Contacts of the strand formed by residues 150 - 159 (chain A) in PDB entry 3AFF
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 TRP 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLU* 3.5 44.3 + - + -
107A VAL* 3.7 24.2 + - + +
114A THR* 3.6 25.7 - - + +
115A ARG 3.6 0.6 + - - -
116A ILE* 3.3 14.7 - - + -
117A SER* 3.0 19.8 + - - -
148A ALA* 3.5 6.3 - - - +
149A SER* 1.3 89.1 + - - +
151A THR* 1.3 63.6 + - - +
170A LEU* 3.7 24.0 - - + -
171A ILE 3.4 11.2 - - - -
172A PRO* 3.4 46.0 - - + -
173A ARG 4.2 0.2 - - - +
176A TYR* 3.4 6.0 + - - -
206A ARG* 3.7 23.1 - - - -
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Residues in contact with THR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 4.0 4.3 - - - -
117A SER* 2.8 28.3 + - - -
150A TRP* 1.3 75.7 - - - +
152A PHE* 1.3 66.4 + - - +
153A VAL* 4.1 15.5 - - + -
169A PHE 3.5 1.2 - - - +
170A LEU* 3.4 3.6 - - - -
171A ILE* 2.9 40.1 + - + +
176A TYR* 3.5 31.4 - - + -
195A LEU* 3.3 26.8 - - + +
197A VAL* 5.7 0.9 - - + -
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A HIS* 3.9 13.0 - + + -
95A HIS* 3.5 25.1 - - + -
96A LEU* 3.9 26.2 - - + -
99A PHE* 3.4 35.7 - + - -
116A ILE* 3.8 15.5 - - + -
117A SER 2.9 18.2 + - - +
118A SER* 3.3 4.3 - - - -
119A SER 2.9 24.3 + - - -
120A TYR* 3.4 36.6 - + + -
151A THR* 1.3 78.7 + - - +
153A VAL* 1.3 63.6 + - - +
168A SER* 4.2 5.6 - - - -
169A PHE 3.3 3.4 - - - +
170A LEU* 3.7 26.0 - - + -
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A SER 3.3 4.9 - - - -
120A TYR* 4.9 0.2 - - - -
135A VAL* 4.5 1.1 - - + -
139A TRP* 3.5 52.0 - - + -
151A THR* 4.1 15.7 - - + -
152A PHE* 1.3 78.7 - - - +
154A GLY* 1.3 59.7 + - - +
168A SER* 3.4 4.3 - - - -
169A PHE* 2.9 56.2 + - + +
171A ILE* 4.0 16.2 - - + -
195A LEU* 4.1 10.1 - - + -
197A VAL* 4.6 5.8 - - + -
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Residues in contact with GLY 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A SER 3.0 12.3 + - - -
120A TYR* 3.6 23.4 - - - +
121A ALA 3.4 6.5 - - - +
122A PRO* 3.5 3.7 - - - +
139A TRP* 2.8 26.8 + - - -
153A VAL* 1.3 74.1 - - - +
155A GLY* 1.3 59.5 + - - -
166A PHE* 5.1 0.9 - - - -
167A GLY 3.3 10.5 - - - -
168A SER* 4.4 2.2 - - - -
169A PHE* 4.9 0.9 - - - -
210A TYR* 5.5 0.4 - - - -
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PRO* 4.3 2.2 - - - -
124A GLY 3.7 7.0 - - - -
153A VAL 4.2 0.2 + - - -
154A GLY* 1.3 73.9 - - - -
156A PRO* 1.4 77.9 - - - +
157A VAL 4.0 0.2 + - - -
166A PHE* 3.7 17.2 - - - -
167A GLY 3.1 27.6 + - - +
169A PHE* 3.7 12.0 - - - -
207A PHE* 4.4 0.2 - - - -
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Residues in contact with PRO 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PRO* 4.8 2.2 - - + -
124A GLY 3.4 14.8 - - - +
125A ALA* 3.6 10.3 - - + +
126A GLY 3.1 23.4 + - - -
155A GLY* 1.4 88.2 - - - +
157A VAL* 1.3 62.9 + - - +
158A ILE* 4.2 16.8 - - + -
163A PRO* 4.3 7.0 - - + -
165A ASP 3.1 14.6 - - - +
166A PHE* 3.6 10.3 - - + -
169A PHE* 3.9 1.6 - - - -
385A PHE* 3.7 16.2 - - + +
163B PRO* 5.1 8.5 - - + -
385B PHE* 4.6 16.6 - - + -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLY 3.3 4.7 - - - -
128A VAL* 3.6 28.3 - - + -
133A TYR* 3.6 18.8 - - + +
156A PRO* 1.3 72.6 - - - +
158A ILE* 1.4 59.9 + - - +
163A PRO* 3.3 4.9 - - - +
164A VAL* 3.0 39.5 + - + -
165A ASP* 2.8 18.7 + - + -
169A PHE* 3.9 10.3 - - + -
207A PHE* 3.4 41.7 - - + -
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ALA* 4.1 15.0 - - + -
126A GLY 2.8 12.2 + - - +
127A VAL* 3.5 26.0 - - + +
128A VAL* 2.9 27.4 + - - +
156A PRO* 4.2 14.6 - - + -
157A VAL* 1.4 78.1 - - - +
159A LYS* 1.3 61.2 + - - +
161A GLY* 3.9 12.1 - - - +
162A ARG* 3.4 21.5 - - - +
163A PRO* 3.8 26.9 - - + -
127B VAL* 5.4 5.8 - - + -
158B ILE* 3.9 28.0 - - + -
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 6.0 0.4 - - - -
128A VAL* 3.7 33.1 - - + +
157A VAL 4.0 0.8 + - - -
158A ILE* 1.3 75.3 - - - +
160A ASP* 1.3 91.5 + - - +
161A GLY 3.0 1.6 + - - -
162A ARG* 2.8 24.6 + - - +
164A VAL* 3.8 27.2 - - + +
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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