Contacts of the strand formed by residues 153 - 162 (chain A) in PDB entry 2XB3
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 LYS 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP* 4.8 8.3 - - - +
71A VAL* 3.8 19.3 - - + -
72A ASN 3.1 12.1 - - - +
73A THR* 3.9 18.6 - - + +
74A VAL* 4.5 0.4 - - - +
149A VAL* 3.2 8.1 - - - +
150A SER 3.1 25.8 + - - +
151A ARG* 3.2 24.0 + - - +
152A GLY* 1.3 85.8 - - - +
154A VAL* 1.3 63.2 + - - +
155A TYR* 3.2 37.2 - - + -
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Residues in contact with VAL 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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70A VAL* 3.7 1.0 - - - +
71A VAL* 3.5 5.2 - - - +
72A ASN* 2.8 37.9 + - + +
74A VAL* 3.3 28.3 - - + -
83A LEU* 4.7 16.4 - - + -
147A ILE* 3.6 26.0 - - + -
148A ALA 3.8 4.5 - - - +
149A VAL* 4.4 15.3 - - + -
153A LYS* 1.3 75.2 - - - +
155A TYR* 1.3 63.9 + - - +
156A THR* 4.2 6.7 + - - +
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Residues in contact with TYR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP 2.8 28.0 + - - -
35A GLY 4.6 2.0 - - - -
36A TYR* 3.8 23.8 - + - -
69A VAL* 4.9 1.3 - - + -
70A VAL 3.4 4.9 - - - +
71A VAL* 3.7 25.8 - - + -
146A SER 3.4 1.7 - - - +
147A ILE* 3.1 23.6 - - - -
148A ALA 3.0 21.4 + - - +
150A SER* 3.5 29.1 + - - -
151A ARG* 3.4 14.2 + - - -
153A LYS* 3.2 35.9 - - + -
154A VAL* 1.3 77.3 - - - +
156A THR* 1.3 61.2 + - - +
157A LEU 4.1 0.4 - - - -
180A PHE* 4.0 7.4 - - + -
182A VAL* 3.9 24.0 - - + -
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Residues in contact with THR 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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68A SER 3.5 1.6 - - - +
69A VAL* 3.3 4.4 - - - +
70A VAL* 2.8 52.7 + - + +
93A LEU* 4.6 16.8 - - + +
145A SER* 4.0 7.0 - - - +
146A SER 3.4 2.2 - - - -
147A ILE* 3.6 28.9 - - + +
154A VAL* 4.2 6.1 + - - +
155A TYR* 1.3 72.4 - - - +
157A LEU* 1.3 64.1 + - - +
158A SER* 3.6 21.1 + - - +
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Residues in contact with LEU 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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38A PHE* 3.5 46.9 - - + -
67A VAL* 3.7 22.0 - - + -
68A SER 3.3 5.8 - - - +
69A VAL* 4.1 4.0 - - + +
145A SER* 3.1 6.1 - - - -
146A SER 2.9 32.0 + - - +
156A THR* 1.3 73.9 - - - +
158A SER* 1.3 66.0 + - - +
159A VAL* 4.4 2.0 - - + -
176A ILE* 4.6 3.6 - - + +
177A VAL* 4.0 36.6 - - + -
180A PHE* 3.7 34.0 - - + -
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Residues in contact with SER 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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66A ASN* 4.1 1.4 - - - +
67A VAL* 3.2 2.1 - - - -
68A SER* 2.8 45.2 + - - -
70A VAL* 6.0 0.9 - - - +
93A LEU* 5.8 0.5 - - - +
98A ILE* 5.0 6.3 - - - +
127A TYR* 3.5 10.5 + - - -
143A ASN* 5.1 3.4 - - - -
144A LEU 3.4 6.5 - - - -
145A SER* 2.7 22.4 + - - -
156A THR* 3.6 11.5 - - - +
157A LEU* 1.3 77.1 + - - +
159A VAL* 1.3 64.3 + - - +
160A SER* 5.6 0.7 - - - -
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Residues in contact with VAL 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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44A TRP* 5.5 0.2 - - + -
66A ASN 3.3 6.5 - - - +
67A VAL* 3.6 20.2 - - + -
143A ASN* 3.3 6.4 + - - +
144A LEU* 3.0 43.3 + - + +
157A LEU* 4.4 2.5 - - + -
158A SER* 1.3 70.5 - - - +
160A SER* 1.3 63.1 + - - +
173A PHE* 3.7 24.2 - - + +
176A ILE* 3.5 39.5 - - + -
177A VAL* 3.3 20.0 - - + -
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Residues in contact with SER 160 (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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65A GLU* 3.3 6.1 - - - -
66A ASN* 3.0 41.4 + - - -
141A ARG* 2.8 32.6 + - - +
142A HIS 3.4 6.3 - - - -
143A ASN* 3.2 29.1 + - - -
158A SER* 5.6 0.7 - - - -
159A VAL* 1.3 76.8 - - - +
161A ALA* 1.3 62.6 + - - +
173A PHE* 3.6 7.4 - - - -
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Residues in contact with ALA 161 (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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65A GLU* 4.4 5.8 - - + -
141A ARG* 3.3 9.9 - - - +
142A HIS 2.8 31.4 + - - -
160A SER* 1.3 76.0 + - - +
162A PRO* 1.3 78.4 - - + +
165A ARG* 4.5 2.9 - - + -
166A TRP* 4.4 7.9 - - + -
169A VAL* 3.8 28.9 - - + -
173A PHE* 3.8 9.0 - - + -
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Residues in contact with PRO 162 (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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62A GLU* 5.1 3.8 - - - +
64A THR* 3.5 30.1 - - + -
65A GLU* 4.0 14.6 - - + -
139A GLN* 3.8 21.5 - - - +
140A GLN 3.7 7.2 - - - +
141A ARG* 3.7 4.2 - - - +
142A HIS 4.5 0.2 - - - -
161A ALA* 1.3 90.0 - - + +
163A GLU* 1.3 66.4 + - - +
164A GLU* 4.2 9.2 - - + +
165A ARG* 2.8 30.1 + - + +
166A TRP* 3.3 7.4 + - - -
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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