Contacts of the strand formed by residues 128 - 134 (chain C) in PDB entry 3F7F
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 128 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ASN* 3.8 29.8 - - + -
121C VAL 4.0 1.8 - - - -
122C ILE* 3.4 33.9 - - + -
126C GLY 5.2 0.4 - - - +
127C SER* 1.3 74.0 - - - +
129C LEU* 1.3 62.0 + - - +
130C THR* 3.5 6.5 + - - -
151C HIS 3.6 5.5 - - - +
153C GLN* 2.7 29.0 + - - +
155C PRO* 3.8 19.1 - - + -
158C PHE* 5.9 4.3 - + + -
166C LEU* 3.9 17.5 - - + -
174C SER* 5.2 4.3 - - - -
186C LEU* 4.0 23.3 - - + -
194C TYR* 3.3 45.5 - + - -
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Residues in contact with LEU 129 (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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28C VAL* 4.0 16.8 - - + -
97C LEU* 3.8 29.4 - - + -
98C PRO* 4.6 0.4 - - + -
119C VAL 4.3 0.2 - - - -
120C ASN* 3.4 6.2 - - - +
121C VAL* 3.0 45.5 + - + +
123C LEU* 4.4 17.0 - - + -
127C SER 3.8 0.6 - - - -
128C PHE* 1.3 77.1 - - - +
130C THR* 1.3 69.2 + - - +
131C LEU* 4.2 9.6 - - + -
150C PHE* 3.8 35.0 - - + -
151C HIS 3.8 6.5 - - - +
152C LEU* 3.8 24.7 - - + +
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Residues in contact with THR 130 (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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118C LEU* 4.0 21.3 - - + -
119C VAL 3.4 2.0 - - - -
120C ASN* 3.2 19.6 + - - +
128C PHE* 3.5 11.3 + - - -
129C LEU* 1.3 81.5 + - - +
131C LEU* 1.3 61.0 + - - +
132C GLN* 4.9 4.9 - - + +
149C TRP 3.4 0.3 - - - +
150C PHE* 2.8 27.8 - - - -
151C HIS* 3.0 31.0 + - + +
153C GLN* 4.4 7.6 + - - -
191C GLY 6.2 0.2 - - - +
192C VAL* 5.2 4.4 + - + -
194C TYR* 4.5 10.9 - - + +
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Residues in contact with LEU 131 (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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28C VAL* 4.3 8.3 - - + -
79C LEU* 4.4 6.7 - - + -
95C ILE* 3.6 36.1 - - + -
97C LEU* 4.9 6.7 - - + -
117C LEU 3.3 2.3 - - - +
118C LEU* 3.4 7.8 - - - +
119C VAL* 2.6 68.2 + - + +
121C VAL* 5.7 1.8 - - + -
129C LEU* 4.5 11.0 - - + -
130C THR* 1.3 74.2 - - - +
132C GLN* 1.3 62.1 + - - +
133C LEU* 4.0 5.2 - - + -
149C TRP* 3.0 35.0 - - + +
150C PHE* 3.6 17.7 - - + -
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Residues in contact with GLN 132 (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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116C GLN* 3.0 30.7 + - - +
117C LEU 3.7 2.9 - - - -
118C LEU* 3.5 26.4 - - + +
130C THR* 4.9 3.9 - - + +
131C LEU* 1.3 71.8 - - - +
133C LEU* 1.3 61.5 + - - +
134C PRO* 3.5 8.2 - - - +
148C GLU 4.3 4.7 + - - +
149C TRP* 2.6 38.4 + - - +
151C HIS* 3.2 32.2 + - + +
191C GLY 4.7 11.7 + - - -
192C VAL* 5.1 1.6 - - - +
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Residues in contact with LEU 133 (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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26C LEU* 4.4 9.6 - - + -
81C PHE* 3.8 23.6 - - + -
93C ILE* 5.6 2.0 - - + -
95C ILE* 3.3 36.1 - - + -
116C GLN* 3.4 2.5 - - - -
117C LEU* 2.7 50.3 + - + +
119C VAL* 4.7 5.2 - - + -
131C LEU* 4.8 4.3 - - + -
132C GLN* 1.3 81.5 - - - +
134C PRO* 1.3 68.8 - - + +
135C LEU* 3.3 0.7 + - - -
137C PHE* 5.0 5.2 - - + -
138C LEU* 4.5 19.0 - - + +
145C LEU* 4.1 19.5 - - + -
149C TRP* 4.6 8.5 - - + -
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Residues in contact with PRO 134 (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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115C GLN 4.0 0.4 - - - +
116C GLN* 3.7 25.1 - - + +
132C GLN 3.5 8.7 - - - +
133C LEU* 1.3 84.5 - - + +
135C LEU* 1.3 66.7 + - - +
136C SER* 2.9 16.6 + - - +
137C PHE* 2.9 21.3 + - + +
138C LEU* 3.3 9.6 + - - +
145C LEU* 4.0 28.7 - - + -
146C ASN 5.8 1.3 - - - +
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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