Contacts of the strand formed by residues 147 - 155 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP* 2.8 31.0 + - - +
145B ASN* 2.9 39.2 + - - +
146B GLN* 1.3 80.2 - - - +
148B ASN* 1.3 61.9 + - - +
149B TYR* 3.3 29.0 - - + +
233B GLU* 3.1 39.8 + - - +
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Residues in contact with ASN 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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139B TYR* 3.3 36.4 + - + +
140B VAL 3.2 3.6 - - - +
141B GLN* 3.5 23.9 + - - +
142B ASP 4.1 0.3 + - - +
146B GLN 4.5 8.8 + - - +
147B ARG* 1.3 81.1 - - - +
149B TYR* 1.3 62.5 + - - +
233B GLU* 3.4 21.9 - - - +
234B SER 3.5 12.2 + - - +
235B GLU* 3.9 7.3 + - - +
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Residues in contact with TYR 149 (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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1B MET* 3.7 43.8 - - + -
14B LEU* 5.8 0.2 - - + -
139B TYR* 3.4 7.3 - - - -
140B VAL* 2.6 53.6 + - + +
142B ASP* 4.0 13.4 + - + -
145B ASN* 4.0 7.4 + - - -
147B ARG* 3.3 46.9 - - + +
148B ASN* 1.3 74.1 - - - +
150B MET* 1.3 64.7 + - - +
231B SER* 4.8 2.9 - - - -
232B VAL* 3.3 13.0 - - - +
233B GLU* 3.5 37.4 + - + -
234B SER 4.0 3.4 - - - -
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Residues in contact with MET 150 (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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53B PHE* 4.2 5.2 - - + -
69B ILE* 3.4 52.9 - - + +
70B GLU 4.7 1.1 - - - +
71B HIS* 4.4 4.7 - - - -
138B GLY 3.3 18.2 - - - +
139B TYR* 3.5 27.8 - - - -
149B TYR* 1.3 73.6 - - - +
151B PHE* 1.3 60.6 + - - +
230B PHE 4.1 0.2 - - - +
231B SER* 3.4 3.1 - - - -
232B VAL* 3.2 32.8 + - + +
234B SER 3.5 17.9 - - - +
235B GLU 4.2 7.0 - - - +
236B TYR 3.5 20.6 - - - +
237B LEU* 3.6 18.5 - - + +
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Residues in contact with PHE 151 (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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3B ILE* 3.5 28.3 - - + -
16B LEU* 4.8 3.8 - - + -
18B HIS* 3.8 22.0 - + - -
69B ILE* 5.5 1.2 - - - +
135B LYS 4.3 1.6 - - - -
136B ASN 3.5 22.2 - - - -
137B ASN* 3.1 19.0 - - - +
138B GLY* 3.0 54.9 + - - +
139B TYR 4.3 0.9 - - - -
140B VAL* 3.6 25.4 - - + -
150B MET* 1.3 77.4 - - - +
152B GLU* 1.3 64.6 + - - +
153B ARG* 3.9 30.1 - - + -
229B GLN* 4.7 2.5 - - + -
230B PHE 3.4 12.1 - - - +
231B SER* 4.0 6.3 - - - -
237B LEU* 3.8 6.9 - - - +
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Residues in contact with GLU 152 (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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69B ILE* 6.1 1.3 - - + +
120B LEU* 4.0 1.4 - - - +
132B SER* 2.8 33.0 + - - -
136B ASN 3.1 4.4 - - - +
137B ASN* 3.1 24.8 + - + +
151B PHE* 1.3 76.7 - - - +
153B ARG* 1.3 77.3 + - - +
154B LEU* 4.0 9.9 - - + -
228B VAL 3.8 1.1 - - - +
229B GLN* 3.3 3.5 - - - +
230B PHE* 3.0 63.8 + - + -
237B LEU* 3.7 7.0 - - + -
239B TYR* 2.5 31.8 + - + +
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Residues in contact with ARG 153 (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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3B ILE* 4.1 15.0 - - - +
4B SER* 3.9 7.5 - - - -
131B GLY 3.7 8.1 - - - +
132B SER* 3.8 7.1 + - - -
135B LYS 3.9 11.9 + - - -
136B ASN* 2.9 44.5 + - + +
151B PHE* 3.9 13.3 - - + -
152B GLU* 1.3 93.8 + - - +
154B LEU* 1.3 63.1 + - - +
155B ASP* 3.7 3.8 + - - +
223B GLU* 3.0 24.9 + - - -
224B LYS* 3.7 37.9 - - - +
227B LYS* 4.0 12.3 - - + -
228B VAL 3.5 5.8 - - - -
229B GLN* 2.9 29.2 + - + -
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Residues in contact with LEU 154 (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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122B PHE* 4.1 17.9 - - + -
130B THR* 3.8 13.0 - - + +
131B GLY* 3.6 22.4 - - - +
132B SER 4.1 0.4 - - - +
152B GLU* 4.0 25.4 - - + +
153B ARG* 1.3 71.8 - - - +
155B ASP* 1.3 66.9 + - - +
156B LEU* 4.4 0.5 - - - +
200B TYR* 3.7 23.7 + - - +
206B TYR* 5.6 0.7 - - + +
208B VAL* 4.1 16.8 - - + -
227B LYS* 3.5 1.5 - - - -
228B VAL* 3.0 31.3 + - - +
230B PHE* 4.1 11.7 - - + -
239B TYR* 3.9 20.9 - - + +
241B VAL* 4.8 5.6 - - + -
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Residues in contact with ASP 155 (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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128B ARG* 2.7 37.7 + - - +
130B THR* 2.9 24.3 + - - +
131B GLY 2.9 20.5 + - - +
133B GLN* 2.7 26.0 + - - +
136B ASN* 4.4 0.7 + - - -
153B ARG 4.4 1.7 - - - +
154B LEU* 1.3 74.4 - - - +
156B LEU* 1.3 64.1 + - - +
160B GLU* 4.0 0.7 - - - +
200B TYR* 5.6 0.2 + - - -
204B ARG* 5.1 2.0 - - - +
206B TYR* 3.6 10.7 + - - -
226B SER 3.7 4.9 - - - -
227B LYS* 2.6 31.3 + - - +
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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