Contacts of the strand formed by residues 370 - 379 (chain I) in PDB entry 5DST
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 370 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I TYR 5.0 1.1 - - - +
190I CYS 5.0 2.5 - - - +
192I PHE* 4.0 13.2 - - + +
193I TYR* 3.6 38.6 - - + +
195I SER* 4.6 8.5 - - - +
360I MET* 3.8 26.5 - - + -
361I LYS 3.6 13.0 - - - +
362I PRO* 4.5 5.2 - - + -
368I ARG 4.6 0.9 - - - +
369I ASP* 1.3 79.7 - - - +
371I ASP* 1.3 63.6 - - - +
372I PHE* 3.6 33.9 + - + -
391I TYR 3.9 0.2 - - - +
392I LYS* 3.3 5.4 - - - +
393I MET* 2.9 37.6 + - + +
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Residues in contact with ASP 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360I MET* 3.0 26.3 - - - +
361I LYS* 2.9 37.3 + - + +
363I ASN* 3.2 39.7 + - - +
364I ALA 4.7 0.9 + - - -
369I ASP* 4.2 0.9 + - - +
370I LEU* 1.3 75.4 - - - +
372I PHE* 1.3 62.2 + - - +
391I TYR 3.7 3.4 - - - +
392I LYS* 3.4 24.3 + - - +
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Residues in contact with PHE 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I CYS* 3.9 21.3 - - + -
221I LEU* 6.2 0.4 - - + -
340I PHE* 3.9 31.2 - + + -
358I ILE* 4.3 16.4 - - + -
359I SER 3.2 7.9 - - - -
360I MET* 3.6 30.7 - - + -
370I LEU* 3.6 41.1 - - + -
371I ASP* 1.3 77.1 - - - +
373I THR* 1.3 70.0 + - - +
374I VAL* 5.1 1.6 - - + -
389I ASN 4.6 0.2 - - - -
390I ASP* 3.5 5.0 - - - +
391I TYR* 2.9 48.6 + - + +
393I MET* 3.8 19.5 - - + -
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Residues in contact with THR 373 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I THR* 3.7 1.6 + - - +
358I ILE* 3.3 3.5 - - - -
359I SER* 2.8 47.3 + - - +
372I PHE* 1.3 76.7 + - - +
374I VAL* 1.3 62.6 + - - +
375I ASP* 3.4 25.7 + - - +
388I SER* 3.8 9.9 - - - +
389I ASN 3.4 4.3 - - - +
390I ASP* 2.9 22.7 + - - +
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Residues in contact with VAL 374 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294I PHE* 4.3 7.2 - - + -
307I LEU* 3.8 29.8 - - + -
340I PHE* 4.8 10.8 - - + -
342I LEU* 5.7 2.9 - - + -
357I THR 3.5 5.8 - - - +
358I ILE* 4.3 20.6 - - + -
372I PHE* 5.1 2.0 - - + -
373I THR* 1.3 76.5 - - - +
375I ASP* 1.3 74.6 + - - +
376I LEU* 4.6 7.7 - - + +
387I VAL 4.0 0.7 - - - +
388I SER* 3.5 1.2 - - - -
389I ASN* 2.9 34.3 + - + +
391I TYR* 3.9 28.3 - - + +
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Residues in contact with ASP 375 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294I PHE* 3.8 3.8 - - - -
356I GLY* 3.0 23.8 - - - -
357I THR* 2.9 31.2 + - + +
373I THR* 3.4 14.0 - - - +
374I VAL* 1.3 73.8 - - - +
376I LEU* 1.3 60.4 + - - +
377I ASP* 5.0 3.8 - - - +
387I VAL 3.2 5.4 - - - +
388I SER* 2.3 34.5 + - - -
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Residues in contact with LEU 376 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294I PHE* 4.7 1.8 - - + -
307I LEU* 4.3 23.8 - - + -
342I LEU* 4.2 28.7 - - + -
346I LEU* 4.1 23.8 - - + -
354I ILE* 3.7 28.7 - - + -
355I TYR 3.6 2.0 - - - +
374I VAL* 4.6 6.5 - - + +
375I ASP* 1.3 76.7 - - - +
377I ASP* 1.3 71.8 + - - +
378I PHE* 4.4 4.5 - - + +
385I THR* 4.4 10.1 - - - +
386I SER* 3.2 2.6 - - - -
387I VAL* 2.7 47.9 + - + +
389I ASN* 6.3 1.3 - - - +
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Residues in contact with ASP 377 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353I GLU 4.3 0.9 - - - +
354I ILE* 3.9 1.2 - - - +
355I TYR* 2.8 49.1 + - + +
356I GLY* 4.6 1.1 - - - -
375I ASP* 5.0 3.1 - - - +
376I LEU* 1.3 81.8 + - - +
378I PHE* 1.3 61.6 + - - +
385I THR 3.7 2.9 - - - -
386I SER* 3.4 25.7 + - - -
387I VAL 4.4 1.6 + - - +
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Residues in contact with PHE 378 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298I ILE* 4.1 3.8 - - + -
346I LEU* 4.4 12.6 - - + -
347I THR 3.8 14.4 - - - -
348I VAL* 3.7 21.8 - - + -
352I GLU* 3.5 36.6 - - + -
353I GLU 3.2 32.8 - - - -
354I ILE* 3.8 9.6 - - + -
355I TYR* 6.1 0.2 - - - -
376I LEU* 4.2 12.5 - - + +
377I ASP* 1.3 74.9 - - - +
379I LYS* 1.3 61.1 + - - +
380I GLY* 3.4 19.5 - - - -
383I CYS* 3.6 28.5 - - - -
384I GLU* 3.2 5.4 - - - +
385I THR* 2.9 38.6 + - - +
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Residues in contact with LYS 379 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D THR 5.9 0.8 + - - -
352I GLU* 5.4 2.1 - - - +
353I GLU 4.7 3.9 + - - +
378I PHE* 1.3 77.1 - - - +
380I GLY* 1.3 63.3 + - - +
383I CYS 4.1 2.2 - - - -
384I GLU* 3.6 35.9 - - + +
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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