Contacts of the strand formed by residues 127 - 134 (chain A) in PDB entry 1IXB
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ARG* 4.0 3.6 - - - -
125A GLY 4.0 1.4 + - - -
126A SER* 1.3 76.4 - - - +
128A TRP* 1.3 60.8 - - - -
143A THR 3.2 12.6 - - - -
145A ASN 3.5 14.4 - - - -
168A VAL* 2.9 38.0 + - - +
169A TRP* 3.4 13.3 - - - +
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Residues in contact with TRP 128 (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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80A ASN* 3.5 43.5 - - + +
81A HIS* 3.8 9.9 - + - -
83A LEU* 5.7 0.4 - - + -
84A PHE* 3.8 25.6 - + + -
123A ARG* 4.3 1.0 - - - +
127A GLY* 1.3 74.1 - - - -
129A ALA* 1.3 58.9 + - - +
130A TRP* 3.4 39.7 - + + +
142A SER* 3.1 8.9 - - - -
143A THR* 2.9 31.4 + - - +
145A ASN 3.2 22.0 + - - -
146A GLN* 2.9 21.9 + - - -
147A ASP 4.4 3.6 - - - -
165A GLY 4.8 1.6 - - - -
166A LEU 3.4 13.7 - - - -
167A ASP* 3.5 52.7 - - + -
168A VAL* 4.0 5.1 - - - +
169A TRP* 3.9 4.9 - - - +
206A MH2 3.8 5.8 - - - -
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Residues in contact with ALA 129 (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 PHE* 3.8 18.0 - - + +
119A ALA* 4.4 5.6 - - + +
120A ALA* 3.7 41.1 - - + +
128A TRP* 1.3 72.8 - - - +
130A TRP* 1.3 64.4 + - - +
141A VAL 3.7 6.3 - - - +
142A SER* 4.2 0.7 - - - -
165A GLY* 3.1 3.6 - - - -
166A LEU* 2.8 35.6 + - + +
168A VAL* 4.8 1.2 - - + +
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Residues in contact with TRP 130 (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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80A ASN* 3.4 34.5 - - + -
83A LEU* 4.1 22.7 - - + -
116A PHE* 3.7 6.5 - - - -
128A TRP* 3.4 40.6 - + + +
129A ALA* 1.3 76.7 - - - +
131A LEU* 1.3 60.4 + - - +
132A VAL* 3.9 17.4 + - + -
140A VAL* 3.3 9.2 - - - +
141A VAL* 2.8 45.1 + - + +
142A SER* 4.1 1.1 - - - -
143A THR* 2.9 27.5 + - + -
147A ASP 4.0 4.3 - - - -
148A SER* 4.8 1.3 - - - -
149A PRO* 3.5 28.0 - - + +
162A PRO* 3.7 26.0 - - + -
164A MET 3.6 15.3 - - - +
165A GLY* 3.9 8.5 - - - -
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Residues in contact with LEU 131 (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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98A LEU* 4.7 4.9 - - + -
102A ILE* 4.2 24.0 - - + -
106A PHE* 4.2 9.0 - - + -
112A PHE* 3.9 27.4 - - + -
116A PHE* 3.9 2.8 - - - -
130A TRP* 1.3 71.3 - - - +
132A VAL* 1.3 53.6 + - - +
138A LEU* 4.1 25.6 - - + -
139A ALA 3.5 15.0 - - - +
140A VAL* 4.8 0.4 - - - +
162A PRO* 3.6 1.7 - - - +
163A ILE* 2.8 55.0 + - + +
164A MET* 3.1 36.1 + - + +
194A TRP* 4.7 3.8 - - + -
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Residues in contact with VAL 132 (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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130A TRP* 3.9 5.1 - - + -
131A LEU* 1.3 76.9 - - - +
133A LEU* 1.3 60.1 + - - +
134A LYS* 4.1 9.0 - - + -
138A LEU* 3.2 10.6 - - - +
139A ALA* 2.8 56.6 + - + +
141A VAL* 3.8 20.2 - - + -
149A PRO* 3.7 33.4 - - + -
159A SER 3.5 19.1 - - - +
160A GLY 4.0 4.5 - - - +
161A PHE 3.1 11.2 - - - +
162A PRO* 4.0 2.2 - - + -
163A ILE* 4.4 0.9 - - - -
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Residues in contact with LEU 133 (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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104A ARG* 5.5 2.0 - - - +
132A VAL* 1.3 72.7 - - - +
134A LYS* 1.3 61.2 + - - +
135A GLY 3.5 26.5 + - - +
136A ASP* 4.2 2.2 - - - -
137A LYS* 3.8 23.8 - - - +
138A LEU* 3.9 17.0 - - + +
160A GLY* 3.4 1.6 - - - -
161A PHE* 2.9 38.2 + - + +
163A ILE* 4.2 8.7 - - + +
201A PHE* 4.2 15.3 - - + -
204A LYS* 3.6 41.3 - - + +
205A LYS* 4.0 8.5 - - - +
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Residues in contact with LYS 134 (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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132A VAL* 4.1 7.6 - - + -
133A LEU* 1.3 77.0 - - - +
135A GLY* 1.3 58.3 + - - +
136A ASP 3.0 9.7 + - - -
137A LYS* 2.9 27.1 + - + +
139A ALA* 4.0 21.4 - - + +
141A VAL* 4.3 13.2 - - - +
153A GLU* 4.3 12.7 + - - -
159A SER* 3.6 33.8 - - - +
160A GLY* 4.1 4.5 - - - -
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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