Contacts of the strand formed by residues 300 - 305 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B SER* 3.6 24.5 - - - +
153B VAL* 4.3 3.6 - - + -
154B ASN 3.6 22.2 - - - +
155B ASN 4.1 3.6 - - - +
156B GLU 3.7 22.9 - - - +
157B ILE* 3.8 7.9 - - - +
158B GLY* 3.6 22.1 - - - +
183B GLN* 4.0 13.2 - - - +
274B ARG* 4.2 9.0 + - - -
297B ALA* 3.7 20.1 + - + +
298B PRO 3.7 0.4 - - - -
299B ASN* 1.3 94.0 + - - +
301B LEU* 1.3 69.0 + - - +
354B ARG* 4.2 8.3 - - + -
355B PHE 3.5 4.9 - - - +
356B SER* 4.6 0.9 - - - -
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Residues in contact with LEU 301 (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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274B ARG* 4.3 19.3 - - + +
277B LEU* 3.6 36.3 - - + -
278B TRP* 3.9 27.6 - - + +
281B ILE* 4.7 1.8 - - + -
289B LEU* 4.0 34.5 - - + -
300B ILE* 1.3 78.6 - - - +
302B ASN* 1.3 57.1 + - - +
303B VAL* 3.8 19.3 - - + -
355B PHE* 2.7 54.6 + - + +
357B LEU* 6.4 1.8 - - + -
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Residues in contact with ASN 302 (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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156B GLU* 2.9 35.9 + - - +
157B ILE* 3.9 15.6 + - + +
289B LEU* 3.7 2.8 - - - +
290B ASN* 2.7 72.8 + - - +
300B ILE* 4.2 1.4 - - - +
301B LEU* 1.3 74.2 - - - +
303B VAL* 1.3 59.7 + - - +
324B SER 5.6 3.2 + - - -
339B LEU* 3.8 13.5 - - - +
352B SER* 4.1 8.5 - - - -
353B ILE 3.4 8.3 - - - +
354B ARG* 3.7 15.5 - - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TRP* 3.6 29.4 - - + -
281B ILE* 4.1 7.2 - - + -
287B VAL* 5.7 1.3 - - + -
288B TYR 3.1 8.7 - - - +
289B LEU* 4.6 1.3 - - - -
290B ASN* 3.8 2.0 - - - -
301B LEU* 3.8 23.1 - - + -
302B ASN* 1.3 78.2 + - - +
304B SER* 1.3 63.7 + - - +
305B PHE* 3.2 35.6 - - + -
352B SER* 3.2 1.2 - - - -
353B ILE 2.8 36.6 + - - +
355B PHE* 3.6 16.6 - - + -
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Residues in contact with SER 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 3.4 6.6 - - - +
288B TYR* 2.7 42.7 + - - -
290B ASN* 2.7 23.4 + - - +
303B VAL* 1.3 74.5 - - - +
305B PHE* 1.3 62.6 + - - +
306B ASN 3.9 0.7 + - - -
344B LEU* 4.6 4.6 - - - +
348B LEU* 3.4 29.6 + - - +
351B SER 3.7 0.7 - - - -
352B SER* 2.5 24.9 + - - -
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Residues in contact with PHE 305 (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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281B ILE* 4.8 4.7 - - + -
284B ILE* 4.7 2.5 - - + -
286B GLU 3.8 4.0 - - - -
287B VAL* 3.8 24.0 - - + -
303B VAL* 3.2 34.1 - - + -
304B SER* 1.3 72.1 - - - +
306B ASN* 1.3 61.2 + - - +
308B VAL* 2.9 29.8 - - + +
313B LEU* 4.0 12.1 - - + -
317B LEU* 5.5 1.8 - - + -
348B LEU* 3.8 1.8 - - - -
351B SER* 2.9 32.4 + - - +
353B ILE* 4.0 18.6 - - + -
355B PHE* 4.6 6.3 - + - -
373B VAL* 3.6 33.0 - - + -
377B ILE* 3.4 30.1 - - + -
381B ARG* 4.7 4.0 - - - +
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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