Contacts of the strand formed by residues 551 - 556 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523B SER* 4.2 10.8 - - - -
540E LEU 5.1 0.2 - - - +
541E VAL* 4.1 13.8 - - - +
543E GLU 6.0 0.2 - - - +
548E SER* 2.8 42.7 + - - +
549E HIS 5.0 0.4 - - - +
550E GLY* 1.3 78.6 - - - +
552E PHE* 1.3 62.8 + - - +
568E PHE* 3.1 3.5 - - - +
569E ASN* 2.8 32.8 + - + -
623E SER* 3.2 24.7 - - - +
624E TYR 4.5 1.8 - - - -
625E VAL* 3.7 32.5 - - + +
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Residues in contact with PHE 552 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B MET* 4.1 26.2 - - + -
527E TRP* 3.7 27.8 - + + -
541E VAL* 4.2 3.1 - - - -
550E GLY 4.0 1.8 - - - -
551E VAL* 1.3 75.6 - - - +
553E LEU* 1.3 78.4 + - - +
554E VAL* 4.7 1.1 - - + -
566E LEU* 3.7 18.6 - - + -
567E THR 3.2 12.8 - - - +
568E PHE* 3.8 11.7 - - + -
601E LEU* 3.8 22.4 - - + -
621E LEU* 3.7 37.9 - - + -
623E SER 2.9 41.8 + - - -
624E TYR* 3.1 12.6 - + + -
625E VAL* 2.9 26.0 + - - +
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Residues in contact with LEU 553 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527E TRP* 3.6 7.9 - - - +
529E HIS* 3.7 26.2 - - + +
532E LEU* 4.0 21.1 - - + -
537E ALA* 4.1 20.4 - - + +
540E LEU* 4.2 11.0 - - + -
541E VAL* 3.9 21.1 - - + -
552E PHE* 1.3 84.1 - - - +
554E VAL* 1.3 79.5 + - - +
555E ARG* 4.0 9.2 - - + +
566E LEU* 3.6 4.9 - - - +
567E THR* 3.0 41.8 + - - +
625E VAL* 4.2 4.9 - - + +
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Residues in contact with VAL 554 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527E TRP* 2.9 37.7 + - + -
528E PHE* 3.6 15.0 - - + -
529E HIS* 2.8 28.9 + - - +
552E PHE* 4.6 1.3 - - + -
553E LEU* 1.3 81.2 - - - +
555E ARG* 1.3 64.2 + - - +
564E CYS* 4.1 15.7 - - + -
565E VAL 3.4 8.1 - - - +
566E LEU* 3.9 19.3 - - + -
579E LEU* 4.3 4.0 - - + -
597E ILE* 3.9 26.0 - - + -
601E LEU* 4.5 7.0 - - + -
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Residues in contact with ARG 555 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528E PHE* 4.9 0.4 - - - -
529E HIS* 5.0 0.2 - - + -
530E GLY 3.2 13.7 - - - +
532E LEU* 3.4 29.5 + - + +
533E SER 3.9 0.4 - - - -
534E ARG* 3.7 15.4 - - - +
537E ALA* 3.7 22.4 - - - +
553E LEU* 4.2 4.3 - - + -
554E VAL* 1.3 76.0 - - - +
556E GLN* 1.3 65.8 + - - +
557E SER* 5.2 1.4 - - - +
558E GLU* 5.8 2.8 + - - +
564E CYS* 3.0 7.4 - - - +
565E VAL* 2.6 65.5 + - + +
567E THR* 3.1 14.3 + - - -
576E HIS* 2.9 28.7 + - - -
813K PTR 2.9 42.2 + - - -
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Residues in contact with GLN 556 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623C SER* 3.3 13.2 - - - -
624C TYR* 2.8 76.1 + - + +
626C PRO* 4.5 7.1 - - - +
528E PHE* 3.4 32.2 - - + -
530E GLY 2.8 10.0 + - - +
531E MET* 3.3 21.0 + - - +
532E LEU 4.4 4.3 - - - +
555E ARG* 1.3 80.9 + - - +
557E SER* 1.3 65.5 + - - +
558E GLU* 3.6 1.4 + - - +
563E GLU 4.0 4.9 - - - +
564E CYS* 4.0 9.5 - - - +
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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