Contacts of the strand formed by residues 296 - 304 (chain B) in PDB entry 3I5D
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 ASN 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 5.4 0.2 - - - -
292B ALA* 6.0 5.5 - - - +
293B PRO 5.3 4.4 + - - -
295B TYR* 1.3 88.7 - - - +
297B PHE* 1.3 74.9 + - - +
298B ARG* 5.6 3.6 + - - +
316B LYS* 4.9 7.3 - - - +
317B GLY 3.1 17.1 - - - +
318B TYR* 3.5 34.6 + - + +
319B GLY 4.9 0.2 - - - +
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Residues in contact with PHE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PRO* 3.6 22.4 - - + -
103B PHE* 3.5 44.4 - + + -
295B TYR* 4.2 18.4 - + - -
296B ASN* 1.3 81.6 - - - +
298B ARG* 1.3 78.0 + - - +
299B PHE* 3.1 30.5 - + + -
315B ILE 3.6 0.5 - - - +
316B LYS* 3.7 0.9 - - - -
317B GLY 2.9 29.6 + - - +
97C GLN* 4.3 32.3 - - + -
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASP* 5.8 5.5 - - - +
171B GLU* 2.7 42.8 + - - +
296B ASN* 5.6 3.6 + - - +
297B PHE* 1.3 87.6 - - - +
299B PHE* 1.3 65.4 + - - +
314B LEU* 3.9 28.4 - - + +
315B ILE 3.3 5.2 - - - +
316B LYS* 4.7 10.3 - - - +
88C ASP* 5.9 0.9 - - - -
90C ALA* 4.2 26.7 - - + +
91C ASP* 4.4 13.2 - - + -
97C GLN* 4.2 13.0 + - - +
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 6.0 3.8 - + - -
95B PRO* 3.8 28.0 - - + -
105B LEU* 4.5 13.7 - - + -
297B PHE* 3.1 33.4 - + + -
298B ARG* 1.3 76.4 - - - +
300B ALA* 1.3 69.7 + - - +
301B LYS* 4.8 8.5 - - + -
314B LEU* 3.4 5.5 - - - +
315B ILE* 2.9 76.6 + - + +
317B GLY* 4.7 8.7 - - - -
91C ASP* 4.3 8.1 - - - +
97C GLN* 4.6 12.3 - - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PHE* 1.3 82.6 - - - +
301B LYS* 1.3 71.8 + - - +
302B TYR* 3.7 38.5 - - + +
312B ARG* 3.9 22.7 - - - +
313B THR 3.3 11.4 - - - +
314B LEU* 4.6 0.9 - - - -
91C ASP* 4.6 4.7 + - + +
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 3.2 40.1 - - + -
310A GLU* 3.7 11.3 + - - -
92B TYR* 2.8 38.4 + - - -
299B PHE* 4.8 8.3 - - + -
300B ALA* 1.3 81.5 - - - +
302B TYR* 1.3 62.7 + - - +
303B TYR* 3.3 26.5 + - + +
312B ARG* 3.1 5.2 - - - -
313B THR* 2.9 40.9 + - + +
315B ILE* 4.5 16.4 - - + +
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR 4.4 2.9 - - - +
167B TRP* 4.3 0.9 - + - -
300B ALA* 3.7 30.8 - - + +
301B LYS* 1.3 73.1 - - - +
303B TYR* 1.3 71.1 + - - +
310B GLU* 4.0 23.6 - - - +
311B THR 3.7 2.0 - - - +
312B ARG* 3.6 34.2 + - + -
91C ASP 3.8 5.1 + - - -
92C TYR* 3.5 48.5 - + - +
301C LYS* 3.2 34.1 - - + -
302C TYR 4.2 5.7 - - - +
303C TYR* 3.7 18.8 - - + -
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Residues in contact with TYR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 3.8 21.2 - - + +
303A TYR* 4.1 1.3 - - - -
304A LYS* 3.3 48.7 - - + +
310A GLU* 3.0 27.4 + - + +
301B LYS* 3.3 35.2 + - + +
302B TYR* 1.3 89.4 - - - +
304B LYS* 1.3 61.9 + - - +
305B ASN* 3.0 9.3 + - - +
310B GLU* 4.0 2.1 - - - +
311B THR* 2.9 47.9 + - - +
312B ARG* 4.9 0.4 - - - -
313B THR* 3.6 23.7 + - - -
303C TYR* 4.0 3.6 - - - -
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LYS 5.4 3.1 - - - +
303B TYR* 1.3 68.8 - - - +
305B ASN* 1.3 68.2 + - - +
306B SER* 3.7 1.2 + - - -
308B GLY* 5.5 5.6 - - - +
309B THR 4.1 4.7 - - - -
310B GLU* 5.0 4.9 - - + +
303C TYR* 3.2 49.1 - - + +
304C LYS 5.2 5.2 - - - +
305C ASN* 6.1 0.3 - - - -
311C THR* 5.6 0.4 - - - +
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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