Contacts of the strand formed by residues 370 - 378 (chain A) in PDB entry 3H44
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 PHE 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A LEU* 5.3 3.1 - - + -
213A HIS* 4.1 7.9 - + - -
215A PHE* 3.5 36.3 - + + -
288A PHE* 3.8 27.1 - + + +
290A GLU 4.5 0.2 - - - -
291A HIS* 3.1 29.4 - - + +
292A PRO* 3.4 24.2 - - + -
319A ILE 3.9 4.3 - - - -
321A ASP 4.1 1.8 - - - +
366A GLY* 3.2 16.8 - - - -
367A ALA* 2.9 61.3 + - + +
369A GLY* 1.3 77.0 - - - +
371A MET* 1.3 62.7 + - - +
372A PHE* 3.7 18.4 - + - -
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Residues in contact with MET 371 (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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291A HIS* 2.8 22.2 + - - -
319A ILE* 2.9 30.9 + - + -
320A PRO 3.7 5.3 - - - +
321A ASP* 4.1 12.1 - - - +
322A LEU* 3.4 31.6 - - - -
323A GLN* 4.5 3.1 - - - -
363A GLN* 3.6 39.9 - - + +
364A LYS 3.5 22.2 - - - +
365A GLU* 4.3 9.9 - - + -
366A GLY 4.0 8.1 - - - +
367A ALA 5.0 0.7 - - - +
370A PHE* 1.3 77.7 - - - +
372A PHE* 1.3 73.0 + - - +
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Residues in contact with PHE 372 (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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205A GLU* 4.5 4.9 - - - -
215A PHE* 3.7 23.6 - + - -
291A HIS* 3.7 9.9 - + - -
292A PRO* 5.0 2.0 - - + -
293A PHE* 3.2 39.9 - + - -
316A THR* 4.2 9.4 - - - +
317A PHE 3.4 9.0 - - - +
318A PRO* 4.7 0.4 - - + -
319A ILE* 3.3 12.8 - - - +
363A GLN* 3.5 0.5 - - - -
364A LYS* 3.0 50.0 + - + +
365A GLU 3.8 15.9 - - - -
366A GLY* 3.7 22.7 - - - -
370A PHE* 3.7 23.3 - + - -
371A MET* 1.3 77.3 - - - +
373A PHE* 1.3 61.1 + - - +
374A ILE* 4.2 11.2 - - + -
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Residues in contact with PHE 373 (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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317A PHE* 2.8 40.1 + + - +
319A ILE* 3.8 11.6 - - + +
331A GLY* 4.1 9.0 - - - -
334A LEU* 3.9 23.1 - - + -
338A ILE* 3.6 29.4 - - + -
362A GLY* 3.4 30.5 - - - -
363A GLN* 3.9 9.0 - - + -
372A PHE* 1.3 76.2 - - - +
374A ILE* 1.3 78.9 - - - +
375A ILE* 4.2 10.1 - - + -
467A VAL* 4.7 10.3 - - + -
471A LEU* 3.7 41.5 - - + -
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Residues in contact with ILE 374 (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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315A VAL 3.4 5.4 - - - +
316A THR* 3.7 22.4 - - + +
360A VAL* 4.0 15.7 - - + +
361A GLY* 2.9 5.7 - - - -
362A GLY 2.7 47.2 + - - +
364A LYS* 3.9 36.8 - - + -
372A PHE* 4.2 7.6 - - + -
373A PHE* 1.3 81.7 - - - +
375A ILE* 1.3 66.4 + - - +
376A ASN* 3.6 30.7 - - - +
3C LEU* 3.8 22.0 - - + -
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Residues in contact with ILE 375 (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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313A LEU 4.0 0.3 - - - +
315A VAL* 2.8 37.3 + - + +
317A PHE* 4.3 20.9 - - + -
338A ILE* 3.8 28.3 - - + -
346A LEU* 4.5 1.1 - - + -
359A LEU* 4.2 20.4 - - + -
360A VAL 3.3 8.3 - - - +
361A GLY* 4.8 0.2 - - - -
373A PHE* 4.2 10.8 - - + -
374A ILE* 1.3 79.9 - - - +
376A ASN* 1.3 68.3 + - - +
394A MET* 3.3 44.6 - - + +
398A ILE* 4.6 16.4 - - + -
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Residues in contact with ASN 376 (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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313A LEU 3.3 8.1 - - - +
314A TYR* 3.3 35.0 - - + +
315A VAL 3.5 12.6 + - - +
359A LEU* 3.2 3.6 - - - -
360A VAL* 2.7 51.7 + - + +
364A LYS* 5.9 2.0 - - - +
374A ILE* 3.6 26.4 - - - +
375A ILE* 1.3 88.9 + - - +
377A VAL* 1.3 63.1 + - - +
2000A DIO 5.7 1.8 + - - -
3C LEU* 5.5 1.6 - - - +
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Residues in contact with VAL 377 (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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312A ASN* 3.5 5.8 - - - +
313A LEU* 3.0 54.9 + - + +
314A TYR* 6.1 0.2 - - - -
350A LEU* 4.5 2.5 - - + -
356A VAL* 3.8 23.1 - - + -
358A THR 3.2 12.8 - - - +
359A LEU* 3.7 28.7 - - + -
376A ASN* 1.3 80.2 - - - +
378A ASP* 1.3 71.9 + - - +
379A LEU* 4.2 2.2 - - + -
390A ILE* 4.6 3.8 - - + -
394A MET* 4.1 14.8 - - + -
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Residues in contact with ASP 378 (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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311A ARG 3.4 2.9 - - - +
312A ASN* 3.3 19.7 - - - +
356A VAL* 3.3 16.8 - - - +
357A ASN* 2.7 48.4 + - - +
358A THR* 3.0 26.3 + - - +
377A VAL* 1.3 78.6 - - - +
379A LEU* 1.3 69.5 + - - +
668A ARG* 6.3 2.0 - - - +
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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