Contacts of the strand formed by residues 550 - 556 (chain A) in PDB entry 3HO5
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 HIS 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A ARG* 2.9 65.4 + - + +
515A ASN* 4.4 14.5 + - - -
549A GLY* 1.3 80.2 + - - -
551A ILE* 1.3 64.5 + - - +
552A LEU* 3.5 8.4 + - + +
566A SER* 3.0 6.7 - - - -
567A SER 2.5 39.6 + - - +
568A SER* 4.3 15.7 - - - -
569A LYS 5.4 0.7 - - - -
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Residues in contact with ILE 551 (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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492A VAL* 3.7 31.1 - - + +
513A ASP 3.6 20.4 - - - +
514A ARG* 2.9 21.6 + - - +
516A GLY* 3.8 1.8 - - - -
518A PHE* 3.8 28.3 - - + -
547A PHE* 3.6 33.4 - - + -
550A HIS* 1.3 72.6 - - - +
552A LEU* 1.3 67.9 + - - +
553A GLY 3.7 22.2 - - - +
554A PHE* 4.2 9.9 - - + -
564A ILE* 3.8 16.4 - - + -
565A LEU 3.6 4.9 - - - +
566A SER* 4.4 0.7 - - - +
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Residues in contact with LEU 552 (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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228A GLN* 4.5 20.0 - - - +
229A PRO* 3.5 32.8 - - + +
230A VAL* 4.1 6.2 - - - +
492A VAL* 3.8 12.8 - - - +
514A ARG* 5.8 2.5 - - + -
550A HIS* 3.9 17.0 - - + +
551A ILE* 1.3 81.5 - - - +
553A GLY* 1.3 58.5 + - - +
565A LEU 2.8 8.9 + - - +
567A SER* 3.7 29.4 - - - +
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Residues in contact with GLY 553 (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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230A VAL 3.4 17.0 + - - -
434A ARG* 6.0 2.5 - - - -
492A VAL* 4.4 3.6 - - - -
551A ILE* 3.7 7.6 - - - +
552A LEU* 1.3 79.2 - - - +
554A PHE* 1.3 77.6 - - - -
564A ILE* 3.8 0.2 - - - -
565A LEU* 3.2 27.4 + - - +
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Residues in contact with PHE 554 (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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231A GLY* 3.3 6.1 - - - -
232A ALA 3.1 18.5 + - - +
434A ARG* 4.3 36.8 + - + +
492A VAL* 3.8 16.8 - - + -
493A GLY 3.6 32.1 - - - -
494A GLY* 4.1 1.1 - - - -
495A PHE* 3.7 35.0 - + + -
512A GLY* 4.1 17.5 - - - -
518A PHE* 4.0 8.5 - + - -
551A ILE* 4.2 13.5 - - + -
553A GLY* 1.3 79.5 - - - -
555A GLY* 1.3 60.2 + - - +
562A VAL* 5.2 0.4 - - + -
563A TYR 3.4 5.4 - - - +
564A ILE* 3.8 25.8 - - + -
565A LEU* 3.6 7.0 - - - +
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Residues in contact with GLY 555 (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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232A ALA* 3.1 20.2 - - - -
554A PHE* 1.3 75.7 - - - +
556A GLU* 1.3 60.8 + - - +
562A VAL* 3.0 14.2 - - - +
563A TYR* 2.9 42.3 + - - -
565A LEU* 4.5 0.7 - - - -
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Residues in contact with GLU 556 (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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232A ALA 3.2 8.6 + - - +
233A LEU* 3.7 3.6 - - + -
234A HIS* 3.7 28.8 + - - +
242A LEU* 3.5 18.8 - - - +
434A ARG* 5.1 9.2 + - - +
439A ARG* 5.8 1.9 + - - -
496A VAL 5.6 4.2 - - - +
498A ARG* 5.3 8.2 + - - +
555A GLY* 1.3 74.4 - - - +
557A ASP* 1.3 71.8 + - - +
560A GLY* 3.7 25.3 - - - +
561A GLU 3.3 7.0 - - - +
562A VAL* 5.3 3.1 - - + -
563A TYR* 4.1 1.7 - - - -
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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