Contacts of the strand formed by residues 129 - 139 (chain C) in PDB entry 1F11
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 GLY 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C GLN* 3.1 33.9 + - - +
125C LEU* 3.2 16.9 + - - +
127C SER 3.3 5.0 - - - -
128C GLY* 1.3 80.3 - - - +
130C ALA* 1.3 60.1 + - - -
181C LEU 4.2 3.8 - - - -
182C THR* 4.7 0.7 - - - -
183C LYS 4.2 2.5 - - - -
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Residues in contact with ALA 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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120C PRO* 3.7 11.7 - - + -
124C GLN* 3.7 3.0 - - - +
125C LEU* 3.6 14.4 - - + -
129C GLY* 1.3 74.3 - - - +
131C SER* 1.3 59.8 + - - +
132C VAL* 4.1 1.0 + - - -
179C LEU 4.0 0.7 - - - +
180C THR* 3.8 0.6 - - - -
181C LEU* 2.8 44.9 + - + +
182C THR 4.1 2.9 - - - +
183C LYS 4.2 0.2 - - - +
186C TYR* 3.5 37.7 - - + -
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Residues in contact with SER 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PRO 4.2 1.6 - - - +
120C PRO* 3.8 19.0 - - - +
124C GLN* 2.8 32.4 + - - +
130C ALA* 1.3 71.2 - - - +
132C VAL* 1.3 63.9 + - - +
133C VAL* 3.7 6.1 + - - +
178C THR* 4.1 9.9 - - - +
179C LEU 3.5 4.5 - - - -
180C THR* 3.5 23.1 + - - +
124D LEU* 5.4 2.8 - - - +
143D LEU* 4.0 19.4 - - - +
145D LYS* 4.0 9.5 - - - +
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Residues in contact with VAL 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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117C ILE* 4.0 4.0 - - + -
118C PHE 3.2 17.0 - - - +
120C PRO* 4.3 17.3 - - + -
130C ALA 5.1 0.4 - - - +
131C SER* 1.3 74.6 - - - +
133C VAL* 1.3 58.4 + - - +
148C TRP* 3.4 33.4 - - + -
178C THR* 3.4 2.4 - - - -
179C LEU* 2.8 42.7 + - + +
181C LEU* 4.7 7.9 - - + -
186C TYR* 4.4 14.4 - - + -
192C TYR* 4.5 15.3 - - + -
209C PHE* 3.7 20.2 - - + -
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 3.4 2.9 - - - +
118C PHE* 2.8 41.2 + - + +
131C SER 3.7 4.6 + - - +
132C VAL* 1.3 73.5 - - - +
134C CYS* 1.3 64.2 + - - +
135C PHE* 3.8 37.9 - - + -
148C TRP* 4.3 1.1 - - - -
176C SER* 5.4 0.9 - - - +
177C SER 3.6 5.8 - - - +
178C THR* 3.6 27.4 - - + +
124D LEU* 3.7 27.6 - - + +
143D LEU* 4.3 19.7 - - + -
188D SER* 5.2 2.5 - - - +
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Residues in contact with CYS 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 VAL* 3.3 25.6 - - - -
116C SER 3.5 4.9 - - - -
117C ILE* 4.4 4.7 - - - -
133C VAL* 1.3 75.5 - - - +
135C PHE* 1.3 64.3 + - - +
136C LEU* 3.7 5.9 - - + +
148C TRP* 3.5 15.7 - - + -
176C SER* 3.4 3.6 - - - -
177C SER* 2.8 42.3 + - - +
194C CYS* 2.0 50.5 - - - -
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Residues in contact with PHE 135 (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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114C THR 3.2 7.1 - - - +
115C VAL* 3.2 2.9 - - - -
116C SER* 3.0 36.8 + - - +
118C PHE* 3.4 28.7 - + - -
133C VAL* 3.8 17.3 - - + -
134C CYS* 1.3 73.4 - - - +
136C LEU* 1.3 61.1 + - - +
137C ASN* 3.7 13.7 - - - +
175C MET 3.8 1.1 - - - -
176C SER* 3.7 17.0 - - - -
124D LEU* 4.3 4.0 - - + -
139D THR* 4.4 2.9 - - + -
141D GLY* 3.7 18.8 - - - -
174D PHE* 3.7 23.1 - + - -
188D SER* 3.8 22.4 - - - -
189D SER 3.7 17.9 - - - -
190D SER* 3.4 20.9 - - - -
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Residues in contact with LEU 136 (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 PRO* 4.2 9.4 - - + -
114C THR 4.0 5.8 - - - -
115C VAL* 4.3 12.1 - - + -
134C CYS* 3.7 26.2 - - + +
135C PHE* 1.3 76.9 - - - +
137C ASN* 1.3 61.5 + - - +
139C PHE* 3.3 13.6 - - + -
144C ILE* 4.2 11.2 - - + -
145C ASN 4.2 1.3 - - - +
146C VAL* 3.3 28.9 - - + -
175C MET* 2.8 56.7 + - + +
177C SER* 4.8 0.7 - - - +
194C CYS* 4.7 1.6 - - - -
196C ALA* 3.5 26.7 - - + -
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Residues in contact with ASN 137 (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 PRO* 3.3 2.8 - - - +
114C THR* 3.0 43.3 + - - +
116C SER* 5.3 0.6 + - - -
135C PHE* 4.1 9.8 - - - +
136C LEU* 1.3 77.1 - - - +
138C ASN* 1.3 81.8 + - - +
139C PHE 3.5 1.1 - - - -
174C SER* 3.4 6.8 + - - -
139D THR* 4.6 9.5 + - - +
169D GLY 5.4 0.2 + - - -
172D HIS* 4.0 12.2 - - - +
174D PHE* 3.6 24.1 - - - -
190D SER* 3.6 20.2 + - - -
192D THR* 4.4 14.3 + - - -
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Residues in contact with ASN 138 (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 ALA* 4.1 6.2 - - - +
112C ALA 3.8 10.4 - - - +
114C THR* 5.6 3.2 + - - +
137C ASN* 1.3 79.3 - - - +
139C PHE* 1.3 60.5 + - - +
170C ASP* 4.2 11.5 + - - +
172C THR* 3.4 28.3 + - + +
173C TYR 3.0 8.3 + - - -
174C SER* 3.0 7.1 + - - -
172D HIS* 2.9 33.8 + - - -
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Residues in contact with PHE 139 (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 ALA* 3.0 13.5 - - - +
113C PRO* 3.5 29.2 - - + -
136C LEU* 3.3 27.8 - - + -
138C ASN* 1.3 74.9 - - - +
140C TYR* 1.3 67.2 + - - +
141C PRO 3.1 20.2 - - - -
142C LYS* 3.4 30.1 - - - -
144C ILE* 3.6 32.5 - - + -
163C TRP* 4.2 5.4 - + - -
172C THR* 3.5 3.7 - - - -
173C TYR* 2.9 50.1 + - + +
174C SER* 3.5 7.2 - - - -
175C MET* 3.6 16.6 - - + -
198C HIS* 4.2 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