Contacts of the strand formed by residues 114 - 118 (chain C) in PDB entry 3IO6
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 SER 114 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ALA 3.5 9.2 + - - -
113C LEU* 1.3 77.1 + - - +
115C LEU* 1.3 62.8 + - - +
116C ILE* 3.6 1.4 + - - -
226C ILE* 3.5 8.0 - - - +
227C ASN 3.0 34.9 + - - +
228C GLY* 5.2 0.5 - - - -
229C PRO* 5.3 0.2 - - - +
232C TRP* 4.9 3.4 - - - -
244C VAL* 3.3 26.8 - - - +
247C LEU* 4.5 2.0 - - - -
319C ALA 4.7 0.4 - - - -
320C THR* 3.8 19.8 + - - -
323C ASN* 3.5 18.4 + - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C SER* 1.3 70.2 - - - +
116C ILE* 1.3 62.2 - - - +
117C TYR* 5.0 0.9 - - + -
125C PRO* 4.2 12.1 - - + -
126C PRO 4.5 5.8 - - - +
132C ILE* 6.5 0.2 - - + -
147C LEU* 4.9 4.0 - - + -
224C MET* 4.1 34.1 - - + -
225C THR 3.9 12.6 - - - +
226C ILE* 4.4 13.7 - - + +
243C GLY 4.0 0.5 - - - +
244C VAL* 3.3 6.9 - - - +
245C THR* 2.8 65.3 + - + +
246C VAL 3.7 11.9 - - - +
247C LEU* 4.4 9.2 - - + +
248C PRO* 4.3 26.5 - - + -
323C ASN* 4.4 0.2 - - - +
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Residues in contact with ILE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C SER 3.9 5.8 - - - +
115C LEU* 1.3 78.3 - - - +
117C TYR* 1.3 61.0 + - - +
217C PHE* 3.4 29.6 - - + -
224C MET* 3.4 2.3 - - - +
225C THR* 2.8 50.2 + - + +
227C ASN* 3.5 37.2 - - + +
228C GLY 4.5 0.2 - - - +
231C ALA* 5.2 0.2 - - + -
232C TRP* 3.7 26.2 - - + +
235C ILE* 4.2 9.6 - - + -
242C TYR* 4.0 19.5 - - + -
243C GLY 3.6 2.5 - - - -
244C VAL* 3.8 12.6 - - + -
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Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 4.5 3.1 - - + -
116C ILE* 1.3 75.1 - - - +
118C ASN* 1.3 59.6 + - - +
119C LYS* 3.6 34.4 + - + +
122C LEU* 3.4 25.6 - - + +
123C PRO 4.5 4.3 + - - -
125C PRO* 3.8 42.0 - - + +
217C PHE* 3.5 5.8 - - - -
223C ALA 3.2 11.4 - - - +
224C MET* 3.9 14.1 - - + -
242C TYR* 3.2 3.8 - - - +
243C GLY* 2.9 65.9 + - - -
244C VAL 4.0 1.9 + - - -
245C THR* 3.9 21.2 - - + -
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Residues in contact with ASN 118 (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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117C TYR* 1.3 68.7 - - - +
119C LYS* 1.3 65.5 + - - +
120C ASP* 3.1 27.7 + - - +
121C LEU* 3.2 25.3 + - + +
122C LEU* 3.0 25.5 + - - +
217C PHE* 3.4 15.3 + - + -
220C GLY* 4.4 13.1 - - - -
222C THR 4.4 5.1 + - - +
223C ALA* 2.9 18.6 + - - +
240C VAL* 3.6 22.3 - - + +
241C ASN 3.3 10.2 - - - +
242C TYR* 4.4 1.1 - - - +
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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