Contacts of the strand formed by residues 418 - 426 (chain A) in PDB entry 2IB8
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 GLY 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ALA 3.4 9.9 - - - -
319A ALA* 4.1 1.3 - - - -
325A PHE 4.4 0.3 - - - +
328A ALA* 3.5 6.6 - - - +
413A CYS* 3.4 3.5 - - - +
414A ASN* 2.8 49.6 + - - +
416A GLY 3.6 1.2 - - - -
417A GLY* 1.3 81.2 - - - +
419A ALA* 1.3 60.8 - - - +
2001B CL 3.7 12.5 - - - +
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Residues in contact with ALA 419 (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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124A LYS* 3.4 10.1 + - - +
317A ASP* 3.3 4.2 - - - -
318A ALA 2.8 32.5 + - - +
328A ALA* 3.4 8.5 - - + +
329A PRO* 3.3 39.9 - - + -
332A ALA* 4.1 4.9 - - + +
412A ILE 3.2 15.3 - - - +
414A ASN* 3.4 3.2 + - - -
418A GLY* 1.3 75.6 - - - +
420A SER* 1.3 60.3 + - - +
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Residues in contact with SER 420 (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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124A LYS* 3.0 14.3 + - - +
127A ALA* 3.6 15.7 - - - +
130A MET* 3.6 21.2 - - - +
131A LYS* 4.5 2.4 - - - +
134A MET* 3.8 12.3 - - - -
316A ALA 3.5 5.2 - - - -
317A ASP* 2.5 22.0 + - - -
332A ALA* 4.2 2.1 - - - +
411A SER* 3.3 2.9 - - - -
412A ILE* 3.0 32.2 + - - -
419A ALA* 1.3 73.7 - - - +
421A ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 421 (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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130A MET* 3.6 4.8 - - - +
134A MET* 4.4 1.2 - - - +
315A PHE* 3.1 7.7 - - - +
316A ALA 2.9 30.8 + - - +
332A ALA* 3.8 33.7 - - + +
333A ALA* 3.9 7.0 - - - +
336A VAL* 4.2 6.1 - - + -
409A LEU* 4.3 3.1 - - + -
410A ALA 3.1 12.3 - - - +
411A SER* 4.0 7.2 - - - -
420A SER* 1.3 76.7 - - - +
422A MET* 1.3 61.7 + - - +
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Residues in contact with MET 422 (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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130A MET* 3.9 17.5 - - + -
133A ILE* 3.7 26.7 - - + -
134A MET* 3.4 33.4 - - + +
137A SER* 5.4 0.2 - - - +
312A ILE* 4.3 13.9 - - + -
314A ALA 3.4 10.8 - - - +
315A PHE* 4.1 8.3 - - + +
336A VAL* 4.8 2.0 - - - -
395A VAL* 4.0 31.4 - - + -
398A LEU* 5.2 0.7 - - - +
408A GLY 3.9 0.5 - - - +
409A LEU* 3.5 6.6 - - - +
410A ALA* 2.9 34.8 + - + +
421A ALA* 1.3 75.9 - - - +
423A LEU* 1.3 62.2 + - - +
424A ILE* 4.0 17.5 + - + +
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Residues in contact with LEU 423 (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 ILE* 3.9 0.5 - - - -
313A VAL* 2.9 42.9 + - + -
314A ALA* 2.8 18.2 + - + +
336A VAL* 4.5 15.5 - - + +
337A LEU* 5.2 2.2 - - + -
340A VAL* 3.6 31.6 - - + -
342A LEU* 3.8 12.8 - - + -
347A ILE* 3.5 31.0 - - + -
407A TYR* 4.2 10.8 - - + -
408A GLY 3.4 15.9 - - - +
409A LEU* 4.3 7.9 - - + +
422A MET* 1.3 72.9 - - - +
424A ILE* 1.3 65.9 + - - +
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Residues in contact with ILE 424 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ILE* 4.1 17.5 - - + -
310A ALA* 4.0 15.3 - - + -
311A ARG 3.2 15.3 - - - +
312A ILE* 4.3 3.4 - - + -
313A VAL* 3.9 3.8 - - - -
395A VAL* 4.2 5.8 - - + +
398A LEU* 3.8 25.8 - - + -
399A THR* 3.6 27.4 - - - +
402A LEU* 3.8 16.2 - - + -
407A TYR* 3.4 7.6 - - - -
408A GLY 3.0 35.0 + - - +
422A MET* 4.0 22.4 - - + +
423A LEU* 1.3 77.6 - - - +
425A GLN* 1.3 60.3 + - - +
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Residues in contact with GLN 425 (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 ALA* 3.3 3.8 - - - -
311A ARG* 2.9 72.0 + - + +
313A VAL* 3.7 1.3 - - + +
405A GLY* 2.9 28.4 + - - +
406A GLU 3.4 12.3 - - - +
407A TYR* 3.6 34.5 + - + -
424A ILE* 1.3 74.2 - - - +
426A LYS* 1.3 69.7 + - - +
427A LEU* 4.1 3.8 - - + +
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Residues in contact with LYS 426 (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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309A LEU* 3.1 36.6 - - - +
310A ALA* 4.2 4.3 - - + -
399A THR* 3.1 28.5 + - - +
400A HIS* 3.5 10.7 + - - +
402A LEU* 2.8 49.2 + - + +
403A LYS* 3.3 26.2 - - - +
404A GLN 3.8 3.4 - - - +
405A GLY* 2.8 25.8 + - - -
406A GLU 2.9 9.4 + - - +
425A GLN* 1.3 75.8 - - - +
427A LEU* 1.3 68.6 + - - +
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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