Contacts of the strand formed by residues 147 - 155 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ASP* 2.8 31.3 + - - +
145A ASN* 2.9 32.1 + - - +
146A GLN* 1.3 81.7 - - - +
148A ASN* 1.3 66.5 + - - +
149A TYR* 3.2 30.0 - - + +
233A GLU* 3.0 39.7 + - - +
3012A SO4 3.0 40.7 + - - -
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Residues in contact with ASN 148 (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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139A TYR* 3.1 34.2 + - + +
140A VAL 3.2 3.4 - - - +
141A GLN* 3.4 27.4 + - - +
146A GLN 4.5 7.8 + - - -
147A ARG* 1.3 84.0 + - - +
149A TYR* 1.3 62.4 - - - +
233A GLU* 3.4 12.7 + - - +
234A SER 3.3 21.4 + - - +
235A GLU* 4.1 7.5 + - - +
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Residues in contact with TYR 149 (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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1A MET* 3.5 46.7 - - + -
14A LEU* 5.9 0.4 - - + -
139A TYR* 3.4 7.5 - - - -
140A VAL* 2.6 52.8 + - + +
142A ASP* 4.0 17.5 - - + -
145A ASN* 4.0 7.3 + - - -
147A ARG* 3.2 40.8 - - + +
148A ASN* 1.3 72.5 - - - +
150A MET* 1.3 66.1 + - - +
231A SER* 4.8 1.8 - - - -
232A VAL* 3.3 11.0 - - - +
233A GLU* 3.3 44.0 - - + -
234A SER 4.0 1.8 - - - -
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Residues in contact with MET 150 (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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53A PHE* 4.0 12.8 - - + -
69A ILE* 3.6 44.0 - - + +
70A GLU 4.6 1.1 - - - +
71A HIS* 4.4 2.5 - - - -
138A GLY* 3.3 17.0 - - - +
139A TYR* 3.5 28.7 - - - -
149A TYR* 1.3 73.7 - - - +
151A PHE* 1.3 63.5 + - - +
231A SER* 3.3 5.1 - - - -
232A VAL* 3.1 31.7 + - + +
234A SER 3.5 17.3 - - - +
235A GLU 4.1 7.0 - - - +
236A TYR 3.6 19.5 - - - +
237A LEU* 3.6 21.0 - - + +
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Residues in contact with PHE 151 (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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3A ILE* 3.7 23.8 - - + -
16A LEU* 4.9 1.6 - - + -
18A HIS* 4.2 19.7 - + - -
69A ILE* 5.6 0.7 - - - +
135A LYS 4.3 3.1 - - - -
136A ASN 3.5 20.2 - - - -
137A ASN* 2.9 37.0 - - - +
138A GLY* 2.9 38.1 + - - -
139A TYR 4.5 0.4 - - - -
140A VAL* 3.7 25.4 - - + -
150A MET* 1.3 75.9 - - - +
152A GLU* 1.3 68.1 + - - +
153A ARG* 3.8 30.3 - - + -
229A GLN* 4.6 2.7 - - + -
230A PHE 3.2 12.1 - - - +
231A SER* 3.8 11.7 - - - -
237A LEU* 3.7 8.2 - - - +
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Residues in contact with GLU 152 (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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69A ILE* 4.1 3.7 - - + +
120A LEU* 4.2 0.9 - - - +
132A SER* 2.5 34.3 + - - -
136A ASN 3.4 4.3 - - - -
137A ASN* 3.1 25.2 + - + +
151A PHE* 1.3 75.1 - - - +
153A ARG* 1.3 75.0 + - - +
154A LEU* 3.9 9.2 - - + -
228A VAL 3.7 0.9 - - - +
229A GLN* 3.2 3.8 - - - +
230A PHE* 2.9 65.5 + - + -
237A LEU* 3.6 9.0 - - + -
239A TYR* 2.5 32.9 + - + +
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Residues in contact with ARG 153 (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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3A ILE* 4.0 20.2 - - - +
4A SER* 4.1 4.2 - - - -
131A GLY 3.6 8.0 - - - +
132A SER* 3.7 8.0 + - - -
135A LYS 4.0 11.3 + - - -
136A ASN* 2.8 49.6 + - + +
151A PHE* 3.8 12.2 - - + -
152A GLU* 1.3 90.2 + - - +
154A LEU* 1.3 60.7 + - - +
155A ASP* 3.9 3.8 + - - +
223A GLU* 3.0 24.2 + - - -
224A LYS* 3.8 35.6 - - - +
227A LYS* 3.9 13.5 - - + -
228A VAL 3.3 6.1 - - - +
229A GLN* 2.9 32.2 + - + -
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Residues in contact with LEU 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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122A PHE* 3.9 17.0 - - + -
130A THR* 3.8 14.4 - - + +
131A GLY* 3.4 15.9 - - - +
132A SER 4.3 0.2 - - - +
152A GLU* 3.9 10.5 - - + +
153A ARG* 1.3 72.4 - - - +
155A ASP* 1.3 64.9 + - - +
200A TYR* 3.5 25.6 - - - +
206A TYR* 5.5 0.4 - - + +
208A VAL* 4.0 15.9 - - + -
227A LYS* 3.4 1.0 - - - -
228A VAL* 2.8 33.9 + - - +
230A PHE* 3.9 24.0 - - + -
239A TYR* 3.9 29.8 - - + +
241A VAL* 4.9 5.2 - - + -
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Residues in contact with ASP 155 (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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128A ARG* 2.5 33.4 + - - +
129A ILE 5.0 0.2 - - - +
130A THR* 2.9 22.4 + - - +
131A GLY 2.9 19.7 + - - +
133A GLN* 3.3 23.7 + - - +
153A ARG 4.3 1.7 - - - +
154A LEU* 1.3 75.7 - - - +
156A LEU* 1.3 66.3 + - - +
160A GLU* 4.2 1.1 - - - +
206A TYR* 3.5 9.7 + - - -
226A SER 3.8 6.5 - - - +
227A LYS* 3.0 33.3 - - - +
488D GLU* 6.4 0.2 - - + -
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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