Contacts of the strand formed by residues 127 - 137 (chain B) in PDB entry 3AA6
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 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B ARG* 4.9 2.9 + - - -
123B ASP* 4.1 4.3 - - - +
124B LEU* 3.0 25.3 + - - +
125B ASP 3.6 0.4 + - - -
126B HIS* 1.3 79.2 - - - +
128B PHE* 1.3 66.7 + - - +
156B VAL 3.4 8.5 - - - -
157B GLN* 4.2 1.2 - - - +
158B GLU* 3.5 22.6 - - - +
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ARG* 4.2 8.5 - - - +
93B LEU* 3.7 24.7 - - + -
96B LEU* 3.6 25.1 - - + -
121B LEU* 4.5 13.0 - - + -
122B TRP 3.4 14.1 - - - +
124B LEU* 3.4 12.4 - - - +
127B GLY* 1.3 75.2 - - - +
129B ALA* 1.3 69.1 + - - +
154B VAL* 5.6 1.1 - - + -
156B VAL* 2.7 70.9 + - + +
158B GLU* 3.9 14.6 - - - -
209B HIS* 3.6 39.0 - + + -
213B ILE* 4.2 12.1 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 3.3 6.9 - - - +
122B TRP* 2.9 65.3 + - + +
124B LEU* 3.9 5.1 - - + +
128B PHE* 1.3 82.5 - - - +
130B GLY* 1.3 58.5 + - - +
154B VAL* 3.1 14.4 - - - +
155B GLU* 4.4 0.2 - - - -
494C PRO* 3.7 17.0 - - + -
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B TYR 3.2 11.9 - - - -
121B LEU* 3.6 13.5 - - - -
122B TRP* 3.7 6.3 - - - -
129B ALA* 1.3 76.6 - - - +
131B VAL* 1.3 61.3 + - - +
132B ILE* 4.9 1.1 - - - -
153B VAL* 3.3 6.4 - - - +
154B VAL* 2.9 41.7 + - - +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TYR* 3.6 36.6 - - + -
118B SER 3.7 0.3 - - - +
119B VAL* 3.2 8.0 - - - +
120B TYR* 2.9 58.3 + - + +
122B TRP* 4.5 2.2 - - + -
130B GLY* 1.3 74.1 - - - +
132B ILE* 1.3 63.5 + - - +
133B LEU* 3.3 30.3 - - + -
151B ILE* 4.0 6.5 - - + -
152B HIS 3.1 10.3 - - - +
153B VAL* 3.9 17.3 - - + -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PHE* 3.7 46.9 - - + -
117B SER* 6.2 0.2 - - - -
118B SER 3.7 2.5 - - - +
119B VAL* 4.1 16.2 - - + -
121B LEU* 6.1 1.1 - - + -
130B GLY* 4.9 0.4 - - - -
131B VAL* 1.3 80.7 - - - +
133B LEU* 1.3 65.6 + - - +
134B ILE* 4.7 7.4 - - + -
150B SER 3.7 1.4 - - - +
152B HIS* 2.8 61.5 + - + +
154B VAL* 4.3 13.7 - - + -
213B ILE* 3.8 27.8 - - + -
217B VAL* 4.0 10.5 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 4.0 12.6 - - + -
60B LEU* 3.6 28.5 - - + +
62B CYS* 3.5 27.1 - - - -
117B SER* 3.2 6.6 - - - -
118B SER 2.8 37.4 + - - +
120B TYR* 3.6 27.8 - - + -
131B VAL* 3.3 28.5 - - + -
132B ILE* 1.3 75.9 - - - +
134B ILE* 1.3 68.2 + - - +
150B SER 3.4 6.5 - - - +
151B ILE* 3.9 21.5 - - + -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 3.5 4.5 - - - +
104B PHE* 5.4 1.1 - - + +
107B TYR* 3.6 29.2 - - + -
108B ARG* 4.1 11.9 - - + -
112B PHE* 3.8 35.7 - - + -
115B GLY* 5.9 0.2 - - - -
116B VAL 3.4 9.2 - - - +
117B SER* 4.2 10.5 - - - -
132B ILE* 4.7 13.9 - - + -
133B LEU* 1.3 80.8 - - - +
135B LYS* 1.3 66.9 + - - +
136B LYS* 5.2 0.2 - - + -
148B TRP* 3.8 1.3 - - - +
149B ASP* 3.3 5.0 - - - -
150B SER* 2.8 44.4 + - - +
152B HIS* 4.8 1.8 - - + -
221B GLU* 3.6 23.1 - - - +
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PRO* 4.7 5.7 - - - +
47B LEU* 3.4 24.6 + - + +
49B ILE* 4.0 25.5 - - + +
60B LEU* 3.5 26.0 - - + +
115B GLY* 3.1 3.5 - - - -
116B VAL* 2.9 32.6 + - + +
134B ILE* 1.3 75.3 - - - +
136B LYS* 1.3 60.9 + - - +
137B ALA* 5.4 1.8 - - + +
147B CYS* 2.8 32.9 - - - -
148B TRP 3.4 8.5 - - - +
149B ASP* 2.6 32.2 + - - +
176B TRP* 5.1 1.4 - - - -
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ALA 3.0 26.6 + - - -
258A LEU* 3.4 25.2 + - + +
112B PHE* 2.9 43.5 + - + +
113B GLU* 4.9 2.3 + - - +
114B GLY* 3.9 7.2 - - - +
115B GLY* 3.7 26.7 - - - +
134B ILE* 4.3 0.4 - - + -
135B LYS* 1.3 76.3 - - - +
137B ALA* 1.3 74.9 + - - +
138B GLY* 5.3 1.1 - - - -
147B CYS* 3.4 4.8 - - - -
148B TRP* 2.8 44.9 + - + +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LEU* 3.9 1.8 - - - -
49B ILE* 6.5 1.1 - - + -
115B GLY* 5.3 1.0 - - - -
135B LYS* 5.4 2.3 - - + +
136B LYS* 1.3 91.1 - - - +
138B GLY* 1.3 68.1 + - - +
139B ASP 4.0 0.2 + - - -
146B GLY 3.6 7.4 - - - +
147B CYS* 4.3 9.8 - - - -
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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