - - -
54C ASN* 3.7 43.3 - - + +
128C MET* 3.7 18.4 - - + -
132C THR* 3.2 28.6 + - + +
133C LEU* 3.6 6.3 - - + +
134C GLU 3.3 0.2 - - - -
135C LEU* 1.3 80.6 - - - +
137C ARG* 1.3 61.9 + - - +
138C ASP 3.1 3.5 + - - -
139C ILE* 3.1 37.8 + - + +
160C LEU* 3.9 24.9 - - + -
161C PRO* 4.2 3.8 - - - -
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Residues in contact with ARG 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C LEU 2.9 15.6 + - - +
134C GLU* 2.9 43.3 + - - +
135C LEU 3.5 2.0 - - - -
136C LEU* 1.3 74.2 - - - +
138C ASP* 1.3 94.9 + - - +
161C PRO* 3.4 17.7 - - - +
163C ARG* 3.9 18.9 - - + +
362C VAL* 5.4 0.9 - - - +
366C ARG* 4.5 3.2 - - - +
472C GLU* 3.8 30.1 + - - +
475C GLU* 4.0 10.3 + - - -
476C ILE* 3.9 19.1 - - - +
479C ARG* 4.4 2.0 - - - +
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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