Contacts of the strand formed by residues 387 - 393 (chain A) in PDB entry 1L7R
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 SER 387 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A GLY 4.6 3.5 + - - -
367A GLY 5.7 0.7 - - - -
385A THR* 3.3 15.2 + - - -
386A GLU* 1.3 79.9 + - - +
388A ALA* 1.3 65.7 + - - +
558A HIS* 3.7 3.1 - - - +
559A ARG* 2.8 62.3 + - - +
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Residues in contact with ALA 388 (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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368A ALA* 5.8 0.9 - - - -
387A SER* 1.3 80.6 - - - +
389A ASP* 1.3 68.3 + - - +
390A THR* 4.2 2.8 + - - +
556A ARG* 3.6 27.4 - - + +
557A ILE 3.2 12.8 - - - +
558A HIS* 4.2 10.5 - - + -
559A ARG* 4.6 1.2 + - - +
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Residues in contact with ASP 389 (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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367A GLY 3.9 0.2 - - - +
368A ALA* 3.6 7.3 - - - +
369A ALA* 2.9 29.5 + - - +
370A ASN* 4.4 2.9 - - - +
388A ALA* 1.3 75.1 - - - +
390A THR* 1.3 61.4 + - - +
428A LEU* 3.7 29.4 - - + +
430A TYR* 2.7 23.3 + - - +
555A ASN 4.0 0.3 - - - +
556A ARG* 3.2 3.1 - - - -
557A ILE* 2.9 34.1 + - - +
559A ARG* 2.7 37.4 + - - -
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Residues in contact with THR 390 (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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370A ASN* 2.9 23.0 + - - +
388A ALA 4.2 3.6 + - - -
389A ASP* 1.3 75.2 - - - +
391A TYR* 1.3 68.3 + - - +
425A ASP* 4.4 1.2 - - - +
554A VAL* 3.4 31.0 - - + -
555A ASN 3.4 8.5 - - - +
556A ARG* 2.7 39.5 + - + +
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Residues in contact with TYR 391 (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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370A ASN* 3.9 0.4 - - - +
389A ASP 5.0 0.2 - - - -
390A THR* 1.3 81.5 - - - +
392A LEU* 1.3 63.5 + - - +
393A TYR* 4.3 4.9 - - + -
425A ASP* 3.6 26.7 - - - +
426A ASP* 3.7 26.7 - - + -
428A LEU* 3.6 40.4 - - + -
460A PHE* 3.4 11.8 - - - -
524A VAL* 4.7 0.7 - - - +
525A SER* 3.1 22.0 + - - -
526A SER* 2.7 38.7 + - - -
554A VAL* 3.5 5.1 - - - +
555A ASN* 3.0 48.0 + - + +
557A ILE* 4.5 7.0 - - + -
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Residues in contact with LEU 392 (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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391A TYR* 1.3 75.4 - - - +
393A TYR* 1.3 61.6 + - - +
394A ASP* 3.9 8.4 + - + +
425A ASP* 4.8 3.0 + - - -
426A ASP* 3.7 17.5 - - - +
552A THR* 3.9 33.2 - - + +
553A ALA 3.5 18.6 - - - +
554A VAL* 3.9 16.4 - - + +
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Residues in contact with TYR 393 (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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391A TYR* 3.9 7.1 + - + -
392A LEU* 1.3 73.1 - - - +
394A ASP* 1.3 77.6 + - - +
395A PRO* 3.6 9.1 - - + +
397A ASP 5.2 0.2 - - - -
398A PRO* 4.6 4.5 - - + -
426A ASP* 5.0 9.2 - - + +
458A THR* 3.7 10.5 - - - -
526A SER* 3.8 32.8 - - - -
527A SER* 3.7 27.2 - - - -
534A ARG* 3.4 14.9 - - - +
535A ASN* 2.8 36.2 + - + -
537A ASN* 3.2 37.2 - - - -
552A THR* 3.3 3.5 - - - -
553A ALA* 2.8 41.8 + - + +
555A ASN* 4.1 5.2 - - - +
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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