Contacts of the strand formed by residues 141 - 145 (chain C) in PDB entry 1FIU
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 141 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLU* 3.3 28.5 - - + +
73C CYS* 3.9 4.5 - - + -
74C SER* 3.6 22.2 - - - +
77C VAL* 5.9 0.7 - - + -
94C VAL* 4.0 19.7 - - + -
95C LYS 3.3 11.4 - - - +
96C GLN* 4.3 5.4 - - + -
97C VAL 4.5 0.2 - - - +
139C PRO* 4.0 1.4 - - - +
140C ASP* 1.3 84.7 - - + +
142C ILE* 1.3 77.8 + - - +
183C SER* 3.8 0.7 - - - -
184C ILE* 2.9 54.7 + - + +
186C CYS* 3.5 24.7 - - - -
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Residues in contact with ILE 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ASN 3.8 0.5 - - - +
94C VAL* 3.5 2.3 - - - -
95C LYS* 3.0 60.0 + - + +
97C VAL* 4.0 14.4 - - + -
104C GLU* 4.0 5.6 - - + +
105C ILE* 5.7 2.0 - - + -
108C TYR* 3.5 41.3 - - + +
139C PRO* 3.8 26.9 - - + -
141C ILE* 1.3 81.0 - - - +
143C VAL* 1.3 63.9 + - - +
144C THR* 3.8 8.3 - - + -
180C LEU* 3.7 19.3 - - + -
182C ALA 3.3 5.4 - - - +
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Residues in contact with VAL 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL* 4.4 6.3 - - + -
81C PHE* 4.6 10.1 - - + -
92C TRP* 4.2 14.1 - - + -
93C ASN 3.2 10.1 - - - +
94C VAL* 4.0 23.3 - - + -
142C ILE* 1.3 77.3 - - - +
144C THR* 1.3 57.4 + - - +
180C LEU* 3.6 4.5 - - - +
181C HIS* 2.7 48.2 + - + +
182C ALA* 3.0 22.4 + - + +
184C ILE* 3.9 26.0 - - + -
284C LEU* 4.5 5.2 - - + -
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Residues in contact with THR 144 (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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91C ASP 3.9 0.3 - - - +
92C TRP* 3.4 12.3 - - - -
93C ASN* 2.9 56.2 + - - +
95C LYS* 5.8 0.4 - - - -
108C TYR* 3.2 45.9 + - + +
142C ILE* 3.8 16.4 - - + -
143C VAL* 1.3 79.5 - - - +
145C ARG* 1.3 62.5 + - - +
146C ASN* 5.0 0.5 + - - -
178C PRO* 4.8 2.1 - - - +
179C LEU 3.2 10.8 - - - +
180C LEU* 4.1 4.7 - - + -
181C HIS 4.1 0.7 - - - +
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Residues in contact with ARG 145 (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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87B ILE* 3.4 30.1 + - - +
285B ALA 3.0 17.2 + - - -
286B VAL* 2.8 35.9 + - - +
88C ARG* 3.6 8.1 - - - +
89C PRO 3.3 24.9 + - - -
90C GLY* 4.0 8.5 - - - -
91C ASP 3.7 8.5 - - - +
92C TRP* 3.5 31.0 - - + -
144C THR* 1.3 73.2 - - - +
146C ASN* 1.3 75.5 + - - +
147C LEU* 4.2 1.2 - - - +
148C ILE* 3.6 11.5 - - - +
170C LEU* 3.9 21.2 - - + +
178C PRO* 3.4 3.5 - - - +
179C LEU* 2.9 46.7 + - + +
181C HIS* 4.7 2.2 - - + +
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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