Contacts of the strand formed by residues 142 - 151 (chain D) in PDB entry 1FBA
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 CYS 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D LEU* 3.8 33.7 - - - -
104D LEU* 3.4 17.0 - - - +
105D GLY 4.4 4.3 - - - -
106D ILE* 3.8 36.6 - - + -
137D TYR* 2.9 21.8 + - + +
138D LYS* 3.4 12.7 + - - +
140D ASP 5.0 0.2 - - - -
141D GLY* 1.3 78.8 - - - +
143D ASP* 1.3 66.6 + - - +
144D PHE 4.5 2.0 - - - +
182D ILE* 3.3 14.5 - - + +
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Residues in contact with ASP 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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18D ILE* 3.8 30.0 - - + +
98D LYS* 4.7 9.7 + - - -
103D ILE* 3.8 26.2 - - + +
104D LEU 2.9 6.7 + - - -
138D LYS* 2.9 31.1 + - - +
141D GLY 4.3 8.3 - - - +
142D CYS* 1.3 77.2 - - - +
144D PHE* 1.3 62.4 + - - +
182D ILE* 3.7 11.6 - - - -
183D VAL* 3.1 18.5 + - - +
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Residues in contact with PHE 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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22D ILE* 3.7 24.7 - - + -
29D ILE* 4.4 9.9 - - + -
75D GLY* 4.2 8.7 - - - -
76D VAL 3.9 17.7 - - - -
77D ILE* 3.8 16.4 - - + -
103D ILE* 3.6 27.1 - - + -
104D LEU 3.4 11.3 - - - +
105D GLY* 3.2 30.3 - - - -
106D ILE* 3.1 26.9 + - - +
142D CYS* 3.7 0.7 - - - +
143D ASP* 1.3 79.2 + - - +
145D ALA* 1.3 65.2 + - - +
182D ILE* 3.6 5.7 - - - +
183D VAL* 3.1 17.9 - - + +
185D ILE* 3.6 32.3 - - + -
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Residues in contact with ALA 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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106D ILE* 3.3 14.1 - - + +
108D VAL* 4.3 12.1 - - + -
134D CYS* 5.5 0.4 - - - -
144D PHE* 1.3 80.2 - - - +
146D LYS* 1.3 61.3 + - - +
173D TYR* 3.4 9.0 - - + +
177D CYS* 3.8 20.2 - - - -
182D ILE* 3.7 17.0 - - + -
183D VAL 2.8 6.8 + - - +
185D ILE* 3.0 32.2 + - - +
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Residues in contact with LYS 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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33D ASP* 2.7 29.0 + - - +
77D ILE* 3.9 35.4 - - + +
106D ILE 3.0 7.1 + - - +
107D LYS* 3.5 24.2 - - + +
108D VAL* 3.0 27.0 + - - +
109D ASP* 3.8 3.0 + - - +
145D ALA* 1.3 76.3 - - - +
147D TRP* 1.3 64.8 + - - +
148D ARG* 4.0 21.0 - - - +
173D TYR* 3.8 2.0 - - - -
185D ILE* 4.4 8.3 - - + +
187D GLU* 3.3 27.7 + - - +
229D LYS* 5.1 9.2 - - + +
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Residues in contact with TRP 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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108D VAL* 4.2 4.5 - - + -
109D ASP* 3.6 23.6 - - + -
124D THR* 3.4 41.3 - - + +
125D GLN 3.6 14.4 - - - -
126D GLY* 3.6 28.9 - - - -
127D LEU* 3.5 26.7 - - + -
130D LEU* 4.5 4.0 - - + -
146D LYS* 1.3 76.6 - - - +
148D ARG* 1.3 62.1 + - - +
149D CYS* 3.7 12.4 - - - -
169D VAL* 4.0 15.5 + - + +
170D LEU* 3.5 20.4 - - + +
173D TYR* 3.5 47.7 + + + -
185D ILE 3.9 3.0 + - - +
187D GLU* 3.3 29.5 + - - +
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Residues in contact with ARG 148 (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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109D ASP* 3.1 17.3 + - - +
112D VAL* 4.6 6.6 - - - +
124D THR* 2.8 29.7 + - - +
146D LYS* 4.0 12.8 - - - +
147D TRP* 1.3 75.0 - - - +
149D CYS* 1.3 63.8 + - - +
150D VAL* 3.6 18.0 - - + +
187D GLU* 3.6 27.3 + - + +
189D GLU* 2.8 31.8 + - - +
191D LEU* 3.8 0.4 - - - +
361D HIS* 2.4 56.8 + - - +
362D ALA 5.4 0.6 - - - +
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Residues in contact with CYS 149 (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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124D THR* 3.6 7.9 - - - -
147D TRP* 3.7 11.4 + - - -
148D ARG* 1.3 75.3 - - - +
150D VAL* 1.3 64.3 + - - +
151D LEU* 5.5 1.3 - - + -
166D ASN* 3.3 29.8 - - + +
169D VAL* 3.6 19.3 - - - -
170D LEU* 3.6 32.1 - - + -
187D GLU 2.9 14.2 + - - +
188D PRO* 4.5 3.8 - - + -
189D GLU* 2.9 30.7 + - - +
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Residues in contact with VAL 150 (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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112D VAL* 4.3 14.8 - - + +
122D VAL* 3.6 27.4 + - + +
124D THR* 4.6 1.8 + - - -
148D ARG* 3.6 37.5 - - + +
149D CYS* 1.3 81.2 - - - +
151D LEU* 1.3 71.7 + - - +
152D LYS* 5.1 0.9 - - - +
162D SER* 4.9 0.9 + - - -
166D ASN* 4.3 2.6 + - - -
189D GLU* 3.5 2.9 - - + +
191D LEU* 3.4 34.3 - - + -
362D ALA* 3.3 34.9 - - + +
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Residues in contact with LEU 151 (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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149D CYS* 5.5 2.2 - - + -
150D VAL* 1.3 77.4 - - - +
152D LYS* 1.3 62.2 + - - +
153D ILE 4.3 0.3 + - - -
158D PRO* 4.5 14.1 - - + -
162D SER* 3.5 34.5 - - - +
163D ILE* 4.8 4.0 - - + +
166D ASN* 3.6 26.0 - - + +
188D PRO* 5.1 6.7 - - + -
189D GLU 2.9 11.5 + - - +
190D VAL* 3.5 14.1 - - + +
191D LEU* 2.9 31.8 + - - +
208D VAL* 3.1 49.4 - - + -
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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