Contacts of the strand formed by residues 147 - 155 (chain D) in PDB entry 1XSK
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 ARG 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D ASP* 2.8 33.2 + - - +
145D ASN* 2.8 36.3 + - - +
146D GLN* 1.3 79.6 - - - +
148D ASN* 1.3 64.0 + - - +
149D TYR* 3.3 29.2 - - + +
233D GLU* 3.0 41.1 + - - +
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Residues in contact with ASN 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D TYR* 3.3 33.3 + - + +
140D VAL 3.2 3.4 - - - +
141D GLN* 3.5 25.7 + - - +
146D GLN 4.4 10.0 + - - +
147D ARG* 1.3 81.9 - - - +
149D TYR* 1.3 63.7 + - - +
233D GLU* 3.5 12.4 + - - +
234D SER 3.2 22.2 + - - +
235D GLU* 4.0 9.2 + - - +
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Residues in contact with TYR 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.6 42.6 - - + -
139D TYR* 3.4 7.5 - - - -
140D VAL* 2.5 60.5 + - + -
142D ASP* 3.9 25.6 + - + -
145D ASN* 4.0 7.8 + - - -
147D ARG* 3.3 33.7 - - + +
148D ASN* 1.3 73.6 - - - +
150D MET* 1.3 64.9 + - - +
231D SER* 4.8 2.9 - - - -
232D VAL* 3.4 11.0 - - - +
233D GLU* 3.5 38.1 - - + -
234D SER 4.1 2.0 - - - -
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Residues in contact with MET 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PHE* 4.3 5.4 - - + -
69D ILE* 3.3 55.2 - - + +
70D GLU* 4.6 0.4 - - - -
71D HIS* 4.4 4.5 - - - -
138D GLY 3.4 14.8 - - - +
139D TYR* 3.6 27.1 - - - -
149D TYR* 1.3 72.7 - - - +
151D PHE* 1.3 61.6 + - - +
231D SER* 3.3 3.3 - - - -
232D VAL* 3.2 33.3 + - + +
234D SER 3.7 6.5 + - - +
235D GLU 3.7 9.4 - - - +
236D TYR* 3.5 29.8 - - - +
237D LEU* 3.7 18.1 - - + +
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Residues in contact with PHE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 3.6 21.1 - - + -
16D LEU* 4.4 7.2 - - + -
18D HIS* 3.8 21.3 - + - -
69D ILE* 5.4 1.4 - - - +
135D LYS 4.2 1.8 - - - -
136D ASN 3.4 21.5 - - - -
137D ASN* 3.0 45.0 - - - +
138D GLY* 3.0 25.4 + - - +
139D TYR 4.5 0.2 - - - -
140D VAL* 3.4 26.7 - - + -
150D MET* 1.3 75.5 - - - +
152D GLU* 1.3 65.0 + - - +
153D ARG* 3.9 30.1 - - + -
229D GLN* 4.6 2.0 - - + -
230D PHE 3.3 13.0 - - - +
231D SER* 3.7 12.6 - - - -
237D LEU* 3.7 7.6 - - - +
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Residues in contact with GLU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ILE* 5.8 1.1 - - + +
120D LEU* 4.1 0.3 - - - +
132D SER* 2.8 33.3 + - - -
136D ASN 3.1 7.4 - - - +
137D ASN* 3.0 22.6 + - + +
151D PHE* 1.3 75.3 - - - +
153D ARG* 1.3 79.1 + - - +
154D LEU* 3.7 15.3 - - + -
228D VAL 3.8 1.3 - - - +
229D GLN* 3.3 2.6 - - - +
230D PHE* 2.9 55.9 + - + +
237D LEU* 3.7 8.3 - - + +
239D TYR* 2.7 36.4 + - + +
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 4.1 15.8 - - - +
4D SER* 3.9 7.7 - - - -
131D GLY 3.5 8.5 - - - +
132D SER* 3.7 6.8 - - - -
133D GLN 4.6 0.5 + - - -
135D LYS 4.0 11.5 + - - -
136D ASN* 2.9 45.4 + - + +
151D PHE* 3.9 11.5 - - + -
152D GLU* 1.3 94.5 + - - +
154D LEU* 1.3 62.1 + - - +
155D ASP* 3.8 0.9 + - - +
223D GLU* 3.0 26.3 + - - -
224D LYS* 3.8 33.2 - - - +
227D LYS* 4.0 16.7 - - + +
228D VAL 3.5 5.4 - - - -
229D GLN* 2.6 31.9 + - + -
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PHE* 4.1 12.1 - - + -
130D THR* 3.7 15.0 - - + +
131D GLY* 3.3 18.2 - - - +
152D GLU* 3.7 28.5 - - + +
153D ARG* 1.3 72.5 - - - +
155D ASP* 1.3 64.0 + - - +
156D LEU* 4.4 0.5 - - - +
200D TYR* 3.7 24.9 - - - +
206D TYR* 5.6 1.1 - - + +
208D VAL* 4.3 13.2 - - + -
227D LYS* 3.4 1.5 - - - -
228D VAL* 2.9 32.1 + - - +
230D PHE* 3.9 13.5 - - + -
239D TYR* 3.9 27.6 - - + +
241D VAL* 5.0 5.8 - - + -
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Residues in contact with ASP 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A GLU* 6.5 0.2 - - + -
128D ARG* 2.7 40.3 + - - +
129D ILE 4.9 0.6 - - - +
130D THR* 2.9 21.1 + - - +
131D GLY 2.9 13.8 + - - +
133D GLN* 3.3 21.0 - - - +
153D ARG 3.8 1.3 + - - +
154D LEU* 1.3 75.3 - - - +
156D LEU* 1.3 63.8 + - - +
160D GLU* 4.0 1.0 - - - +
206D TYR* 3.6 10.9 + - - -
226D SER* 3.7 6.1 + - - +
227D LYS* 3.0 34.0 + - - +
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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