Contacts of the strand formed by residues 300 - 305 (chain A) in PDB entry 1P3W
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 ILE 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 3.6 25.1 - - - +
153A VAL* 4.3 3.1 - - + -
154A ASN 3.6 22.2 - - - +
155A ASN 4.1 3.4 - - - +
156A GLU 3.8 13.2 - - - +
157A ILE* 3.8 9.3 - - - +
158A GLY* 3.6 28.5 - - - +
183A GLN* 3.9 12.6 - - + +
274A ARG* 4.1 10.3 + - - +
297A ALA* 3.9 21.3 + - + +
298A PRO 3.6 0.8 - - - -
299A ASN* 1.3 92.9 + - - +
301A LEU* 1.3 69.7 - - - +
354A ARG* 4.4 9.2 - - + -
355A PHE 3.5 2.2 - - - -
356A SER* 4.5 1.3 - - - -
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Residues in contact with LEU 301 (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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274A ARG* 4.3 18.4 - - + +
277A LEU* 3.6 34.8 - - + -
278A TRP* 4.0 39.0 - - + +
281A ILE* 4.6 3.1 - - + -
289A LEU* 4.3 24.2 - - + -
293A LEU* 5.2 2.5 - - + -
300A ILE* 1.3 79.5 - - - +
302A ASN* 1.3 60.4 + - - +
303A VAL* 4.0 9.6 - - + -
354A ARG* 3.4 0.7 - - - -
355A PHE* 2.6 57.4 + - + +
357A LEU* 6.3 1.8 - - + -
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Residues in contact with ASN 302 (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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156A GLU* 3.0 36.5 + - - +
157A ILE* 3.9 14.4 + - - +
289A LEU* 3.7 2.7 - - - +
290A ASN* 2.7 72.7 + - - +
300A ILE* 4.3 1.6 - - - +
301A LEU* 1.3 73.4 - - - +
303A VAL* 1.3 62.5 + - - +
324A SER 5.5 3.8 + - - -
339A LEU* 4.0 12.5 - - - +
352A SER* 4.1 8.8 - - - -
353A ILE 3.3 8.2 - - - +
354A ARG* 3.8 14.4 - - - +
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Residues in contact with VAL 303 (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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278A TRP* 3.4 36.8 - - + -
281A ILE* 4.3 5.6 - - + -
287A VAL* 5.5 1.3 - - + -
288A TYR 3.1 11.2 - - - +
289A LEU* 4.2 2.9 - - - -
290A ASN* 3.9 2.5 - - - +
301A LEU* 4.0 17.0 - - + -
302A ASN* 1.3 79.7 + - - +
304A SER* 1.3 62.5 + - - +
305A PHE* 3.3 34.8 - - + -
352A SER* 3.3 0.7 - - - -
353A ILE 2.8 32.5 + - - +
355A PHE* 3.9 16.8 - - + -
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Residues in contact with SER 304 (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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287A VAL* 3.4 5.4 - - - +
288A TYR* 2.8 41.7 + - - +
290A ASN* 2.8 22.3 + - - +
303A VAL* 1.3 73.4 - - - +
305A PHE* 1.3 63.4 + - - +
306A ASN 3.9 1.1 + - - -
344A LEU* 4.7 6.1 - - - +
348A LEU* 3.7 29.5 + - - -
351A SER 3.5 4.5 - - - -
352A SER* 2.4 24.5 + - - -
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Residues in contact with PHE 305 (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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281A ILE* 4.7 4.7 - - + -
284A ILE* 4.8 2.0 - - + -
286A GLU 3.9 4.0 - - - -
287A VAL* 3.7 24.9 - - + -
303A VAL* 3.3 36.8 - - + -
304A SER* 1.3 72.7 - - - +
306A ASN* 1.3 60.1 + - - +
308A VAL* 2.8 31.5 - - + +
313A LEU* 3.8 11.9 - - + -
317A LEU* 5.8 1.6 - - + -
348A LEU* 3.9 1.1 - - - -
351A SER* 2.9 32.3 + - - +
353A ILE* 4.0 17.7 - - + -
355A PHE* 4.6 7.4 - + - -
373A VAL* 3.7 32.1 - - + -
377A ILE* 3.3 33.9 - - + -
381A ARG* 4.4 4.5 - - - +
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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