Contacts of the strand formed by residues 551 - 556 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A LEU 4.8 0.9 - - - +
541A VAL* 3.9 19.6 - - - +
543A GLU 5.5 0.7 - - - +
548A SER* 2.8 37.3 + - - +
549A HIS 5.1 0.4 - - - +
550A GLY* 1.3 76.7 - - - +
552A PHE* 1.3 61.0 + - - +
568A PHE* 3.2 3.3 - - - +
569A ASN* 2.9 26.7 + - - +
623A SER* 3.2 24.0 - - - +
624A TYR 4.7 1.3 - - - -
625A VAL* 3.5 31.0 - - + +
523C SER* 4.1 12.8 - - - +
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Residues in contact with PHE 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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527A TRP* 3.9 21.8 - + + -
541A VAL* 4.1 3.8 - - - -
550A GLY 3.8 3.8 - - - -
551A VAL* 1.3 75.6 - - - +
553A LEU* 1.3 67.5 + - - +
554A VAL* 4.8 1.1 - - + -
566A LEU* 3.9 17.0 - - + -
567A THR 3.3 12.8 - - - +
568A PHE* 3.8 10.5 - - + -
601A LEU* 4.1 17.3 - - + -
605A ARG* 5.9 0.4 - - + -
621A LEU* 3.7 38.4 - - + -
622A VAL 4.5 2.2 - - - -
623A SER* 2.9 43.0 + - - -
624A TYR* 3.0 20.1 - + + +
625A VAL 3.0 24.6 + - - -
531C MET* 4.0 26.7 - - + -
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Residues in contact with LEU 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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527A TRP* 3.6 7.0 - - - -
529A HIS* 3.6 24.7 - - + +
532A LEU* 3.9 22.0 - - + -
537A ALA* 4.0 29.2 - - + +
540A LEU* 4.1 13.2 - - + -
541A VAL* 4.2 10.3 - - + -
552A PHE* 1.3 83.6 - - - +
554A VAL* 1.3 79.3 + - - +
555A ARG* 4.1 12.6 - - + +
566A LEU* 3.7 5.0 - - - +
567A THR* 3.0 35.2 + - - +
625A VAL* 4.2 9.6 - - + -
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Residues in contact with VAL 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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527A TRP* 3.0 33.2 + - + -
528A PHE* 3.6 13.7 - - + -
529A HIS* 2.9 27.4 + - - -
552A PHE* 4.8 2.2 - - + -
553A LEU* 1.3 81.5 - - - +
555A ARG* 1.3 68.9 + - - +
564A CYS* 4.2 5.6 - - + -
565A VAL 3.4 9.9 - - - +
566A LEU* 3.8 20.0 - - + -
579A LEU* 4.2 9.6 - - + -
597A ILE* 3.9 24.7 - - + -
601A LEU* 4.3 12.6 - - + -
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Residues in contact with ARG 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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528A PHE* 4.8 0.9 - - - -
529A HIS* 5.1 0.4 - - + -
530A GLY 3.2 12.6 - - - +
532A LEU* 3.6 26.0 + - + +
533A SER 4.2 0.2 - - - -
534A ARG* 3.8 18.2 - - - +
537A ALA* 3.5 24.2 - - - +
553A LEU* 4.1 8.1 - - + -
554A VAL* 1.3 75.7 - - - +
556A GLN* 1.3 64.8 + - - +
557A SER* 5.5 0.4 - - - +
558A GLU* 6.0 3.4 - - - +
564A CYS* 3.2 7.5 - - - +
565A VAL* 2.7 57.7 + - + +
567A THR* 2.9 15.2 + - - -
576A HIS* 2.9 29.7 + - - -
813G PTR 2.9 39.6 + - - -
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Residues in contact with GLN 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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528A PHE* 3.4 33.4 - - + -
530A GLY* 2.7 17.0 + - - +
531A MET* 3.5 35.3 + - + +
532A LEU 4.3 4.7 - - - +
555A ARG* 1.3 82.1 + - - +
557A SER* 1.3 68.2 - - - +
558A GLU* 3.6 2.1 + - - +
563A GLU 4.4 2.2 - - - +
564A CYS* 3.9 14.0 - - - -
565A VAL 5.0 0.2 - - - -
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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