Contacts of the strand formed by residues 142 - 148 (chain B) in PDB entry 1XUQ
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 LEU 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.9 19.3 - - + -
105B ALA* 3.6 42.4 - - + +
106B ILE* 3.7 20.4 - - + +
109B LYS* 3.6 33.6 - - + +
110B PHE* 4.1 12.1 - - + -
135B LEU* 4.0 17.9 - - + -
136B VAL 3.2 15.7 - - - +
137B VAL* 4.3 6.7 - - + -
140B GLY 4.3 1.3 + - - +
141B GLU* 1.3 72.9 - - - +
143B GLU* 1.3 65.2 + - - +
161B VAL* 4.7 1.6 - - + -
199B TYR* 3.9 21.1 - - + +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LYS* 5.3 7.0 - - - +
110B PHE* 4.6 2.2 - - - -
135B LEU* 3.5 7.0 - - - +
136B VAL* 2.8 43.9 + - + +
138B ASN* 3.1 26.7 + - + +
139B ASN* 4.9 3.1 + - - -
141B GLU* 4.2 11.1 - - + +
142B LEU* 1.3 79.0 - - - +
144B VAL* 1.3 61.1 + - - +
145B THR* 4.1 9.7 - - + +
158B LYS* 3.0 28.2 + - - -
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 3.8 15.8 - - + -
116B PHE* 3.7 31.2 - - + -
119B GLU* 3.7 43.0 + - + +
120B PHE* 4.1 10.1 - - + +
123B ALA* 3.6 29.8 - - + -
134B TRP 3.3 10.1 - - - +
135B LEU* 4.6 0.9 - - + -
143B GLU* 1.3 74.3 - - - +
145B THR* 1.3 66.6 + - - +
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Residues in contact with THR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 4.2 10.2 - - - +
133B ALA* 3.7 1.7 - - - -
134B TRP* 2.9 50.1 + - - +
136B VAL* 4.1 19.6 - - + +
143B GLU* 3.9 21.0 + - + +
144B VAL* 1.3 80.0 - - - +
146B SER* 1.3 67.5 + - - +
147B THR* 5.0 2.5 - - - +
153B PRO* 4.9 2.6 - - - +
156B GLU* 5.7 3.4 + - - +
158B LYS* 4.5 9.4 - - + +
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 3.9 23.5 + - - +
127B ARG* 2.9 39.7 + - - +
132B TRP 3.1 17.3 - - - -
133B ALA* 4.4 1.6 - - - -
134B TRP* 4.3 1.1 - - - -
145B THR* 1.3 78.7 - - - +
147B THR* 1.3 65.4 + - - +
148B PRO* 4.6 0.3 - - - +
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Residues in contact with THR 147 (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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127B ARG* 3.6 7.7 + - - -
131B GLY* 3.1 4.9 - - - -
132B TRP* 3.0 35.2 + - - +
134B TRP* 3.0 25.7 + - + +
145B THR* 5.0 3.1 - - - +
146B SER* 1.3 79.5 - - - +
148B PRO* 1.3 67.7 + - + +
151B ASP* 2.9 33.4 + - + +
152B SER 4.6 0.2 - - - -
153B PRO* 4.3 9.6 - - + -
156B GLU* 3.7 23.3 - - - +
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Residues in contact with PRO 148 (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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74B ARG* 5.7 0.2 - - - +
127B ARG* 3.5 28.0 - - - +
130B SER 3.7 5.4 - - - +
146B SER 4.6 0.4 - - - +
147B THR* 1.3 87.1 - - + +
149B ASN* 1.3 70.9 + - - +
151B ASP* 2.9 53.7 + - + +
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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