Contacts of the strand formed by residues 354 - 360 (chain A) in PDB entry 5I35
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 GLU 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A ALA 3.6 8.3 - - - +
348A ARG* 4.4 14.1 - - + +
352A GLY 3.3 9.6 + - - +
353A ARG* 1.3 76.6 - - - +
355A VAL* 1.3 66.2 + - - +
446A GLU* 3.8 4.0 - - - +
447A LEU* 3.2 48.7 + - + +
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Residues in contact with VAL 355 (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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346A LEU* 3.5 9.9 - - - +
347A ALA* 3.0 51.3 + - + +
349A MSE 4.1 26.7 - - + -
353A ARG* 4.1 8.5 - - - +
354A GLU* 1.3 83.2 - - - +
356A ALA* 1.3 60.8 + - - +
357A MSE 4.4 3.1 - - + -
434A VAL* 4.1 22.2 - - + -
437A LEU* 4.9 2.9 - - + -
444A THR* 3.9 16.2 - - + -
445A THR 3.4 13.7 - - - +
446A GLU* 4.4 1.6 - - - -
447A LEU* 3.9 7.0 - - - +
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Residues in contact with ALA 356 (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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336A PHE* 4.4 3.6 - - + -
344A VAL* 3.8 14.6 - - + -
345A HIS 3.6 4.7 - - - -
346A LEU* 4.7 0.2 - - - -
355A VAL* 1.3 72.3 - - - +
357A MSE 1.3 63.7 + - - +
358A LYS 3.8 0.2 + - - -
443A LEU 3.7 1.7 - - - +
444A THR* 3.4 3.2 - - - -
445A THR* 2.8 33.7 + - - +
447A LEU* 4.2 9.8 - - + +
700A ANP 3.8 40.6 - - + +
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Residues in contact with MSE 357 (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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316A LEU* 4.1 24.9 - - + -
320A LEU* 4.4 3.4 - - + -
324A TRP* 4.8 6.3 - - + -
328A LEU* 4.3 8.5 - - - -
331A PHE* 4.0 17.7 - - + -
343A GLN 3.6 1.0 - - - +
344A VAL* 3.2 3.9 - - - -
345A HIS* 2.8 44.2 + - + +
347A ALA* 3.9 26.7 - - + -
355A VAL* 4.4 1.3 - - + -
356A ALA* 1.3 74.5 - - - +
358A LYS* 1.3 60.5 + - - +
359A ILE* 3.7 13.9 + - + +
437A LEU* 3.8 30.5 - - + -
442A VAL* 4.3 6.7 - - + -
444A THR* 3.5 27.1 - - + +
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Residues in contact with LYS 358 (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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339A ALA* 4.2 9.0 - - + -
343A GLN 3.5 4.3 - - - +
344A VAL* 3.6 23.1 - - + +
356A ALA 3.8 1.4 + - - +
357A MSE 1.3 70.6 - - - +
359A ILE* 1.3 61.2 + - - +
408A TYR* 3.0 34.5 + - + +
411A GLU* 2.8 36.6 + - - -
442A VAL* 3.3 5.7 - - - +
443A LEU* 2.8 48.4 + - + +
507A ASP* 4.6 0.4 + - - -
700A ANP 2.9 51.1 + - + -
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Residues in contact with ILE 359 (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 MSE 4.0 25.2 - - + +
315A THR* 3.8 21.3 - - + -
316A LEU* 3.8 29.4 - - + -
331A PHE* 4.1 17.3 - - + -
342A GLY* 3.2 1.3 - - - -
343A GLN 2.7 34.7 + - - +
345A HIS* 3.6 27.1 - - + +
357A MSE 3.9 13.0 - - + +
358A LYS* 1.3 79.2 - - - +
360A GLN* 1.3 75.0 + - - +
408A TYR* 4.8 1.8 - - - -
441A HIS 3.8 2.0 - - - -
442A VAL* 4.3 5.8 - - + -
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Residues in contact with GLN 360 (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 MSE 4.4 3.2 - - - +
315A THR* 2.8 29.2 + - + -
341A ILE* 3.4 20.4 - - + +
342A GLY* 4.1 0.2 - - - -
359A ILE* 1.3 77.8 - - - +
361A TYR* 1.3 63.1 + - - +
362A PRO* 4.2 0.3 - - - +
364A VAL* 3.8 18.8 + - + +
365A ALA 5.1 1.0 + - - -
406A CYS* 2.8 34.8 + - - +
408A TYR* 3.5 28.0 - - + +
440A PRO 3.7 12.9 + - - -
441A HIS* 2.9 44.4 + - + +
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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