Contacts of the strand formed by residues 551 - 556 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540D LEU 4.9 0.7 - - - +
541D VAL* 3.9 15.6 - - - +
543D GLU 5.6 1.1 - - - +
548D SER* 2.7 46.1 + - - +
549D HIS 5.1 0.2 - - - -
550D GLY* 1.3 78.3 - - - +
552D PHE* 1.3 61.0 + - - +
568D PHE* 3.1 3.1 - - - +
569D ASN* 2.7 31.2 + - - +
623D SER* 3.0 24.9 - - - +
624D TYR 4.5 1.3 - - - -
625D VAL* 3.5 32.1 - - + +
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Residues in contact with PHE 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D TRP* 4.0 15.7 - + + -
541D VAL* 4.1 3.6 - - - -
550D GLY 3.7 9.2 - - - -
551D VAL* 1.3 75.6 - - - +
553D LEU* 1.3 77.7 + - - +
554D VAL* 4.8 1.1 - - + -
566D LEU* 3.7 20.6 - - + -
567D THR 3.0 14.8 - - - +
568D PHE* 3.6 11.7 - - + +
601D LEU* 3.6 26.9 - - + -
621D LEU* 3.9 26.9 - - + -
622D VAL 4.6 1.6 - - - -
623D SER* 2.9 45.5 + - - -
624D TYR* 3.2 26.9 - + + -
625D VAL* 3.0 27.0 + - - +
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Residues in contact with LEU 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D TRP 3.6 6.3 - - - -
529D HIS* 3.7 23.8 - - + +
532D LEU* 3.9 24.0 - - + -
537D ALA* 4.1 13.7 - - + +
540D LEU* 4.1 14.6 - - + -
541D VAL* 4.1 19.7 - - + -
552D PHE* 1.3 84.4 - - - +
554D VAL* 1.3 81.2 + - - +
555D ARG* 4.0 12.6 - - + +
566D LEU* 3.6 5.0 - - - +
567D THR* 2.9 42.7 + - - +
624D TYR* 4.9 0.4 - - - -
625D VAL* 4.5 2.7 - - + +
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Residues in contact with VAL 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D TRP* 3.0 40.5 + - + +
528D PHE* 3.5 19.1 - - + -
529D HIS* 2.8 28.1 + - - -
552D PHE* 4.7 1.3 - - + -
553D LEU* 1.3 81.1 - - - +
555D ARG* 1.3 67.9 + - - +
564D CYS* 4.5 5.4 - - + -
565D VAL 3.4 8.1 - - - +
566D LEU* 4.2 16.6 - - + -
579D LEU* 4.2 16.6 - - + -
597D ILE* 4.5 10.3 - - + -
601D LEU* 4.2 12.1 - - + -
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Residues in contact with ARG 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528D PHE* 4.7 1.3 - - - -
529D HIS* 5.1 0.4 - - + -
530D GLY 3.3 13.9 - - - +
532D LEU* 3.6 28.7 + - + +
533D SER 4.5 0.2 - - - -
534D ARG* 3.7 19.2 - - - +
537D ALA* 3.6 23.2 - - - +
553D LEU* 4.1 3.8 - - + -
554D VAL* 1.3 75.7 - - - +
556D GLN* 1.3 65.6 + - - +
557D SER* 5.3 1.0 - - - +
558D GLU* 5.9 2.2 - - - +
564D CYS* 3.2 7.4 - - - +
565D VAL* 2.7 66.4 + - + +
567D THR* 2.8 17.3 + - - +
576D HIS* 3.1 23.4 + - - -
813J PTR 2.7 43.4 + - - -
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Residues in contact with GLN 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D LEU* 6.0 1.2 - - - +
528D PHE* 3.2 32.6 - - + -
530D GLY 2.8 13.1 + - - +
531D MET* 3.5 17.3 + - - +
532D LEU 4.3 7.6 - - - +
555D ARG* 1.3 78.1 + - - +
557D SER* 1.3 66.3 + - - +
558D GLU* 3.6 1.4 + - - +
564D CYS* 4.0 14.7 - - - -
623F SER* 3.2 12.2 + - - -
624F TYR* 2.8 74.8 + - + +
626F PRO* 4.5 7.1 - - - +
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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