Contacts of the strand formed by residues 249 - 256 (chain A) in PDB entry 3I5G
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 GLY 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A PHE* 1.3 78.0 - - - +
250A LYS* 1.3 62.6 + - - -
269A THR* 3.2 4.3 - - - -
270A TYR* 2.8 46.1 + - - -
271A LEU* 4.9 0.6 - - - +
462A LEU* 4.8 1.6 - - - -
463A ASP 3.3 11.0 - - - -
464A ILE* 4.0 20.1 - - - +
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Residues in contact with LYS 250 (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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183A THR* 5.9 4.8 - - - +
224A ILE* 6.2 0.2 - - - -
228A ASN* 3.9 26.4 + - - +
231A LEU* 4.0 22.8 - - + +
232A GLU* 5.6 4.4 + - - +
246A SER* 5.4 4.4 + - - -
248A PHE* 3.3 27.4 - - + -
249A GLY* 1.3 73.4 - - - +
251A PHE* 1.3 59.6 + - - +
252A ILE* 3.9 27.5 + - + +
267A ILE* 4.1 13.0 - - + -
268A GLU 3.7 2.2 - - - -
269A THR* 4.0 9.0 - - + -
461A VAL 3.5 4.0 - - - +
462A LEU* 3.5 3.0 - - - +
463A ASP* 3.0 54.1 + - + +
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Residues in contact with PHE 251 (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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171A SER* 4.0 20.6 - - - -
250A LYS* 1.3 73.7 - - - +
252A ILE* 1.3 59.8 + - - +
253A ARG* 3.4 26.1 + - + +
267A ILE* 3.5 3.8 - - - -
268A GLU* 3.0 62.9 + - + +
270A TYR* 4.0 15.0 - + + -
458A PHE* 4.1 11.9 - + - -
460A GLY* 3.6 29.2 - - - -
461A VAL 3.4 16.6 - - - -
462A LEU* 3.8 20.0 - - + -
658A LEU* 5.6 2.5 - - + -
661A ASN* 5.2 10.8 - - + -
662A LEU* 4.5 11.9 - - + -
665A THR* 5.1 4.5 - - + -
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Residues in contact with ILE 252 (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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186A THR* 4.0 26.2 - - + -
190A ILE* 4.1 11.9 - - + -
224A ILE* 3.9 42.0 - - + -
228A ASN* 5.9 0.2 - - - +
250A LYS* 3.9 32.1 - - + +
251A PHE* 1.3 68.1 - - - +
253A ARG* 1.3 60.9 + - - +
254A ILE* 3.5 8.2 + - + +
265A ALA* 5.6 0.2 - - + -
266A ASP 3.8 8.1 - - - +
267A ILE* 4.2 14.1 - - + -
459A ILE 3.8 0.9 - - - +
460A GLY* 3.3 2.4 - - - -
461A VAL* 2.9 40.8 + - + +
463A ASP* 6.5 0.7 - - + -
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Residues in contact with ARG 253 (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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251A PHE* 3.4 26.4 + - + +
252A ILE* 1.3 71.7 - - - +
254A ILE* 1.3 60.6 + - - +
255A HIS* 3.5 17.1 + - - +
265A ALA* 3.2 3.9 - - - -
266A ASP* 3.0 67.4 + - - +
268A GLU* 3.3 37.6 + - - +
455A ARG* 4.9 1.0 - - - +
458A PHE* 3.5 47.9 - - + -
460A GLY* 3.9 5.8 - - - -
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Residues in contact with ILE 254 (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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190A ILE* 3.2 53.2 - - + +
193A PHE* 4.1 14.4 - - + -
220A LEU* 4.0 17.5 - - + -
224A ILE* 4.8 0.7 - - + -
252A ILE* 4.4 14.1 - - + +
253A ARG* 1.3 72.4 - - - +
255A HIS* 1.3 64.6 + - - +
256A PHE* 3.4 26.3 - - + -
262A ILE* 4.6 4.5 - - + -
264A GLY 3.7 9.6 - - - +
265A ALA* 4.6 5.6 - - + -
458A PHE* 3.2 1.7 - - - -
459A ILE 3.0 36.8 + - - +
461A VAL* 5.3 2.5 - - + -
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Residues in contact with HIS 255 (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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253A ARG* 3.5 21.6 + - - +
254A ILE* 1.3 72.7 - - - +
256A PHE* 1.3 72.8 + - - +
262A ILE* 3.6 3.5 - - - -
263A ALA 2.9 18.0 + - - -
264A GLY 2.8 21.2 + - - +
265A ALA* 4.0 4.7 - - - -
266A ASP* 2.9 29.9 + - - -
455A ARG* 3.2 59.8 + - + +
456A GLN 5.9 0.2 - - - -
457A PHE 3.3 9.2 + - - +
458A PHE* 3.5 31.0 - + + +
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Residues in contact with PHE 256 (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 TYR* 3.7 12.3 - + - -
163A MET* 3.5 32.3 - - + -
193A PHE* 3.8 30.3 - - + -
254A ILE* 3.4 24.5 - - + -
255A HIS* 1.3 76.4 - - - +
257A GLY* 1.3 62.0 + - - +
260A GLY* 3.2 26.7 - - - -
261A LYS 3.1 12.3 - - - +
262A ILE* 3.6 21.5 - - + -
263A ALA* 3.7 6.7 - - - +
455A ARG 3.6 0.2 - - - -
456A GLN* 2.6 32.9 + - - +
457A PHE* 2.9 13.5 + - + +
458A PHE* 4.4 1.8 - - - -
459A ILE* 3.9 24.2 - - + -
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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