Contacts of the strand formed by residues 238 - 247 (chain A) in PDB entry 1P4J
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 VAL 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 4.1 22.4 - - + +
66A ARG* 3.7 27.6 - - + -
67A TRP* 3.5 30.4 - - + +
70A THR* 3.1 15.1 + - - +
71A GLN* 3.3 16.3 + - - -
102A LEU* 5.6 0.9 - - + -
229A PRO* 3.6 31.9 - - + -
230A VAL 3.4 9.9 - - - +
231A PRO* 4.3 4.3 - - + -
236A ASN 4.5 1.3 - - - +
237A VAL* 1.3 79.9 - - - +
239A ASN* 1.3 64.0 + - - +
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Residues in contact with ASN 239 (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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67A TRP* 3.6 2.4 + - - -
71A GLN* 4.0 3.8 - - - +
74A TYR* 2.7 31.8 + - - -
144A LEU 5.2 0.6 + - - +
147A MET* 4.0 2.0 + - - +
148A ALA* 3.4 27.3 - - + +
152A LEU 3.0 22.6 + - - -
154A ALA* 3.6 21.6 + - - +
229A PRO* 3.6 5.2 - - - +
230A VAL* 2.8 43.0 + - + +
237A VAL* 3.7 6.8 - - - +
238A VAL* 1.3 77.2 - - - +
240A THR* 1.3 64.6 + - - +
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Residues in contact with THR 240 (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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67A TRP* 3.0 21.6 + - + -
71A GLN* 3.5 14.7 + - - +
144A LEU* 5.7 0.7 - - - +
154A ALA 3.9 3.5 + - - +
155A TYR* 3.4 27.6 - - + +
156A GLY 3.1 20.1 + - - +
227A ASP* 3.8 32.3 - - + +
228A THR 3.7 4.0 - - - +
230A VAL* 4.3 4.4 - - - +
239A ASN* 1.3 77.9 - - - +
241A MET* 1.3 74.0 + - - +
242A ARG* 4.0 7.6 + - + +
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Residues in contact with MET 241 (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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89A PHE* 3.9 31.4 - - + -
91A MET* 4.0 26.9 - - + -
131A LEU* 6.0 0.4 - - + -
144A LEU* 4.0 17.7 - - + -
156A GLY 3.3 12.3 - - - +
226A TYR 3.6 2.1 - - - +
227A ASP* 3.5 1.7 - - - -
228A THR* 3.0 58.5 + - + +
230A VAL* 4.0 12.1 - - + +
240A THR* 1.3 74.3 - - - +
242A ARG* 1.3 59.5 + - - +
243A LEU* 3.8 33.0 + - + +
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Residues in contact with ARG 242 (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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155A TYR* 6.0 1.3 - - + +
156A GLY 2.7 10.3 + - - +
157A TYR* 3.3 30.4 - - + -
158A GLY 3.1 21.3 + - - +
196A PHE* 4.0 33.2 - - - +
225A PRO* 3.4 29.8 - - + +
226A TYR 3.5 3.4 - - - +
227A ASP* 2.7 38.6 + - - +
240A THR* 4.0 7.3 - - + +
241A MET* 1.3 74.0 - - - +
243A LEU* 1.3 62.6 + - - +
244A TRP* 4.1 8.1 + - + -
306A ASP* 2.6 44.7 + - - -
309A ARG* 4.2 3.4 - - - +
310A ARG* 3.9 15.1 - - - +
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Residues in contact with LEU 243 (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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89A PHE* 4.0 12.6 - - + -
131A LEU* 3.7 29.2 - - + -
158A GLY* 3.4 31.6 - - - +
159A ILE 3.8 5.6 - - - +
160A ARG* 3.6 24.0 - - + +
182A TRP* 5.8 2.7 - - + -
224A MET 3.8 0.2 - - - +
225A PRO* 3.6 1.5 - - - +
226A TYR* 2.9 39.3 + - + +
228A THR* 5.3 3.1 - - - +
241A MET* 3.8 38.8 - - + +
242A ARG* 1.3 75.6 - - - +
244A TRP* 1.3 63.2 + - - +
245A SER 3.9 0.2 + - - -
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Residues in contact with TRP 244 (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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157A TYR* 3.5 29.3 - + - -
158A GLY 2.9 27.8 + - - +
159A ILE* 3.6 11.6 - - - +
160A ARG* 3.0 20.2 + - - -
196A PHE 4.2 5.4 - - - -
198A LEU* 3.9 21.5 - - + -
223A ALA* 3.6 26.7 - - + -
224A MET 3.5 2.5 - - - -
225A PRO* 3.5 41.5 - - + -
242A ARG* 4.1 4.0 - - - -
243A LEU* 1.3 74.1 - - - +
245A SER* 1.3 58.7 + - - +
298A PHE* 3.7 23.0 - - + -
299A VAL* 4.3 9.9 - - + -
302A ALA* 3.5 32.8 - - + -
303A THR* 3.2 24.2 + - - +
306A ASP* 3.9 13.0 - - - -
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Residues in contact with SER 245 (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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160A ARG* 4.1 19.8 + - - -
223A ALA* 3.5 2.4 - - - -
224A MET* 2.8 44.4 + - - +
226A TYR* 3.6 23.8 + - - -
244A TRP* 1.3 73.7 - - - +
246A ALA* 1.3 67.2 + - - +
247A LYS* 3.7 1.9 + - - +
276A SER* 3.9 10.0 + - - -
298A PHE* 3.7 2.5 - - - -
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Residues in contact with ALA 246 (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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221A VAL* 4.2 2.9 - - + -
222A LEU 3.5 5.2 - - - -
245A SER* 1.3 77.0 + - - +
247A LYS* 1.3 64.0 + - - +
272A ALA 3.8 21.8 - - - +
273A GLU* 3.9 19.2 - - - +
275A ILE* 3.9 15.0 - - + -
276A SER* 2.9 21.2 + - - +
298A PHE* 3.6 17.7 - - + -
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Residues in contact with LYS 247 (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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197A THR* 5.9 0.4 - - + -
221A VAL* 3.8 4.3 - - - +
222A LEU* 2.7 58.7 + - + +
224A MET* 4.5 35.4 - - + -
245A SER* 4.7 3.4 - - - +
246A ALA* 1.3 77.5 - - - +
248A ALA* 1.3 62.5 + - - +
269A ARG* 4.3 15.0 - - - +
273A GLU* 3.6 18.7 + - - +
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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