Contacts of the helix formed by residues 118 - 129 (chain C) in PDB entry 3OMA
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 GLY 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C GLY* 3.3 26.4 - - - +
33C TYR* 3.7 5.6 - - - -
34C LEU* 4.1 9.9 - - - -
113C PRO 2.8 9.1 + - - -
114C ALA 3.2 10.8 + - - -
116C PHE 3.3 0.4 - - - -
117C GLY* 1.3 76.5 - - - +
119C PHE* 1.3 61.5 + - - +
122C TYR* 3.2 25.3 + - - +
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Residues in contact with PHE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.5 30.5 - - + -
114C ALA 3.2 12.4 + - - -
115C LEU* 3.5 13.2 + - + +
118C GLY* 1.3 71.3 - - - +
120C GLY* 1.3 60.8 + - - +
121C ASN 3.4 0.2 - - - -
122C TYR* 5.4 0.2 - - + -
123C PHE* 3.0 35.8 + + - +
228C PHE* 3.3 23.8 - - + -
297C ILE* 3.9 16.8 - - + -
432C ILE* 3.8 24.2 - - + -
435C GLY* 3.6 7.9 - - - -
436C ILE* 3.5 34.3 - - + -
439C TRP* 3.5 28.9 - + + -
443C MET* 4.2 13.2 - - + -
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Residues in contact with GLY 120 (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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115C LEU 3.0 9.7 + - - -
116C PHE 3.1 13.7 + - - -
119C PHE* 1.3 77.4 - - - +
121C ASN* 1.3 60.0 + - - +
124C MET* 3.1 28.1 + - - +
125C PRO* 3.8 1.0 - - - +
133C MET* 3.9 2.9 - - - +
208C MET* 4.0 7.7 - - - +
228C PHE* 3.7 3.8 - - - -
232C ILE* 3.7 25.4 - - - -
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Residues in contact with ASN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C HIS* 3.0 37.5 + - - +
29C ILE* 3.5 11.7 - - - +
30C GLY* 3.8 4.7 - - - -
33C TYR* 3.6 10.1 - - - -
116C PHE 3.3 3.6 + - - -
117C GLY* 2.8 28.7 + - - +
118C GLY 3.5 1.2 + - - -
119C PHE 3.4 0.2 - - - -
120C GLY* 1.3 74.6 - - - +
122C TYR* 1.3 60.8 + - - +
125C PRO* 3.3 9.7 - - - +
133C MET* 3.2 20.4 - - + +
139C ASN* 3.4 30.8 + - - +
204C GLY* 6.1 1.5 - - - -
207C ASN* 6.0 0.5 - - - +
208C MET* 3.5 11.9 - - - +
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Residues in contact with TYR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C DMU 5.0 2.2 + - - -
26C HIS* 3.3 27.3 + - - -
27C LYS* 3.3 54.3 - - + +
30C GLY* 4.5 1.6 - - - -
31C VAL* 3.7 23.6 - - + -
34C LEU* 6.2 0.4 - - + -
118C GLY 3.2 16.4 + - - +
119C PHE* 4.6 0.9 - - + -
121C ASN* 1.3 79.1 - - - +
123C PHE* 1.3 92.5 + + + +
126C LEU* 3.3 15.6 - - + +
442C LYS* 5.1 0.7 - - + -
443C MET* 3.4 43.4 + - + -
545C PRO* 4.6 1.2 - - - +
546C PRO* 3.6 19.9 - - + +
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Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 3.0 20.8 + + - +
122C TYR* 1.3 109.6 - + + +
124C MET* 1.3 60.3 + - - +
125C PRO* 3.4 2.7 - - - -
126C LEU* 3.3 13.9 + - + +
127C HIS* 2.8 46.2 + - + -
228C PHE* 4.1 4.7 - - + -
439C TRP* 3.2 69.1 - + + -
442C LYS* 4.1 9.0 - - + -
443C MET* 4.0 14.8 - - + -
539C GLU* 3.8 26.0 - - + -
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Residues in contact with MET 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE 4.0 1.2 + - - -
120C GLY* 3.1 22.3 + - - +
123C PHE* 1.3 77.1 - - - +
125C PRO* 1.4 62.0 - - - +
127C HIS* 3.4 8.2 + - - +
128C ILE* 3.2 45.2 + - - +
133C MET* 3.9 17.5 - - + -
208C MET* 3.7 47.1 - - + +
211C THR* 4.1 7.2 - - + -
212C PHE* 4.4 15.3 - - + -
228C PHE* 4.2 3.2 - - + -
229C ALA* 4.0 23.6 - - + +
232C ILE* 4.1 18.2 - - + -
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Residues in contact with PRO 125 (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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26C HIS* 3.7 23.1 - - + +
120C GLY 3.8 1.3 - - - +
121C ASN 3.3 25.1 - - - +
122C TYR 4.0 2.0 - - - +
123C PHE 3.5 2.9 - - - -
124C MET* 1.4 93.7 - - + +
126C LEU* 1.3 59.7 + - - +
128C ILE* 3.3 10.7 + - + -
129C GLY 3.0 9.7 + - - -
130C ALA* 2.9 49.5 + - + +
132C ASP 4.7 4.5 - - - -
133C MET* 3.6 22.0 - - + -
211C THR* 5.0 0.4 - - + -
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Residues in contact with LEU 126 (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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26C HIS* 3.6 21.8 - - + +
27C LYS* 4.8 4.7 - - + -
122C TYR* 3.3 39.9 - - + +
123C PHE* 3.3 13.4 + - + +
125C PRO* 1.3 80.0 - - - +
127C HIS* 1.3 60.2 + - - +
129C GLY* 3.7 2.9 + - - +
130C ALA 4.9 2.2 - - - +
538C LEU* 3.1 30.5 - - - +
539C GLU* 3.9 30.7 - - + -
542C LEU* 3.8 25.7 - - + +
546C PRO* 4.4 7.6 - - + -
550C THR* 4.0 13.2 - - - +
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Residues in contact with HIS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C PHE* 2.8 24.3 + + + +
124C MET* 3.7 5.1 - - - +
125C PRO 3.2 0.4 - - - -
126C LEU* 1.3 78.3 - - - +
128C ILE* 1.3 58.6 + - - +
129C GLY 3.4 0.9 - - - -
220C MET* 3.4 18.9 - - - +
226C PRO* 3.4 28.0 - - + +
228C PHE* 3.7 29.0 - + + +
229C ALA* 4.2 9.2 + - + -
300C HIS* 3.3 28.0 - + - -
439C TRP* 3.9 11.5 - + - -
537C THR* 3.7 12.3 + - - -
538C LEU* 3.7 7.1 + - - +
539C GLU* 3.0 39.8 + - - -
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Residues in contact with ILE 128 (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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124C MET* 3.2 33.1 + - - +
125C PRO* 3.5 7.9 - - + +
127C HIS* 1.3 77.2 - - - +
129C GLY* 1.3 57.5 + - - +
130C ALA* 3.8 18.2 - - + -
211C THR* 3.3 29.6 - - + +
212C PHE* 4.0 8.5 - - + -
215C MET 4.3 0.4 - - - +
216C ARG* 3.5 23.9 - - + -
217C ALA* 3.0 24.3 + - - +
220C MET* 3.8 15.6 - - - +
225C VAL* 3.7 29.2 - - + -
229C ALA* 4.0 8.5 - - + -
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Residues in contact with GLY 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PRO 3.0 4.6 + - - -
126C LEU* 3.7 3.1 + - - -
127C HIS 3.4 4.2 - - - -
128C ILE* 1.3 79.5 - - - +
130C ALA* 1.3 59.9 + - - +
131C PRO* 4.2 3.1 - - - +
215C MET 4.2 0.5 - - - +
217C ALA* 3.5 24.7 + - - +
538C LEU* 3.6 18.8 - - - +
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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