Contacts of the strand formed by residues 551 - 556 (chain B) in PDB entry 2HDX
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 VAL 551 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540B LEU 5.1 0.7 - - - +
541B VAL* 4.2 13.8 - - - +
548B SER* 2.8 40.0 + - - +
549B HIS 4.9 0.9 - - - +
550B GLY* 1.3 78.2 - - - +
552B PHE* 1.3 63.5 + - - +
568B PHE* 3.1 4.7 - - - +
569B ASN 2.8 26.2 + - - -
622B VAL* 6.1 0.2 - - + -
623B SER* 3.1 27.1 - - - +
624B TYR 4.5 1.1 - - - -
625B VAL* 3.6 30.7 - - + +
523F SER* 5.3 8.5 - - - -
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Residues in contact with PHE 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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527B TRP* 4.1 11.7 - - + -
541B VAL* 4.1 4.9 - - - -
550B GLY 3.8 9.2 - - - -
551B VAL* 1.3 77.2 - - - +
553B LEU* 1.3 69.0 + - - +
554B VAL* 4.9 0.9 - - + -
566B LEU* 3.9 16.8 - - + -
567B THR 3.2 13.2 - - - +
568B PHE* 3.8 10.3 - - + +
601B LEU* 3.9 21.8 - - + -
621B LEU* 3.8 31.4 - - + -
622B VAL 4.6 0.7 - - - -
623B SER* 2.9 43.1 + - - -
624B TYR* 3.0 30.3 - + + -
625B VAL* 2.8 26.3 + - - +
531F MET* 4.3 19.7 - - + -
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Residues in contact with LEU 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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527B TRP 3.7 6.3 - - - -
529B HIS* 3.5 28.5 - - + +
532B LEU* 4.2 5.6 - - + -
537B ALA* 4.0 14.6 - - + +
540B LEU* 3.9 38.8 - - + -
541B VAL* 3.8 17.9 - - + -
552B PHE* 1.3 82.2 - - - +
554B VAL* 1.3 80.3 + - - +
555B ARG* 4.3 7.4 - - + +
566B LEU* 3.8 2.3 - - - +
567B THR* 3.0 42.4 + - - +
624B TYR* 5.0 0.2 - - - -
625B VAL* 4.3 4.7 - - + +
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Residues in contact with VAL 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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527B TRP* 3.1 34.4 + - + +
528B PHE* 3.7 9.6 - - + -
529B HIS* 2.9 28.1 + - - +
552B PHE* 4.8 2.0 - - + -
553B LEU* 1.3 79.9 - - - +
555B ARG* 1.3 64.4 + - - +
564B CYS* 4.1 17.9 - - + -
565B VAL 3.4 9.6 - - - +
566B LEU* 3.9 20.6 - - + -
579B LEU* 4.2 4.7 - - + -
597B ILE* 3.7 26.5 - - + -
601B LEU* 4.3 9.0 - - + -
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Residues in contact with ARG 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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528B PHE* 4.9 0.7 - - - -
530B GLY 3.2 13.7 - - - +
532B LEU* 3.5 28.7 + - + +
534B ARG* 3.7 16.3 - - - +
537B ALA* 3.3 27.1 - - - +
553B LEU* 4.4 4.7 - - + -
554B VAL* 1.3 76.5 - - - +
556B GLN* 1.3 66.9 + - - +
557B SER* 5.2 0.8 - - - +
558B GLU* 5.8 3.0 - - - +
564B CYS* 3.2 7.8 - - - +
565B VAL* 2.7 62.0 + - + +
567B THR* 2.8 16.7 + - - +
576B HIS* 3.2 22.4 + - - -
813H PTR 2.8 42.4 + - - -
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Residues in contact with GLN 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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522B LEU* 6.1 1.2 - - - +
528B PHE* 3.4 32.6 - - + -
530B GLY 2.7 14.9 + - - +
531B MET* 3.6 14.3 + - - +
532B LEU 4.4 5.0 - - - +
555B ARG* 1.3 79.8 + - - +
557B SER* 1.3 64.2 + - - +
558B GLU* 3.5 2.4 + - - +
564B CYS* 4.1 13.1 - - - -
565B VAL 5.1 0.2 - - - -
623E SER* 3.0 13.5 - - - -
624E TYR* 2.8 77.9 + - + +
626E PRO* 4.4 8.9 - - - +
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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