Contacts of the strand formed by residues 550 - 556 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514B ARG* 3.3 62.8 + - + +
515B ASN* 4.4 16.0 + - + +
549B GLY* 1.3 77.6 + - - -
551B ILE* 1.3 64.0 + - - +
552B LEU* 3.3 5.2 + - + +
566B SER* 3.1 21.2 - - - -
567B SER 2.9 20.0 + - - +
568B SER* 4.5 14.1 - - - -
569B LYS* 5.6 2.0 - - + -
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Residues in contact with ILE 551 (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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492B VAL* 3.3 35.1 - - + +
512B GLY 5.1 0.7 - - - -
513B ASP 3.4 22.7 - - - +
514B ARG* 2.8 19.1 + - - +
516B GLY* 3.7 1.8 - - - -
518B PHE* 3.7 29.8 - - + -
547B PHE* 3.4 35.4 - - + -
550B HIS* 1.3 70.4 - - - +
552B LEU* 1.3 65.6 + - - +
553B GLY 3.8 21.8 - - - +
554B PHE* 4.1 13.0 - - + -
564B ILE* 4.3 11.2 - - + -
565B LEU 3.5 5.2 - - - +
566B SER* 4.4 0.7 - - - -
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Residues in contact with LEU 552 (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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228B GLN* 4.6 20.0 - - + +
229B PRO* 3.4 25.8 - - + +
230B VAL* 3.9 11.4 - - + +
247B LYS* 6.3 1.1 - - + -
492B VAL* 4.1 10.6 - - - +
514B ARG* 4.4 19.7 - - - +
550B HIS* 3.6 19.7 - - + +
551B ILE* 1.3 77.7 - - - +
553B GLY* 1.3 55.7 + - - +
565B LEU 2.7 12.8 + - - +
566B SER 4.6 0.2 - - - -
567B SER* 3.9 31.0 - - - +
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Residues in contact with GLY 553 (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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230B VAL 3.5 16.5 + - - -
434B ARG* 5.9 3.6 - - - -
492B VAL* 4.7 2.5 - - - -
551B ILE* 3.7 6.4 - - - +
552B LEU* 1.3 80.5 - - - +
554B PHE* 1.3 68.7 + - - -
564B ILE* 3.5 3.6 - - - -
565B LEU* 2.7 40.2 + - - +
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Residues in contact with PHE 554 (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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231B GLY* 3.6 3.7 - - - -
232B ALA 3.4 16.1 + - - +
434B ARG* 4.2 36.0 + - + +
492B VAL* 3.9 16.8 - - + -
493B GLY* 3.4 35.0 - - - -
494B GLY* 3.8 5.6 - - - -
495B PHE* 3.7 32.8 - + + -
512B GLY* 4.3 12.6 - - - -
518B PHE* 4.1 9.4 - + - -
551B ILE* 4.1 16.8 - - + -
553B GLY* 1.3 75.7 - - - -
555B GLY* 1.3 60.8 + - - +
562B VAL* 5.0 0.2 - - + -
563B TYR 3.3 15.9 - - - +
564B ILE* 3.8 21.3 - - + -
565B LEU* 3.6 4.7 - - - -
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Residues in contact with GLY 555 (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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232B ALA* 3.1 22.4 - - - -
554B PHE* 1.3 74.5 - - - +
556B GLU* 1.3 60.8 + - - +
562B VAL* 3.3 12.8 - - - +
563B TYR* 3.0 43.9 + - - -
565B LEU* 3.8 0.6 - - - +
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Residues in contact with GLU 556 (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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232B ALA 3.2 9.0 + - - +
233B LEU* 3.6 8.8 - - + -
234B HIS* 3.5 22.3 + - - +
242B LEU* 3.4 17.8 - - - +
434B ARG* 4.9 12.6 + - - +
439B ARG* 5.5 4.5 + - - -
495B PHE* 6.1 1.0 - - - +
496B VAL 5.4 5.2 - - - +
498B ARG* 5.7 5.4 - - - +
555B GLY* 1.3 75.5 - - - +
557B ASP* 1.3 76.2 + - - +
560B GLY* 3.9 16.7 - - - +
561B GLU 3.3 11.7 - - - +
562B VAL* 5.0 5.2 - - + -
563B TYR* 3.9 2.9 - - - -
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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