Contacts of the strand formed by residues 387 - 393 (chain B) in PDB entry 2H4Q
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 387 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A PHE* 4.2 4.9 - + - -
258A ILE* 3.8 20.9 - - + -
259A LEU 3.3 15.5 - - - +
260A LEU* 4.0 11.4 - - + -
271A LEU* 4.0 4.0 - - - +
301A LEU* 5.0 1.3 - - + -
302A PRO* 4.6 5.4 - - + -
304A PHE* 3.9 21.5 - + - -
383B VAL* 3.2 29.6 - - + -
385B HIS 3.5 7.9 - - - -
386B PRO* 1.3 74.7 - - - +
388B HIS* 1.3 76.9 + - - +
389B PHE* 3.7 26.2 - + + -
404B ARG* 3.4 5.0 - - - +
405B PHE* 3.0 65.1 + + + +
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Residues in contact with HIS 388 (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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16A PHE* 3.6 17.6 - + - -
258A ILE* 3.4 2.3 - - - -
259A LEU* 2.9 49.0 + - + +
271A LEU* 4.0 12.2 - - + +
274A LEU* 4.0 17.2 - - + +
275A GLU* 2.9 45.4 + - + +
278A LEU* 4.2 14.8 - - + +
387B PHE* 1.3 83.4 - - - +
389B PHE* 1.3 62.5 + - - +
390B PHE* 5.7 1.6 - - + -
402B PHE* 4.0 21.3 - + + -
403B GLY 3.4 6.1 - - - +
404B ARG* 3.9 12.8 - - + -
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Residues in contact with PHE 389 (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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29A PHE* 3.6 38.6 - + - -
256A MET* 3.8 28.3 - - + -
257A PHE 3.1 13.2 - - - +
258A ILE* 4.1 7.4 - - + -
304A PHE* 3.9 28.9 - + - -
306A LEU* 4.2 9.4 - - + -
351A VAL* 4.5 5.4 - - + -
387B PHE* 3.7 27.4 - + + -
388B HIS* 1.3 75.3 - - - +
390B PHE* 1.3 69.4 + - - +
391B ILE* 5.3 2.5 - - + -
402B PHE* 3.5 2.5 - - - -
403B GLY* 2.8 54.5 + - - +
404B ARG 4.1 2.0 - - - -
405B PHE* 4.2 9.9 - - + -
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Residues in contact with PHE 390 (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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244A MET* 5.0 4.5 - - - -
255A SER 3.7 0.3 - - - +
256A MET* 3.3 3.8 - - - +
257A PHE* 2.8 77.3 + + + -
259A LEU* 6.1 4.3 - - + -
283A LEU* 3.7 33.7 - - + -
287A ALA* 4.3 12.6 - - + -
388B HIS* 5.7 1.8 - - + -
389B PHE* 1.3 80.7 - - - +
391B ILE* 1.3 62.1 + - - +
392B ARG* 4.2 19.1 - - + -
399B ILE* 4.0 22.7 - - + -
401B PHE 3.1 18.4 - - - +
402B PHE* 3.7 26.5 - + + -
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Residues in contact with ILE 391 (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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29A PHE* 5.4 1.1 - - + -
195A PHE* 4.0 24.0 - - + -
249A TYR* 4.1 9.2 - - + +
254A LEU* 4.3 15.3 - - + -
255A SER 3.4 8.1 - - - +
256A MET* 3.9 21.5 - - + -
351A VAL* 4.8 3.6 - - + -
358A THR* 3.9 20.6 - - + -
360A ALA* 3.8 28.9 - - + -
389B PHE* 5.3 1.6 - - + -
390B PHE* 1.3 75.2 - - - +
392B ARG* 1.3 60.9 + - - +
399B ILE* 3.7 2.6 - - - -
400B LEU* 2.9 28.5 + - + -
401B PHE* 2.9 29.3 + - + +
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Residues in contact with ARG 392 (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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246A GLU* 5.0 2.4 + - - -
254A LEU* 3.1 30.2 - - - +
255A SER 2.9 10.8 + - - +
257A PHE* 3.6 30.0 - - + -
287A ALA* 4.0 16.3 + - - +
288A ASP* 3.1 37.6 + - - -
390B PHE* 4.0 17.5 + - + -
391B ILE* 1.3 74.4 - - - +
393B HIS* 1.3 66.7 + - - +
394B ASN* 3.2 37.4 + - - +
397B LYS* 3.7 31.9 - - - +
398B THR 3.4 17.3 - - - +
399B ILE* 4.4 3.4 - - - +
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Residues in contact with HIS 393 (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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104A ALA* 4.8 16.4 + - + +
105A PHE* 3.5 35.1 - + + -
109A ARG* 5.7 1.8 + - - -
112A TYR* 5.3 3.5 + - - -
114A LEU* 4.5 7.9 - - + -
253A GLU* 3.8 12.8 + - + +
254A LEU* 4.0 19.3 - - + +
392B ARG* 1.3 68.7 - - - +
394B ASN* 1.3 53.1 + - - +
395B LYS* 3.9 18.5 - - + +
396B SER* 2.7 41.2 + - - +
397B LYS* 2.8 35.9 + - - -
398B THR 2.9 12.4 + - - +
400B LEU* 4.4 6.5 - - + +
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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