Contacts of the strand formed by residues 554 - 558 (chain A) in PDB entry 1N7D
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 554 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ILE* 5.9 2.9 - - + -
545A ILE* 5.7 5.4 - - + -
546A THR 4.5 4.3 - - - +
547A LEU* 4.6 9.8 - - + +
552A GLY 3.8 0.2 + - - -
553A ARG 1.3 67.1 - - - -
555A TYR* 1.3 54.1 - - - +
556A TRP* 4.2 8.7 - - + -
565A SER 4.0 0.9 - - - -
566A SER* 2.2 43.1 - - - -
567A ILE* 2.0 48.9 + - + +
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Residues in contact with TYR 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ILE* 3.3 6.6 - - - +
546A THR* 3.2 31.7 + - + +
547A LEU* 5.8 0.4 - - - -
553A ARG 3.8 2.2 + - - +
554A LEU* 1.3 74.3 - - - +
556A TRP* 1.3 56.6 + - - +
564A ILE* 5.0 6.1 - - + -
565A SER 3.5 4.7 - - - -
566A SER* 4.1 6.3 - - - +
590A LEU* 2.6 32.3 - - + +
592A VAL* 4.1 15.0 - - + -
597A VAL* 6.0 0.2 - - + -
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Residues in contact with TRP 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ILE* 4.8 14.6 - - + -
535A VAL* 4.3 26.9 - - + -
537A GLU 6.0 1.3 - - - -
538A ASN* 5.9 4.3 - - - -
539A ILE* 4.9 10.0 - - + +
542A PRO* 5.2 4.9 - - + -
543A ASN 5.4 1.1 - - - +
544A GLY 4.1 0.9 - - - +
545A ILE* 3.5 25.4 - - + -
554A LEU* 4.1 9.9 - - + -
555A TYR* 1.3 76.6 - - - +
557A VAL* 1.3 70.3 + - - +
558A ASP* 2.7 41.7 + - - -
564A ILE* 3.0 20.8 - - - +
565A SER* 2.7 59.4 + - - +
566A SER 4.1 0.2 - - - -
567A ILE* 3.5 30.7 - - + -
574A ARG* 4.3 9.6 - - + -
590A LEU* 3.2 5.8 - - - +
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Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A PRO 3.4 0.5 - - - -
543A ASN* 2.5 69.5 + - + +
544A GLY 3.6 3.6 + - - +
556A TRP* 1.3 78.9 - - - +
558A ASP* 1.3 60.6 + - - +
563A SER 4.0 2.0 - - - +
564A ILE* 4.0 11.0 - - + -
587A PRO* 3.1 36.6 - - + -
589A SER 3.6 8.7 - - - +
590A LEU* 3.1 31.0 - - + -
599A TRP* 4.9 4.7 - - + -
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Residues in contact with ASP 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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538A ASN 4.6 3.5 - - - +
539A ILE* 3.6 17.1 - - - +
541A TRP 3.4 6.5 - - - +
542A PRO* 4.0 2.8 - - - +
556A TRP* 2.7 39.7 + - - -
557A VAL* 1.3 75.4 - - - +
559A SER* 1.3 61.6 + - - +
561A LEU* 2.9 57.5 - - + +
563A SER* 2.9 26.3 + - - +
564A ILE 5.5 0.2 + - - -
565A SER* 5.0 1.9 + - - -
587A PRO* 3.5 6.1 - - - +
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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