Contacts of the strand formed by residues 119 - 124 (chain C) in PDB entry 3RIE
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 ASN 119 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LYS* 1.3 79.4 - - + +
120C VAL* 1.3 68.2 + - - +
142C ASN* 2.7 37.3 + - + +
144C ASP* 4.6 1.2 + - - -
189C THR* 3.6 39.6 + - - +
190C TYR* 3.5 17.7 - - - -
191C ASP* 3.0 33.2 + - - +
192C VAL 3.7 0.7 + - - -
221C LYS* 5.8 0.9 - - - -
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Residues in contact with VAL 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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111C MET* 3.9 28.9 - - + -
117C PRO* 4.5 7.0 - - + -
119C ASN* 1.3 86.2 + - - +
121C LEU* 1.3 69.0 + - - +
134C LEU* 3.6 35.9 - - + -
140C VAL* 4.6 8.1 - - + -
142C ASN 3.0 11.2 + - - +
143C ILE* 3.4 6.0 - - + +
144C ASP* 3.0 24.4 + - - +
190C TYR* 3.8 3.8 - - - -
192C VAL* 3.4 26.9 - - + +
194C ILE* 4.3 2.9 - - + -
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C VAL* 1.3 75.4 - - - +
122C VAL* 1.3 75.7 + - - +
123C VAL* 3.7 22.2 - - + -
144C ASP* 3.4 24.7 - - + +
145C ILE 4.4 0.2 - - - -
146C CYS* 4.0 8.7 - - + +
182C PHE* 3.9 18.2 - - + -
183C LEU* 3.6 31.9 - - + -
190C TYR* 3.6 26.1 - - + +
192C VAL 3.0 8.5 + - - +
193C ILE* 3.3 15.3 - - + -
194C ILE* 2.7 32.1 + - - -
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Residues in contact with VAL 122 (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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120C VAL* 5.0 0.2 - - + -
121C LEU* 1.3 78.8 - - - +
123C VAL* 1.3 66.7 + - - +
124C GLY 4.0 14.6 - - - +
125C GLY* 4.1 7.9 - - - +
130C ILE* 3.8 28.0 - - + -
131C ILE* 4.3 12.8 - - + -
134C LEU* 3.6 28.9 - - + -
143C ILE* 4.6 1.3 - - + -
144C ASP 2.9 11.9 + - - +
145C ILE* 3.3 14.4 - - + +
146C CYS 2.9 26.3 + - - -
194C ILE* 3.4 9.6 - - + +
196C ASP* 4.6 1.6 - - + -
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 3.7 29.2 - - + -
122C VAL* 1.3 70.4 - - - +
124C GLY* 1.3 66.3 + - - +
146C CYS* 3.7 3.1 - - + -
179C ALA* 3.3 33.0 - - + -
183C LEU* 4.8 1.6 - - + -
193C ILE* 4.2 13.0 - - + -
194C ILE 2.9 10.4 + - - +
195C VAL* 3.9 15.9 - - + -
196C ASP* 2.9 27.9 + - - +
207C LEU* 3.7 24.9 - - + -
212C PHE* 4.1 12.3 - - + -
401C MTA 4.5 0.7 - - + -
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Residues in contact with GLY 124 (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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122C VAL* 4.0 1.0 - - - +
123C VAL* 1.3 78.3 - - - +
125C GLY* 1.4 63.2 + - - -
126C GLY 3.2 3.7 + - - -
145C ILE* 3.3 20.6 - - - +
146C CYS 2.8 14.1 + - - -
147C GLU* 3.7 6.9 - - - +
196C ASP 3.6 2.9 - - - -
197C SER* 4.9 0.9 - - - -
401C MTA 3.5 35.2 + - - -
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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