Contacts of the strand formed by residues 145 - 152 (chain C) in PDB entry 1XFB
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 PHE 145 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 3.6 29.8 - - + -
30C ILE* 4.4 7.9 - - + -
76C GLY* 4.3 5.6 - - - -
77C VAL 3.7 22.4 - - - -
78C ILE* 3.6 20.0 - - + -
104C VAL* 3.6 21.3 - - + -
105C VAL 3.2 20.2 - - - -
106C GLY* 2.9 42.5 - - - -
107C ILE* 3.2 8.8 + - - +
143C ALA 3.7 0.2 - - - -
144C ASP* 1.3 82.4 - - - +
146C ALA* 1.3 61.6 + - - +
183C ILE* 3.7 5.8 - - - +
184C VAL* 2.9 22.7 - - + +
186C ILE* 3.6 34.5 - - + -
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Residues in contact with ALA 146 (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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107C ILE* 3.2 18.2 - - + +
109C VAL* 3.9 17.5 - - + -
135C CYS* 5.7 0.7 - - - -
145C PHE* 1.3 79.5 - - - +
147C LYS* 1.3 61.8 + - - +
174C TYR* 3.2 10.3 - - + +
178C CYS* 4.1 11.2 - - - -
183C ILE* 3.7 14.6 - - + +
184C VAL 2.8 7.5 + - - +
186C ILE* 2.8 31.9 + - - +
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Residues in contact with LYS 147 (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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32C ALA* 5.1 0.6 - - - +
34C ASP* 3.2 32.7 + - - +
78C ILE* 4.0 28.9 - - + -
107C ILE 3.0 5.1 + - - -
108C LYS* 3.4 11.7 - - + +
109C VAL* 3.0 27.5 + - - +
110C ASP* 3.9 1.9 + - - +
146C ALA* 1.3 76.5 - - - +
148C TRP* 1.3 63.9 + - - +
149C ARG* 4.2 16.2 - - - +
174C TYR* 3.3 4.7 - - - -
186C ILE* 4.0 8.7 - - + +
188C GLU* 2.8 28.8 + - - +
230C LYS* 3.0 32.1 - - + +
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Residues in contact with TRP 148 (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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109C VAL* 4.0 2.9 - - + -
110C ASP* 3.6 22.7 - - + -
125C THR* 3.3 35.4 - - + -
126C GLN 3.5 0.7 - - - -
127C GLY* 3.4 27.8 - - - -
128C LEU* 3.4 39.3 - - + -
131C LEU* 4.4 4.9 - - + -
147C LYS* 1.3 76.3 - - - +
149C ARG* 1.3 64.6 + - - +
150C CYS* 3.6 12.4 - - - -
170C VAL* 3.3 25.9 - - + +
171C LEU* 3.6 18.8 - - + +
174C TYR* 3.3 49.9 + + + -
186C ILE 3.7 1.8 + - - -
188C GLU* 3.3 24.8 + - - +
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Residues in contact with ARG 149 (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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108C LYS* 5.7 2.9 - - - +
110C ASP* 3.2 18.3 + - - +
113C VAL* 5.6 2.4 + - - +
125C THR* 2.8 21.4 + - - +
147C LYS* 4.2 12.1 - - - +
148C TRP* 1.3 76.0 - - - +
150C CYS* 1.3 70.7 + - - +
151C VAL* 3.4 31.2 - - + +
188C GLU* 3.3 33.0 - - + +
190C GLU* 2.4 44.0 + - - +
192C LEU* 4.3 6.5 - - - +
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Residues in contact with CYS 150 (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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125C THR* 3.3 9.2 - - - -
148C TRP* 3.6 24.0 + - - -
149C ARG* 1.3 78.7 - - - +
151C VAL* 1.3 65.5 + - - +
152C LEU* 5.6 2.0 - - + -
167C ASN* 3.3 36.8 - - + +
170C VAL* 4.6 2.7 - - - -
171C LEU* 3.6 26.5 - - + -
188C GLU 3.0 13.3 + - - +
189C PRO* 4.5 6.5 - - + -
190C GLU* 3.2 22.1 + - - +
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Residues in contact with VAL 151 (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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113C VAL* 4.7 12.9 - - + +
123C THR* 3.5 30.4 + - - +
124C THR 5.9 0.2 - - - -
125C THR* 4.5 1.6 + - - -
149C ARG* 3.4 39.9 - - + +
150C CYS* 1.3 82.8 - - - +
152C LEU* 1.3 72.7 + - - +
153C LYS* 5.9 0.2 - - + -
167C ASN* 4.2 3.3 + - - +
190C GLU 3.4 3.6 - - - +
192C LEU* 3.5 40.4 - - + -
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Residues in contact with LEU 152 (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 GLU* 5.5 0.7 - - - +
123C THR 5.2 0.2 - - - +
150C CYS* 5.6 1.6 - - + -
151C VAL* 1.3 81.5 - - - +
153C LYS* 1.3 61.6 + - - +
159C PRO* 5.0 9.2 - - + -
163C ALA* 3.8 19.3 - - + +
164C ILE* 4.6 12.3 - - + -
167C ASN* 3.5 33.9 - - + +
189C PRO* 5.6 6.1 - - + -
190C GLU 2.8 12.2 + - - +
191C ILE* 4.2 12.6 - - + -
192C LEU* 2.9 31.8 + - - +
209C VAL* 3.3 46.2 - - + -
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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