Contacts of the strand formed by residues 553 - 558 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483C ILE 3.0 7.8 + - - +
484C VAL* 3.3 7.1 - - + -
485C THR* 2.8 32.4 + - - -
528C VAL* 4.1 3.6 - - - -
529C ASP* 3.1 37.0 - - + -
530C ALA* 3.8 4.5 - - - -
531C THR* 3.6 36.6 - - + -
542C ALA* 3.5 20.9 - - + -
545C LYS* 4.0 31.0 - - + -
546C GLY* 3.7 33.4 - - - -
549C LEU* 3.7 18.8 - - + -
551C ARG 3.7 1.5 + - - +
552C PRO* 1.3 74.5 - - - +
554C LEU* 1.3 53.1 + - - +
555C ILE* 3.7 20.2 - - + -
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Residues in contact with LEU 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C PHE* 3.6 33.7 - - + -
473C LEU* 4.0 14.8 - - + -
485C THR* 3.3 19.1 - - + +
487C VAL* 3.9 13.7 - - + -
519C PHE* 3.4 30.1 - - + +
520C VAL 4.4 0.2 - - - +
523C ALA* 3.8 21.8 - - + -
528C VAL* 4.1 4.7 - - + +
529C ASP 3.0 7.7 + - - +
530C ALA* 3.0 28.7 - - + +
531C THR 3.0 6.1 + - - -
553C PHE* 1.3 76.2 - - - +
555C ILE* 1.3 77.5 + - - +
556C GLU 4.1 3.1 - - - +
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Residues in contact with ILE 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C VAL* 3.8 24.5 - - + -
485C THR 2.6 10.8 + - - +
486C VAL* 3.3 10.1 - - + +
487C VAL 2.8 26.5 + - - -
531C THR* 3.2 9.9 - - + +
533C ALA* 3.8 28.3 - - + -
539C LEU* 4.0 10.3 - - + -
542C ALA* 3.7 35.9 - - + +
543C LEU* 3.8 16.4 - - + +
553C PHE* 3.7 15.5 - - + -
554C LEU* 1.3 83.6 - - - +
556C GLU* 1.3 62.2 + - - +
557C VAL* 3.8 2.6 + - + -
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Residues in contact with GLU 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C VAL* 3.6 10.8 - - - +
489C ASN* 3.0 33.5 + - + +
517C VAL 4.0 2.8 - - - +
518C ASP* 3.9 5.9 - - - +
519C PHE* 3.0 42.6 + - + +
520C VAL* 3.5 20.1 + - + +
531C THR 3.0 7.1 + - - -
532C ARG* 3.4 24.6 + - + +
533C ALA 2.9 26.9 + - - +
554C LEU* 4.1 2.6 - - + +
555C ILE* 1.3 72.1 - - - +
557C VAL* 1.3 65.8 + - - +
558C PRO* 4.2 2.5 - - - +
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Residues in contact with VAL 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C MET* 3.6 24.7 - - + -
387C VAL* 4.0 13.2 - - + -
486C VAL* 3.9 25.4 - - + -
487C VAL 2.9 11.7 + - - +
488C VAL* 3.4 6.4 - - + -
489C ASN 2.8 26.4 + - - -
533C ALA* 3.4 14.4 - - + +
539C LEU* 4.0 21.8 - - + -
555C ILE* 4.1 5.4 - - + -
556C GLU* 1.3 81.8 - - - +
558C PRO* 1.4 77.4 - - - +
559C VAL* 3.9 2.0 - - + +
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Residues in contact with PRO 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380C ASP 5.6 0.2 - - - -
381C GLY* 3.9 13.7 - - - -
382C MET 2.9 21.7 + - - -
489C ASN* 3.6 10.8 - - + +
532C ARG* 3.5 39.5 - - - +
533C ALA 3.4 13.5 - - - +
534C THR* 4.0 18.4 - - + -
556C GLU* 4.0 4.9 - - + +
557C VAL* 1.4 86.8 - - - +
559C 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