Contacts of the strand formed by residues 263 - 268 (chain B) in PDB entry 4ISO
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 PHE 263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 4.7 0.2 - - - -
41A ILE* 3.5 30.5 - - + -
57A HIS* 4.6 3.8 - + - -
58A CYS* 3.7 15.7 - - - -
60A TYR* 3.6 42.4 - + - +
303A GOL 3.5 28.3 - - - -
261B GLY* 4.1 6.7 - - - -
262B SER* 1.3 73.9 - - - +
264B PRO* 1.4 69.0 - - - +
265B ARG* 3.4 15.5 + - - +
279B VAL* 3.5 1.7 - - - +
280B TYR* 2.8 59.0 + - + +
281B GLY 3.8 6.7 - - - -
282B GLY* 3.6 23.1 - - - -
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Residues in contact with PRO 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 3.3 38.6 + - + +
40A HIS 5.2 0.2 - - - +
41A ILE* 3.7 13.7 - - + -
262B SER 3.3 11.6 - - - +
263B PHE* 1.4 81.8 - - - +
265B ARG* 1.3 71.4 + - - +
266B TRP* 5.4 2.2 - - - -
277B SER* 6.5 0.9 - - - -
278B PHE 3.7 6.5 - - - +
279B VAL* 4.7 8.5 - - + -
291B LEU* 4.4 11.3 - - - +
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Residues in contact with ARG 265 (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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38A GLN* 5.0 0.2 - - - +
60A TYR* 2.9 39.4 - - - +
303A GOL 3.0 28.1 + - - -
263B PHE* 3.5 18.6 - - - +
264B PRO* 1.3 81.3 + - - +
266B TRP* 1.3 68.7 + - - +
277B SER* 3.3 7.4 - - - -
278B PHE* 2.9 50.4 + - + +
280B TYR* 3.6 24.8 - - + -
289B ASN* 2.8 39.3 + - - +
290B TYR 3.3 18.2 - - - +
291B LEU* 3.8 19.5 - - - +
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Residues in contact with TRP 266 (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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264B PRO 5.5 1.2 + - - -
265B ARG* 1.3 83.5 + - - +
267B TYR* 1.3 60.1 + - - +
275B CYS 3.8 10.1 - - - -
276B LYS* 3.2 28.5 - - - -
277B SER* 3.7 23.1 - - - -
278B PHE* 3.7 3.2 - - - -
289B ASN* 3.4 6.6 - - - -
290B TYR* 2.8 39.3 + - - +
291B LEU 3.7 10.6 + - - -
292B ARG* 3.5 5.8 - - - +
293B GLU* 3.3 59.7 - - + +
296B CYS* 4.1 20.2 - - + -
401B PEG 5.9 0.8 + - - -
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Residues in contact with TYR 267 (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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252B ALA 5.1 0.9 - - - -
253B SER* 5.7 0.7 - - - -
254B ASN* 3.6 43.9 + - + -
266B TRP* 1.3 74.5 - - - +
268B TYR* 1.3 71.0 + - - +
269B ASP* 4.0 21.1 + - + -
275B CYS* 3.3 1.0 - - - -
276B LYS* 2.8 78.6 + - + +
277B SER 3.8 11.2 - - - -
278B PHE* 3.7 17.9 - + + -
288B ASN* 3.3 30.1 - - - +
296B CYS* 3.6 6.7 - - - -
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Residues in contact with TYR 268 (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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250B CYS* 3.4 26.7 - - + +
252B ALA 4.6 0.7 - - - +
267B TYR* 1.3 77.1 - - - +
269B ASP* 1.3 57.8 + - - +
270B PRO* 3.5 19.6 - - + +
273B GLN* 3.3 41.7 + - - +
274B ILE* 3.8 10.1 - - - -
275B CYS* 3.9 11.7 - - - -
288B ASN* 2.8 31.3 + - - +
296B CYS* 3.5 8.7 - - - -
297B ILE* 6.3 0.4 - - - -
300B CYS* 3.3 49.4 + - + -
301B ARG* 4.6 4.5 - - - -
302B GLY 3.8 3.7 + - - -
303B VAL* 2.9 44.7 + - + -
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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