Contacts of the strand formed by residues 138 - 147 (chain D) 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 VAL 138 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 4.1 11.9 - - + -
133D GLN* 3.5 37.5 - - + +
134D THR* 3.9 2.9 - - - +
136D SER 3.7 7.6 - - - +
137D MET* 1.3 80.5 - - - +
139D THR* 1.3 71.2 + - - +
140D LEU* 4.2 5.6 - - + -
191D VAL 3.8 0.5 - - - +
192D THR* 3.5 1.7 - - - -
193D VAL* 2.6 50.7 + - + +
195D SER* 4.6 11.7 - - - -
200D ARG* 4.1 25.1 - - - +
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Residues in contact with THR 139 (chain D).
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* 5.3 7.1 - - - +
116C SER* 3.8 28.0 + - - +
118C PHE* 3.3 23.1 - - + -
135C PHE* 4.4 3.6 - - + -
137C ASN* 4.6 8.1 + - - +
126D PRO* 4.0 7.6 - - - +
138D VAL* 1.3 72.6 - - - +
140D LEU* 1.3 80.9 + - - +
190D SER* 4.2 15.7 - - - -
191D VAL 3.5 7.6 - - - +
192D THR* 3.2 21.0 + - - +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C PHE* 4.2 1.8 - - - -
124D LEU 3.8 3.6 - - - +
126D PRO* 3.4 36.1 - - + -
138D VAL* 4.2 6.3 - - + +
139D THR* 1.3 80.1 - - - +
141D GLY* 1.3 59.6 + - - +
157D TRP* 4.3 5.4 - - + -
190D SER* 3.2 4.9 - - - -
191D VAL* 2.8 43.8 + - + +
193D VAL* 4.5 8.5 - - + -
200D ARG* 3.4 39.0 - - + +
206D VAL* 3.7 25.4 - - + -
223D ILE* 3.7 19.7 - - + -
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Residues in contact with GLY 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C PHE* 4.0 1.8 - - - -
135C PHE* 3.7 12.1 - - - -
124D LEU* 2.7 50.8 + - - +
140D LEU* 1.3 75.6 - - - +
142D CYS* 1.3 59.7 + - - +
157D TRP* 3.8 4.0 - - - -
189D SER 3.3 9.6 - - - -
223D ILE* 3.6 9.2 - - - +
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Residues in contact with CYS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL* 4.0 14.4 - - - -
122D TYR 3.6 11.4 - - - -
123D PRO* 4.7 1.6 - - - -
124D LEU* 4.2 3.9 - - - +
141D GLY* 1.3 76.9 - - - -
143D LEU* 1.3 61.3 + - - +
144D VAL* 3.8 3.8 + - + +
154D VAL* 4.8 5.8 - - + -
157D TRP* 3.8 12.8 - - + -
188D SER* 3.3 4.0 - - - -
189D SER* 2.8 33.7 + - - +
208D CYS* 2.0 50.0 - - - -
210D VAL* 4.8 1.1 - - - -
221D LYS* 4.8 2.7 - - - -
223D ILE* 4.7 6.3 - - - -
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLN* 5.0 1.1 - - - +
131C SER* 4.0 22.4 - - - +
133C VAL* 4.3 16.6 - - + -
178C THR* 4.9 8.1 - - + +
120D SER 3.2 4.9 - - - +
121D VAL* 3.6 1.1 - - - -
122D TYR* 2.8 55.8 + - + +
124D LEU* 4.2 16.9 - - + +
142D CYS* 1.3 70.8 - - - +
144D VAL* 1.3 61.2 + - - +
145D LYS* 3.9 28.7 - - + -
186D THR* 4.1 15.0 - - + -
187D LEU 3.5 15.7 - - - +
188D SER* 3.8 12.8 - - - -
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PRO* 3.4 32.8 - - + -
120D SER 3.6 4.0 - - - +
121D VAL* 4.6 4.9 - - + -
142D CYS* 3.8 6.5 + - - +
143D LEU* 1.3 75.4 - - - +
145D LYS* 1.3 57.9 + - - +
147D TYR* 3.9 14.7 - - + -
152D VAL* 4.6 6.7 - - + -
154D VAL* 4.3 14.1 - - + -
186D THR* 3.6 1.9 - - - +
187D LEU* 2.9 42.5 + - + +
210D VAL* 3.3 38.8 - - + -
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Residues in contact with LYS 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLN* 4.1 6.7 - - - +
131C SER* 4.0 17.0 - - - +
180C THR* 4.9 11.5 - - - +
119D PRO* 4.6 0.7 - - - -
120D SER* 2.9 43.5 + - - -
122D TYR* 3.9 25.5 - - + -
143D LEU* 3.9 22.9 - - + -
144D VAL* 1.3 76.1 - - - +
146D GLY* 1.3 63.3 + - - +
147D TYR* 3.7 1.6 - - - -
179D GLN* 3.8 28.9 + - - +
185D TYR 4.1 0.2 - - - -
186D THR* 3.4 19.5 - - + -
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Residues in contact with GLY 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D THR* 3.5 12.8 - - - +
118D PRO 3.3 14.9 - - - +
120D SER* 5.4 0.9 + - - -
145D LYS* 1.3 77.9 - - - +
147D TYR* 1.3 57.5 + - - -
179D GLN* 3.9 15.8 - - - +
184D LEU* 4.0 18.6 - - - +
185D TYR 2.8 14.1 + - - -
186D THR* 3.4 3.2 + - - -
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Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D THR 3.3 8.7 - - - +
119D PRO* 3.4 26.7 - - + -
144D VAL* 3.9 27.8 - - + -
146D GLY* 1.3 76.3 - - - +
148D PHE* 1.3 68.0 + - - +
149D PRO 3.7 18.8 - - - -
150D GLU* 3.0 26.8 + - - -
152D VAL* 3.0 31.9 - - + +
176D ALA* 3.2 18.2 - - - +
184D LEU* 3.7 3.2 - - - -
185D TYR* 2.7 69.9 + + + +
186D THR* 3.9 4.0 - - - -
187D LEU* 3.4 4.4 - - + +
212D HIS* 3.7 9.6 - + - +
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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