Contacts of the strand formed by residues 553 - 558 (chain D) in PDB entry 2IHU
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 PHE 553 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483D ILE 3.1 7.3 + - - +
484D VAL* 3.3 7.3 - - + +
485D THR* 2.8 26.9 + - - +
528D VAL* 4.3 2.7 - - - -
529D ASP* 3.3 24.0 - - + -
530D ALA* 3.8 12.1 - - - -
531D THR* 3.6 28.7 - - + -
542D ALA* 3.3 27.8 - - - -
545D LYS* 3.8 32.1 - - + -
546D GLY* 3.6 24.2 - - - +
549D LEU* 3.7 19.3 - - + -
551D ARG 3.7 2.2 + - - +
552D PRO* 1.3 74.3 - - - +
554D LEU* 1.3 59.7 + - - +
555D ILE* 3.8 23.6 - - + -
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Residues in contact with LEU 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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466D PHE* 3.5 34.3 - - + -
473D LEU* 4.1 12.1 - - + -
485D THR* 3.4 16.6 - - + +
487D VAL* 3.7 17.7 - - + -
519D PHE* 3.5 30.3 - - + +
520D VAL* 4.4 0.7 - - - +
523D ALA* 3.8 21.1 - - + -
528D VAL* 4.2 4.4 - - + +
529D ASP 2.9 8.3 + - - +
530D ALA* 3.0 7.8 - - + +
531D THR 2.9 25.5 + - - +
553D PHE* 1.3 74.6 - - - +
555D ILE* 1.3 78.8 + - - +
556D GLU 4.0 3.4 - - - +
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Residues in contact with ILE 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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484D VAL* 3.8 23.6 - - + -
485D THR 2.7 11.5 + - - +
486D VAL* 3.3 9.8 - - + +
487D VAL 2.8 26.9 + - - -
531D THR* 3.3 7.2 - - + +
533D ALA* 3.8 29.2 - - + -
539D LEU* 3.9 12.3 - - + -
542D ALA* 3.7 39.5 - - + +
543D LEU* 3.7 17.0 - - + +
553D PHE* 3.8 10.5 - - + -
554D LEU* 1.3 80.5 - - - +
556D GLU* 1.3 62.3 + - - +
557D VAL* 3.8 5.1 + - + -
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Residues in contact with GLU 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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487D VAL* 3.6 9.4 - - - +
489D ASN* 2.9 31.7 + - + +
517D VAL 3.9 3.6 - - - +
518D ASP* 3.8 5.4 - - - +
519D PHE* 2.8 49.3 + - + +
520D VAL* 3.5 20.9 + - + +
531D THR 2.9 6.9 + - - -
532D ARG* 3.4 19.6 + - + +
533D ALA 2.9 26.2 + - - +
554D LEU* 4.0 2.8 - - + +
555D ILE* 1.3 72.1 - - - +
557D VAL* 1.3 66.2 + - - +
558D PRO* 4.2 4.0 - - + +
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Residues in contact with VAL 557 (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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382D MET* 3.7 24.2 - - + -
387D VAL* 4.1 13.0 - - + -
486D VAL* 3.9 24.7 - - + -
487D VAL 2.8 12.8 + - - +
488D VAL* 3.3 7.1 - - + -
489D ASN 2.9 24.3 + - - -
533D ALA 3.4 15.9 - - - +
539D LEU* 3.9 22.9 - - + -
555D ILE* 3.9 5.4 - - + -
556D GLU* 1.3 81.5 - - - +
558D PRO* 1.4 76.6 - - - +
559D VAL* 3.8 2.1 - - + +
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Residues in contact with PRO 558 (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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380D ASP 4.6 4.3 - - - +
381D GLY* 4.0 15.0 - - - -
382D MET 2.9 21.8 + - - -
489D ASN* 3.5 13.7 - - + +
532D ARG* 3.5 36.3 - - - +
533D ALA 3.5 13.0 - - - +
534D THR* 4.2 12.1 - - + -
556D GLU* 4.1 6.7 - - + +
557D VAL* 1.4 89.1 - - - +
559D VAL* 1.3 61.8 + - - +
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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