Contacts of the strand formed by residues 550 - 554 (chain X) in PDB entry 1T6B
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 550 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493X PHE* 3.5 38.8 - + - -
494X ASN* 4.5 0.2 - - - -
495X GLY* 3.8 17.5 - - - -
533X PHE* 4.5 7.9 - + - -
542X TYR* 4.7 5.6 - + + -
545X LYS* 3.8 38.1 - - + -
546X ASP 3.6 20.0 - - - -
547X ILE* 3.1 19.9 + - + +
548X THR 3.1 0.2 - - - -
549X GLU* 1.3 81.7 - - + +
551X ASP* 1.3 56.0 + - - +
552X PHE* 4.2 1.1 - - + -
575X TYR* 2.5 31.0 + - - -
591X ILE* 3.7 15.5 - - + -
592X ARG 3.4 4.0 - - - +
593X ASP* 3.5 32.5 - - + -
594X LYS* 3.7 2.9 - - - -
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Residues in contact with ASP 551 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550X PHE* 1.3 72.5 - - - +
552X PHE* 1.3 77.0 + - - +
553X ASN* 3.9 3.8 + - - +
575X TYR* 4.0 4.5 - - - -
590X LEU 3.2 8.1 - - - +
591X ILE* 3.2 4.3 - - - +
592X ARG* 2.8 63.3 + - + +
594X LYS* 3.9 18.6 - - + +
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Residues in contact with PHE 552 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523X LEU* 3.8 26.5 - - + -
527X LEU* 4.0 8.3 - - + -
547X ILE* 3.7 26.9 - - + -
550X PHE 4.4 2.9 - - - -
551X ASP* 1.3 84.3 + - - +
553X ASN* 1.3 62.2 + - - +
554X PHE* 3.7 29.0 - + + -
574X ILE* 4.0 16.8 - - + -
575X TYR* 3.6 34.9 + + - -
578X LEU* 4.1 13.0 - - + -
589X ILE* 4.1 12.8 - - + -
590X LEU 3.8 1.3 - - - -
591X ILE* 3.7 28.0 - - + -
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Residues in contact with ASN 553 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301X SER* 5.4 0.2 + - - -
320X VAL* 3.4 23.6 + - - +
321X SER* 3.4 5.0 + - - +
322X ALA* 3.0 30.5 + - - +
551X ASP* 3.9 11.5 + - - +
552X PHE* 1.3 75.0 + - - +
554X PHE* 1.3 65.8 + - - +
589X ILE* 3.6 2.8 - - - +
590X LEU* 2.7 53.8 + - + +
592X ARG* 3.9 19.3 + - - +
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Residues in contact with PHE 554 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320X VAL 4.8 0.3 - - - +
321X SER* 3.6 10.4 + - - -
322X ALA* 3.3 15.3 + - - -
523X LEU* 5.0 2.2 - - + -
552X PHE* 3.7 34.1 - + + -
553X ASN* 1.3 80.3 + - - +
555X ASP* 1.3 63.8 + - - +
558X THR* 3.8 12.1 - - + -
559X SER* 3.7 34.5 + - - +
562X ILE* 4.0 32.5 - - + -
574X ILE* 3.7 20.2 - - + -
588X ASN 3.6 3.8 - - - +
589X ILE* 3.7 41.5 - - + -
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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