Contacts of the strand formed by residues 551 - 556 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523D SER* 4.1 10.5 - - - +
540F LEU 4.9 0.9 - - - +
541F VAL* 3.9 16.6 - - - +
543F GLU 5.5 1.1 - - - +
548F SER* 2.7 50.6 + - - +
549F HIS 5.0 0.4 - - - +
550F GLY* 1.3 74.4 - - - +
552F PHE* 1.3 61.4 + - - +
568F PHE* 3.1 3.5 - - - +
569F ASN 2.7 30.5 + - - -
622F VAL* 6.1 0.7 - - + -
623F SER* 3.2 24.9 - - - +
624F TYR 4.6 1.8 - - - -
625F VAL* 3.5 30.7 - - + +
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Residues in contact with PHE 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D MET* 4.4 18.8 - - + -
527F TRP* 3.9 13.5 - + + -
541F VAL* 4.0 4.5 - - - -
550F GLY 3.7 3.8 - - - -
551F VAL* 1.3 74.7 - - - +
553F LEU* 1.3 79.4 + - - +
554F VAL* 5.0 0.7 - - + -
566F LEU* 4.0 16.8 - - + -
567F THR 3.1 14.8 - - - +
568F PHE* 3.7 10.8 - - + +
601F LEU* 3.8 22.9 - - + -
621F LEU* 3.7 35.9 - - + -
622F VAL 4.5 2.2 - - - -
623F SER* 3.0 43.5 + - - -
624F TYR* 3.2 27.2 - + + -
625F VAL* 2.9 27.0 + - - +
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Residues in contact with LEU 553 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527F TRP* 3.6 7.2 - - - -
529F HIS* 3.7 37.5 - - + +
532F LEU* 4.1 4.3 - - + -
537F ALA* 4.0 36.6 - - + +
540F LEU* 4.1 17.9 - - + -
541F VAL* 4.1 12.1 - - + -
552F PHE* 1.3 84.5 - - - +
554F VAL* 1.3 80.1 + - - +
555F ARG* 4.0 9.6 - - + +
566F LEU* 3.8 2.3 - - - +
567F THR* 3.0 34.6 + - - +
625F VAL* 4.2 3.1 - - + +
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Residues in contact with VAL 554 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527F TRP* 2.9 39.5 + - + -
528F PHE* 3.4 15.3 - - + -
529F HIS 2.9 27.7 + - - -
552F PHE* 4.8 1.1 - - + -
553F LEU* 1.3 80.7 - - - +
555F ARG* 1.3 61.4 + - - +
564F CYS* 4.2 12.6 - - + -
565F VAL 3.3 9.4 - - - +
566F LEU* 3.8 19.1 - - + -
579F LEU* 4.2 17.3 - - + -
597F ILE* 4.5 11.9 - - + -
601F LEU* 4.3 10.5 - - + -
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Residues in contact with ARG 555 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528F PHE* 4.8 1.1 - - - -
529F HIS* 5.1 0.4 - - + -
530F GLY 3.2 12.3 - - - +
532F LEU* 3.5 30.3 + - + +
533F SER 4.2 0.7 - - - -
534F ARG* 3.7 18.0 - - - +
537F ALA* 3.5 23.6 - - - +
553F LEU* 4.0 4.9 - - + +
554F VAL* 1.3 74.8 - - - +
556F GLN* 1.3 65.7 + - - +
557F SER* 5.2 0.4 - - - +
558F GLU* 5.6 2.6 - - - +
564F CYS* 3.2 7.0 - - - +
565F VAL* 2.7 61.1 + - + +
567F THR* 2.9 16.6 + - - +
576F HIS* 3.1 25.3 + - - -
813L PTR 2.9 41.6 + - - -
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Residues in contact with GLN 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B SER* 3.2 20.4 - - - -
624B TYR* 3.0 73.5 + - + +
626B PRO* 5.0 4.6 - - - +
522F LEU* 6.2 1.0 - - - +
528F PHE* 3.7 23.8 - - + -
530F GLY 2.7 13.3 + - - +
531F MET* 3.4 15.4 + - - +
532F LEU 4.3 4.0 - - - +
555F ARG* 1.3 84.7 + - - +
557F SER* 1.3 63.6 + - - +
558F GLU* 3.6 1.7 + - - +
564F CYS* 3.9 14.1 - - - -
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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