Contacts of the strand formed by residues 551 - 555 (chain A) in PDB entry 2H3W
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 LEU 551 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A LEU* 4.0 22.0 - - + -
438A GLN* 4.1 8.1 - - - +
441A TYR* 3.8 28.7 - - + -
449A CYS* 3.8 10.5 - - - -
450A ALA 3.5 3.0 + - - +
451A THR* 3.4 30.2 - - + +
452A TYR 2.8 26.9 + - - -
549A PHE* 2.9 6.7 - - - +
550A ASN* 1.3 86.5 - - - +
552A SER* 1.3 60.0 + - - +
553A THR* 4.0 4.5 - - + -
574A TYR* 3.9 19.5 - - + -
576A ILE* 3.9 28.0 - - + -
603A MET* 4.7 1.8 - - - -
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Residues in contact with SER 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A TYR* 3.8 9.3 - - - -
549A PHE* 4.1 2.4 + - - -
551A LEU* 1.3 72.1 - - - +
553A THR* 1.3 60.3 + - - +
566A PHE* 3.3 10.7 - - - -
569A VAL* 3.5 31.6 - - - +
574A TYR 3.1 14.2 + - - +
575A GLY* 4.9 0.2 - - - -
576A ILE 2.9 23.2 + - - -
1602A HC5 3.3 34.7 - - - -
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Residues in contact with THR 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A GLN* 3.3 24.3 + - - +
437A LEU* 3.6 31.2 - - + -
451A THR* 4.7 2.9 - - + -
452A TYR* 2.7 29.7 + - - +
453A GLU* 3.4 5.4 - - - +
454A SER* 3.2 19.1 + - - -
551A LEU* 4.4 6.1 - - + -
552A SER* 1.3 86.0 + - - +
554A ALA* 1.3 67.4 + - - +
566A PHE* 4.2 3.4 - - - -
576A ILE* 3.0 20.9 - - + -
578A TYR* 4.7 3.1 - - - -
1602A HC5 4.0 1.6 - - - -
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Residues in contact with ALA 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A GLU* 4.9 3.6 - - - -
454A SER* 3.2 19.1 - - - +
553A THR* 1.3 83.0 - - - +
555A GLN* 1.3 61.4 + - - +
566A PHE* 4.5 4.3 - - + -
576A ILE 3.2 4.0 + - - -
577A CYS* 3.5 7.4 - - - -
578A TYR* 3.3 28.0 + - - -
1601A COA 4.4 2.9 - - + +
1602A HC5 3.0 38.6 - - + +
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Residues in contact with GLN 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A PRO* 5.6 0.2 - - - +
430A ASP* 2.8 46.2 + - - +
453A GLU* 4.6 3.1 + - - +
454A SER 5.3 1.2 + - - -
554A ALA* 1.3 73.6 - - - +
556A VAL* 1.3 60.8 + - - +
557A PRO* 3.0 33.7 - - + +
578A TYR* 3.5 13.1 + - + +
580A PRO* 3.1 43.3 - - + +
1601A COA 3.1 59.1 + - + +
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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