Contacts of the strand formed by residues 370 - 378 (chain B) in PDB entry 3N56
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B LEU* 5.2 4.7 - - + -
213B HIS* 3.8 15.5 - - - -
215B PHE* 3.6 30.3 - + + -
288B PHE* 3.7 22.9 - + + +
291B HIS* 3.4 27.1 - - + -
292B PRO* 3.5 29.4 - - + -
319B ILE 4.1 4.3 - - - -
321B ASP* 4.2 4.9 - - - +
366B GLY* 3.5 18.8 + - - -
367B ALA* 2.7 61.1 + - + +
369B GLY* 1.3 77.7 - - - +
371B MET* 1.3 64.5 + - - +
372B PHE* 3.7 17.0 - + - -
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Residues in contact with MET 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B HIS* 2.9 21.1 + - - -
319B ILE* 3.0 21.9 + - + +
320B PRO 3.5 15.3 - - - +
321B ASP* 3.9 9.0 - - - +
322B LEU* 3.2 34.1 - - + -
323B GLN* 4.3 6.7 - - + +
363B GLN* 3.5 37.5 - - + +
364B LYS 3.2 20.4 - - - +
365B GLU* 3.9 20.6 - - + +
366B GLY 4.1 6.1 - - - +
370B PHE* 1.3 75.2 - - - +
372B PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLU* 4.5 4.3 - - - -
215B PHE* 3.7 23.6 - + - -
291B HIS* 3.6 15.7 - + - -
292B PRO* 4.9 1.3 - - + -
293B PHE* 3.4 33.4 - + - -
316B THR* 4.1 18.8 - - + -
317B PHE 3.4 9.0 - - - +
318B PRO* 4.8 0.2 - - + -
319B ILE* 3.3 15.1 - - - +
363B GLN* 3.9 1.6 - - - -
364B LYS* 2.9 50.6 + - + +
365B GLU 3.8 16.2 - - - -
366B GLY* 3.7 22.9 - - - -
370B PHE* 3.7 23.3 - + - -
371B MET* 1.3 77.6 - - - +
373B PHE* 1.3 62.8 + - - +
374B ILE* 4.6 2.0 - - + -
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Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B THR* 3.4 2.9 - - - -
317B PHE* 2.8 45.8 + + + +
319B ILE* 4.3 9.9 - - + -
331B GLY* 4.1 12.6 - - - -
334B LEU* 3.8 27.1 - - + -
338B ILE* 3.7 33.0 - - + -
362B GLY* 3.5 28.7 - - - -
363B GLN* 4.2 7.4 - - + -
372B PHE* 1.3 73.4 - - - +
374B ILE* 1.3 78.9 + - - +
375B ILE* 4.5 6.1 - - + -
467B VAL* 4.8 8.5 - - + -
471B LEU* 3.9 37.0 - - + -
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B VAL 3.2 9.9 - - - +
316B THR* 4.1 17.3 - - + +
360B VAL* 4.3 13.0 - - + +
361B GLY* 3.4 0.3 - - - -
362B GLY 2.9 45.0 + - - +
364B LYS* 4.2 39.5 - - + +
372B PHE* 4.6 0.4 - - + -
373B PHE* 1.3 82.7 - - - +
375B ILE* 1.3 70.1 + - - +
376B ASN* 3.3 32.8 - - - +
2D PRO* 4.3 17.7 - - + -
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Residues in contact with ILE 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LEU 4.0 0.9 - - - +
315B VAL* 2.9 36.8 + - + +
317B PHE* 4.2 21.8 - - + -
338B ILE* 3.9 29.4 - - + -
346B LEU* 4.5 1.3 - - + -
359B LEU* 4.2 24.5 - - + -
360B VAL 3.4 3.8 - - - +
373B PHE* 4.5 10.1 - - + -
374B ILE* 1.3 79.5 - - - +
376B ASN* 1.3 62.3 + - - +
394B MET* 3.6 42.3 - - + +
398B ILE* 4.3 18.4 - - + -
471B LEU* 5.9 0.2 - - + -
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Residues in contact with ASN 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LEU 3.3 8.5 - - - +
314B TYR* 3.3 43.9 - - + +
315B VAL 3.5 3.6 + - - +
316B THR* 5.2 0.2 + - - -
359B LEU* 3.4 3.6 - - - +
360B VAL* 2.9 41.4 + - + +
374B ILE* 3.3 37.2 - - - +
375B ILE* 1.3 81.0 - - - +
377B VAL* 1.3 62.3 + - - +
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Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ASN* 3.5 6.9 + - - +
313B LEU* 2.9 64.9 + - + +
350B LEU* 4.6 1.8 - - + -
356B VAL* 3.8 22.7 - - + -
358B THR 3.5 11.2 - - - +
359B LEU* 3.7 29.2 - - + -
376B ASN* 1.3 80.3 - - - +
378B ASP* 1.3 69.7 + - - +
379B LEU* 4.2 3.1 - - + -
390B ILE* 4.6 0.7 - - + -
394B MET* 4.2 14.4 - - + -
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Residues in contact with ASP 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B ARG 3.5 1.6 - - - +
312B ASN* 3.1 22.7 - - - +
356B VAL* 3.3 21.3 - - - +
357B ASN* 2.8 45.0 + - - +
358B THR* 3.3 28.0 + - - +
377B VAL* 1.3 77.9 - - - +
379B LEU* 1.3 64.0 + - - +
668B ARG* 6.0 1.1 + - - -
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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