Contacts of the strand formed by residues 377 - 382 (chain A) in PDB entry 4PBZ
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 ILE 377 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A PHE* 5.2 3.3 - - - +
336A SER* 3.7 23.0 + - - +
337A GLY* 3.1 24.4 + - - +
340A ARG 3.6 13.7 - - - +
341A ARG 3.6 33.7 - - - +
342A LEU* 3.7 14.4 - - + +
370A HIS* 5.2 0.2 - - + -
373A HIS* 3.8 37.5 - - + +
375A ALA 3.3 0.4 + - - +
376A LYS* 1.3 80.4 - - - +
378A SER* 1.3 62.7 + - - +
379A ASP 3.8 15.7 - - - +
392A SER* 4.5 8.7 - - - -
393A VAL 3.6 11.2 - - - +
394A SER* 4.2 0.2 - - - +
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Residues in contact with SER 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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44A SER 3.8 21.5 + - - -
45A LEU* 3.8 27.6 - - - +
129A ARG* 5.3 5.2 + - - -
321A PHE* 5.4 6.1 - - - +
322A GLN* 5.1 5.0 - - - +
336A SER* 5.4 1.1 - - - -
376A LYS* 3.4 7.8 + - - +
377A ILE* 1.3 75.2 - - - +
379A ASP* 1.3 62.1 + - - +
393A VAL 2.8 12.7 + - - -
395A GLU* 3.5 31.5 + - - +
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Residues in contact with ASP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU 3.7 9.8 - - - +
46A THR* 3.3 9.7 + - - -
47A ALA* 2.9 36.4 + - - +
129A ARG* 4.6 5.7 + - - -
131A ARG* 3.2 22.3 + - - -
322A GLN* 2.8 32.9 + - - -
377A ILE* 3.6 5.4 - - - +
378A SER* 1.3 81.4 - - - +
380A PHE* 1.3 78.5 + - - +
392A SER* 3.6 0.2 - - - -
393A VAL* 3.0 30.3 + - + +
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Residues in contact with PHE 380 (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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47A ALA* 4.2 6.8 - - - +
322A GLN* 3.5 18.8 + - + -
324A GLN* 3.8 37.3 - - + +
334A ALA* 3.5 43.7 - - + -
335A SER 4.2 0.4 - - - -
336A SER* 3.3 37.9 - - - -
342A LEU* 3.5 27.1 - - + -
379A ASP* 1.3 88.3 + - - +
381A SER* 1.3 67.7 + - - +
382A TRP* 4.1 6.7 - + - -
390A ILE* 4.1 11.2 - - + -
391A CYS 3.1 14.1 - - - +
392A SER* 3.8 3.8 - - - -
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Residues in contact with SER 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.8 6.3 - - - -
48A GLN* 3.5 25.3 - - - +
49A TRP* 2.9 38.7 + - - +
66A LEU* 5.1 0.2 - - - -
324A GLN* 5.6 2.2 - - - -
380A PHE* 1.3 78.9 - - - +
382A TRP* 1.3 62.8 + - - +
390A ILE* 3.6 3.8 - - - -
391A CYS* 2.8 34.1 + - - -
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Residues in contact with TRP 382 (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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49A TRP* 3.4 6.8 - - - +
324A GLN* 2.9 36.7 + - + +
325A TRP 3.3 16.4 + - - -
326A SER* 3.7 23.1 - - - -
327A PRO* 3.5 21.5 - - + +
328A HIS* 6.1 0.7 - - - -
332A ILE* 3.7 27.4 - - + -
333A LEU 4.2 0.2 - - - -
334A ALA* 3.6 30.5 - - + +
344A VAL* 4.1 10.3 - - + -
380A PHE* 4.3 3.8 - + - -
381A SER* 1.3 76.1 + - - +
383A ASN* 1.3 61.6 + - - +
384A PRO* 3.4 6.8 - - - +
388A TRP* 4.2 33.2 - + - -
389A VAL 3.6 10.5 - - - -
390A ILE* 3.6 31.0 - - + -
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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