Contacts of the strand formed by residues 553 - 559 (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 ALA 553 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LEU* 3.5 2.6 - - - -
393A TYR* 2.8 39.8 + - + +
453A SER* 4.0 0.4 - - - +
454A SER* 3.6 4.5 - - - +
455A ALA* 4.0 15.3 - - + -
458A THR* 4.3 0.4 - - - +
537A ASN* 3.6 26.0 - - - +
552A THR* 1.3 77.1 - - - +
554A VAL* 1.3 64.4 + - - +
555A ASN* 3.5 22.3 + - - +
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Residues in contact with VAL 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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390A THR* 3.4 29.4 - - + -
391A TYR 3.5 5.6 - - - +
392A LEU* 3.9 17.7 - - + -
452A SER 4.2 0.2 - - - +
453A SER* 3.6 2.8 - - - -
454A SER* 2.9 40.7 + - - +
553A ALA* 1.3 71.8 - - - +
555A ASN* 1.3 60.5 + - - +
556A ARG* 5.2 5.9 - - + +
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Residues in contact with ASN 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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390A THR* 3.4 5.0 - - - +
391A TYR* 3.0 50.5 + - + -
393A TYR* 4.1 4.9 - - - +
452A SER 3.5 1.6 - - - -
453A SER* 2.6 35.0 + - - -
458A THR* 3.1 16.8 + - - +
460A PHE* 3.7 22.7 - - + -
526A SER* 2.8 22.8 + - - -
553A ALA* 3.5 13.0 + - - +
554A VAL* 1.3 76.5 - - - +
556A ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 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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388A ALA* 3.6 24.6 - - + +
389A ASP 3.2 12.1 - - - +
390A THR* 2.7 30.7 + - + +
451A VAL* 3.3 9.0 - - - +
452A SER* 2.9 43.8 + - - +
460A PHE* 4.5 0.2 - - - -
554A VAL* 5.2 5.3 - - + +
555A ASN* 1.3 77.1 - - - +
557A ILE* 1.3 66.6 + - - +
558A HIS* 3.6 25.4 + - + -
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Residues in contact with ILE 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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363A LEU* 3.9 28.3 - - + -
388A ALA* 3.2 5.2 - - - -
389A ASP* 2.9 32.6 + - + +
391A TYR* 4.5 3.1 - - + +
428A LEU* 3.4 31.2 - - + -
430A TYR* 4.0 6.5 - - - +
449A LEU* 4.4 7.0 - - + -
450A PHE 3.7 4.0 - - - +
451A VAL* 3.5 26.9 - - + -
460A PHE* 3.8 20.4 - - + -
524A VAL* 3.8 16.8 - - + -
556A ARG* 1.3 74.8 - - - +
558A HIS* 1.3 69.3 + - - +
559A ARG* 4.0 2.8 + - + +
565A SER* 4.4 3.8 - - - +
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Residues in contact with HIS 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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386A GLU* 5.4 1.6 - - - +
387A SER 3.7 6.1 - - - +
388A ALA* 4.2 12.6 - - + -
450A PHE* 2.8 24.2 + - + +
451A VAL* 4.0 3.4 - - - -
452A SER* 2.8 39.4 + - - -
500A ILE* 3.5 29.9 - - + +
556A ARG* 3.6 24.3 + - + -
557A ILE* 1.3 72.9 - - - +
559A ARG* 1.3 59.4 + - - +
563A HIS* 3.4 26.4 - + + +
565A SER* 2.6 30.1 + - - -
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Residues in contact with ARG 559 (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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363A LEU* 3.6 24.0 - - + +
364A GLY* 3.2 34.6 + - - +
365A GLY 2.9 25.2 + - - +
367A GLY 3.0 27.7 + - - -
369A ALA* 4.4 4.0 - - - +
376A GLY* 5.5 0.8 - - - -
383A SER* 4.9 2.1 - - - -
385A THR* 3.5 4.5 + - - +
386A GLU* 3.6 4.7 + - - +
387A SER* 2.8 61.4 + - - +
388A ALA 4.6 1.5 + - - +
389A ASP* 2.7 36.5 + - - +
430A TYR* 3.8 11.5 - - - -
557A ILE* 4.7 2.5 - - + +
558A HIS* 1.3 75.7 - - - +
560A GLY* 1.3 58.4 + - - +
563A HIS 3.2 5.4 - - - -
565A SER* 4.7 4.0 - - - +
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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