Contacts of the strand formed by residues 310 - 317 (chain A) in PDB entry 5IZL
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 HIS 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A LEU* 1.3 76.5 - - - +
311A THR* 1.3 63.2 + - - +
312A VAL* 3.2 31.5 + - + +
420A VAL 3.6 1.4 - - - +
421A THR* 3.5 0.8 - - - -
422A CYS* 3.0 50.7 + - - +
423A PRO 3.6 12.3 + - - -
424A ARG* 3.6 44.3 + - + +
450A LEU* 4.2 7.9 - - + +
453A GLY* 3.9 19.0 + - - -
455A GLU* 3.7 31.4 + - - +
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Residues in contact with THR 311 (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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262A LYS* 3.8 17.3 - - - +
309A LEU 5.5 0.4 - - - +
310A HIS* 1.3 74.1 - - - +
312A VAL* 1.3 59.4 + - - +
313A HIS* 5.2 4.8 + - - -
419A PRO* 5.0 8.2 - - - +
420A VAL 3.3 9.0 - - - -
421A THR* 3.1 33.0 - - + +
455A GLU* 3.2 34.5 + - - +
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Residues in contact with VAL 312 (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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310A HIS* 3.2 40.8 - - + +
311A THR* 1.3 76.6 - - - +
313A HIS* 1.3 63.9 + - - +
314A ALA 3.5 11.4 - - - +
315A ALA* 5.1 2.9 - - + -
416A PHE* 3.8 23.4 - - + -
419A PRO* 3.2 5.7 - - - +
420A VAL* 3.0 42.5 + - + +
422A CYS* 4.3 11.0 - - - -
450A LEU* 5.3 1.6 - - + -
453A GLY* 3.6 15.0 - - - -
454A LEU 3.5 8.1 - - - +
455A GLU* 4.4 0.4 - - - +
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Residues in contact with HIS 313 (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 THR* 5.2 5.3 + - - -
312A VAL* 1.3 75.3 - - - +
314A ALA* 1.3 59.8 + - - +
415A GLU* 3.9 0.5 - - - -
416A PHE* 3.0 37.2 + - - +
418A LYS 5.5 0.2 - - - -
419A PRO* 3.7 32.4 - - + +
454A LEU 3.1 2.5 + - - +
455A GLU 3.0 29.3 + - - -
456A ASP 3.4 14.6 - - - -
457A ARG* 3.6 25.4 + - + +
459A TYR* 4.1 19.7 + - + -
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Residues in contact with ALA 314 (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 VAL* 3.5 7.0 - - - +
313A HIS* 1.3 79.8 - - - +
315A ALA* 1.3 65.5 + - - +
413A LEU* 4.6 2.0 - - + -
414A VAL 3.1 16.2 - - - +
415A GLU* 4.1 3.4 - - + -
416A PHE* 3.7 6.1 - - - -
454A LEU* 2.8 36.2 + - + -
459A TYR* 3.6 35.4 - - + +
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Residues in contact with ALA 315 (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 VAL* 5.1 1.3 - - + -
314A ALA* 1.3 81.5 - - - +
316A LEU* 1.3 62.5 + - - +
317A ILE* 3.8 3.8 + - + -
413A LEU* 3.6 6.9 - - - +
414A VAL* 3.0 30.4 + - + +
416A PHE* 4.2 12.6 - - + -
450A LEU* 3.4 33.9 - - + -
452A HIS 3.2 11.9 - - - +
453A GLY* 4.1 4.5 - - - -
454A LEU* 4.3 3.1 - - - +
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Residues in contact with LEU 316 (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 ALA* 1.3 71.4 - - - +
317A ILE* 1.3 61.0 + - - +
351A PHE* 4.8 4.5 - - + -
367A PHE* 4.0 31.2 - - + -
369A PHE* 3.7 36.6 - - + -
411A TRP* 6.0 1.1 - - + -
412A ALA 3.6 10.1 - - - +
413A LEU* 3.5 29.2 - - + -
451A LEU* 2.9 26.7 + - - +
452A HIS* 2.8 28.5 + - + +
454A LEU* 5.2 6.7 - - + -
463A PHE* 5.4 2.9 - - + -
464A LEU* 5.5 1.1 - - + -
467A LEU* 3.8 23.1 - - + -
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Residues in contact with ILE 317 (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 ALA* 4.2 4.7 - - + +
316A LEU* 1.3 74.2 - - - +
318A SER* 1.3 71.6 + - - +
319A VAL* 3.5 7.1 - - + +
411A TRP* 4.5 2.9 - - - +
412A ALA* 3.1 31.3 + - + +
414A VAL* 3.8 26.7 - - + -
416A PHE* 6.3 0.2 - - + -
428A VAL* 3.6 32.1 - - + -
446A PHE* 4.1 16.2 - - + -
448A GLY* 5.4 0.2 - - - -
449A ILE 3.1 10.5 - - - +
450A LEU* 3.1 48.9 - - + -
451A LEU* 4.2 1.8 - - - +
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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