Contacts of the strand formed by residues 121 - 127 (chain C) in PDB entry 5FFO
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 LEU 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C VAL* 3.9 33.5 - - + +
118C PRO* 3.4 15.3 + - + +
119C VAL 3.1 8.6 - - - +
120C LEU* 1.3 78.0 - - - +
122C SER* 1.3 57.5 + - - +
123C ARG 4.0 4.0 - - - +
124C ALA* 3.7 24.5 - - + -
172C THR* 3.8 25.6 - - + +
175C VAL* 4.6 12.3 - - + -
176C ARG* 2.7 34.8 + - - +
179C LEU* 4.9 5.2 - - + -
231C LEU* 4.5 19.3 - - + -
232C MET 4.3 4.5 - - - +
233C ALA* 4.0 7.6 - - + -
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Residues in contact with SER 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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77C LYS* 3.8 35.7 - - - +
120C LEU 3.3 5.5 + - - -
121C LEU* 1.3 77.2 - - - +
123C ARG* 1.3 64.9 + - - +
172C THR* 3.5 14.7 + - - +
176C ARG* 4.1 4.0 + - - +
232C MET* 2.2 35.6 + - - +
234C THR* 5.0 0.2 - - - -
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Residues in contact with ARG 123 (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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121C LEU* 4.1 1.9 - - - +
122C SER* 1.3 85.1 + - - +
124C ALA* 1.3 61.3 + - - +
125C GLU* 3.5 34.8 + - + +
170C ASP* 3.5 27.9 + - - +
172C THR* 3.5 7.9 - - - +
230C LEU 4.1 0.3 - - - +
231C LEU 3.6 0.3 - - - -
232C MET* 2.8 61.4 + - + +
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Residues in contact with ALA 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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121C LEU* 3.7 17.9 - - + -
123C ARG* 1.3 74.1 - - - +
125C GLU* 1.3 60.4 + - - +
170C ASP* 4.5 0.2 - - - -
171C VAL* 3.1 25.9 + - - +
172C THR* 2.7 19.0 + - - -
175C VAL* 3.7 20.2 - - + -
229C LEU* 4.5 1.1 - - + -
230C LEU 3.5 7.0 - - - -
231C LEU* 3.7 24.7 - - + -
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Residues in contact with GLU 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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123C ARG* 3.5 36.4 + - + +
124C ALA* 1.3 72.6 - - - +
126C LEU* 1.3 62.5 + - - +
127C ARG* 3.0 38.8 + - - +
168C SER* 4.0 17.1 + - - -
169C PHE 3.4 10.8 - - - +
170C ASP* 4.2 10.3 - - + +
229C LEU* 3.9 2.2 - - - -
230C LEU* 3.1 35.7 + - + +
232C MET* 3.3 22.0 - - + +
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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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104C MET* 3.9 26.9 - - + -
106C PHE* 4.1 20.4 - - + -
125C GLU* 1.3 70.1 - - - +
127C ARG* 1.3 59.6 + - - +
128C LEU* 3.9 18.9 + - + +
141C LEU* 5.3 8.5 - - + -
168C SER* 3.2 1.2 - - - -
169C PHE* 2.7 49.8 + - + +
171C VAL* 3.9 10.9 - - + +
188C PHE* 4.2 25.4 - - + -
227C PRO 5.3 0.2 - - - -
228C PHE 3.7 24.9 - - - +
229C LEU* 3.7 16.7 - - + +
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Residues in contact with ARG 127 (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 SER 2.4 31.9 + - - -
55C THR* 4.4 7.9 + - - +
57C ASP* 3.1 24.2 + - - +
58C ARG* 5.7 2.4 - - - +
125C GLU* 3.0 40.4 + - - +
126C LEU* 1.3 72.3 - - - +
128C LEU* 1.3 68.0 + - - +
166C TRP* 3.6 22.8 - - - +
167C LEU 3.4 7.2 - - - +
168C SER* 3.6 20.9 + - - -
227C PRO* 3.7 0.5 - - - +
228C PHE* 3.1 49.7 + - + +
230C LEU* 3.6 23.7 - - + +
232C MET* 4.7 3.0 - - - +
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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