Contacts of the strand formed by residues 553 - 558 (chain A) in PDB entry 1DY7
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 PRO 553 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.3 4.3 - - + -
172A THR 3.2 11.0 - - - +
173A LEU* 4.6 0.7 - - + -
520A SER* 3.4 10.9 - - - -
521A VAL 3.9 5.2 - - - +
522A TRP* 3.5 12.3 - - - +
529A SER* 3.2 30.3 - - - +
530A ALA 3.8 16.4 - - - +
531A LEU* 3.5 23.1 - - + -
550A LEU* 3.8 19.7 - - + +
551A VAL 3.3 4.7 - - - +
552A THR* 1.3 88.7 - - - +
554A THR* 1.3 63.0 + - - +
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Residues in contact with THR 554 (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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171A VAL* 4.9 0.4 - - - +
172A THR* 3.1 30.0 + - - +
174A ARG* 4.1 13.6 - - + +
199A VAL 4.7 1.7 + - - -
200A HIS 5.8 0.2 + - - -
506A VAL* 4.5 9.4 - - - +
507A GLN* 3.9 0.8 - - - +
520A SER* 2.6 25.4 + - - -
522A TRP* 3.6 37.0 - - + +
552A THR 3.7 7.4 - - - +
553A PRO* 1.3 77.7 - - - +
555A GLY* 1.3 72.5 + - - +
556A LYS* 3.3 6.9 + - - +
602A DHE 4.2 22.0 + - + +
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Residues in contact with GLY 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER 3.8 0.5 - - - +
171A VAL* 3.4 2.3 - - - +
172A THR* 2.8 35.7 + - - -
200A HIS 5.2 1.9 + - - -
507A GLN* 3.4 7.9 - - - -
554A THR* 1.3 85.3 + - - +
556A LYS* 1.3 60.5 + - - +
557A PHE* 4.0 12.3 - - - -
602A DHE 3.6 22.9 - - - +
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Residues in contact with LYS 556 (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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169A PHE* 4.4 7.4 - - + -
170A SER 3.4 4.7 - - - -
171A VAL* 3.9 22.9 - - + -
506A VAL 3.1 9.5 + - - -
507A GLN* 2.7 70.4 + - - +
509A GLU* 3.5 18.0 - - + +
518A TRP* 3.4 39.5 - - + -
519A PHE 4.2 1.6 - - - -
520A SER* 2.8 33.2 + - - +
531A LEU* 4.4 8.7 - - + -
554A THR 3.3 3.0 + - - +
555A GLY* 1.3 77.7 - - - +
557A PHE* 1.3 64.2 + - - +
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Residues in contact with PHE 557 (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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169A PHE* 3.4 2.7 - - - -
170A SER* 2.8 41.4 + - - +
172A THR* 5.1 1.8 - - - -
200A HIS 4.7 0.2 - - - -
201A ILE* 3.8 9.6 - - + -
202A SER* 3.5 46.7 - - - +
203A ARG* 3.2 26.0 - - - -
204A LEU* 5.2 3.3 - - + +
391A ARG* 3.8 11.4 - - - -
507A GLN* 3.5 10.1 - - - -
509A GLU* 3.5 2.0 - - - -
555A GLY* 4.0 8.1 - - - -
556A LYS* 1.3 84.5 - - - +
558A ASN* 1.3 64.5 + - - +
559A VAL* 3.5 3.1 + - - +
562A THR* 3.5 14.6 - - - +
602A DHE 3.5 46.9 - - + -
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Residues in contact with ASN 558 (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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166A GLU 3.4 14.8 + - - -
167A ASN* 3.6 14.1 + - - -
168A LEU 3.4 12.3 + - - -
169A PHE* 3.7 14.8 - - + +
509A GLU* 2.7 16.2 + - - +
510A PHE 3.2 25.6 - - - +
512A LYS 3.6 16.5 + - - +
557A PHE* 1.3 70.3 - - - +
559A VAL* 1.3 64.3 + - - +
560A TYR* 3.2 10.3 + - - +
561A ASN* 2.9 32.6 + - + +
562A THR* 2.7 29.5 + - - -
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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