Contacts of the helix formed by residues 381 - 391 (chain S) in PDB entry 1I84
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 ASN 381 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378S MET* 4.4 13.7 - - - +
379S PRO 6.0 0.2 - - - -
380S ASP* 1.3 78.4 + - - +
382S THR* 1.3 67.9 + - + +
383S ALA 2.7 5.2 + - - -
384S ALA* 3.2 5.3 + - - +
385S GLN* 2.6 33.6 + - + +
395S VAL* 6.3 2.0 - - + -
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Residues in contact with THR 382 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361S GLN* 5.7 0.3 + - - -
380S ASP* 3.0 29.4 + - - +
381S ASN* 1.3 71.4 - - + +
383S ALA* 1.3 82.5 + - - +
385S GLN* 2.9 27.3 - - - +
386S LYS* 2.7 32.9 + - - +
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Residues in contact with ALA 383 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361S GLN* 4.0 12.9 - - - +
364S ASN* 4.4 6.7 - - + +
365S ILE* 3.6 35.7 - - + +
366S VAL* 4.9 3.4 - - + +
378S MET* 4.9 1.1 - - + -
380S ASP* 4.3 14.5 + - + +
381S ASN 2.7 4.7 + - - +
382S THR* 1.3 88.1 + - - +
384S ALA* 1.3 60.6 + - - +
386S LYS* 2.8 14.0 + - - +
387S VAL* 3.1 14.6 + - - +
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Residues in contact with ALA 384 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365S ILE* 3.3 31.2 - - + +
378S MET* 5.2 14.6 - - + -
380S ASP 5.0 0.2 + - - -
381S ASN* 3.2 3.4 + - - +
383S ALA* 1.3 75.9 - - - +
385S GLN* 1.3 66.8 + - - +
386S LYS 3.2 0.2 - - - -
387S VAL* 3.8 4.7 - - - -
388S CYS* 2.8 27.9 + - - +
395S VAL* 4.7 4.3 - - + -
398S PHE* 3.9 21.5 - - + -
399S THR* 5.8 4.0 - - + +
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Residues in contact with GLN 385 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381S ASN* 2.6 32.1 + - + +
382S THR* 2.9 35.1 - - - +
384S ALA* 1.3 80.3 - - - +
386S LYS* 1.3 72.4 + - + +
388S CYS* 3.7 3.5 + - - +
389S HIS* 3.7 11.4 + - - +
395S VAL* 3.9 18.8 - - + +
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Residues in contact with LYS 386 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306S LEU* 3.5 43.2 - - + +
308S GLU* 3.0 28.1 + - - +
361S GLN* 3.6 27.5 - - + +
382S THR* 2.7 26.4 + - - +
383S ALA 2.8 6.0 + - - +
385S GLN* 1.3 81.4 - - + +
387S VAL* 1.3 56.9 + - - +
389S HIS* 2.5 40.2 + - - +
390S LEU* 3.3 7.2 + - - +
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Residues in contact with VAL 387 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358S SER* 4.5 3.5 - - - +
361S GLN* 3.2 20.8 - - + +
362S LEU* 3.2 65.7 - - + +
365S ILE* 4.2 9.4 - - + -
383S ALA 3.1 5.3 + - - +
384S ALA* 3.8 10.8 - - - +
386S LYS* 1.3 78.9 - - - +
388S CYS* 1.3 62.7 + - - +
389S HIS 3.1 1.4 + - - -
390S LEU* 3.1 13.3 + - - +
391S MET* 3.1 29.3 + - + +
398S PHE* 4.6 7.0 - - + -
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Residues in contact with CYS 388 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384S ALA 2.8 21.7 + - - +
385S GLN 4.1 3.4 - - - +
386S LYS 2.9 0.2 + - - -
387S VAL* 1.3 73.6 - - - +
389S HIS* 1.3 57.3 + - - +
391S MET 3.8 1.1 - - - -
392S GLY 3.5 0.5 + - - -
393S ILE* 3.2 51.4 + - + +
394S ASN* 3.7 5.4 - - - -
395S VAL* 3.9 19.1 - - + +
398S PHE* 3.2 53.4 - - - -
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Residues in contact with HIS 389 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306S LEU* 5.3 7.2 - - + -
354S ARG* 5.5 8.3 + - - -
385S GLN 3.7 6.9 + - - +
386S LYS* 2.5 25.1 + - - +
388S CYS* 1.3 69.9 - - - +
390S LEU* 1.3 72.5 + - + +
391S MET 3.1 1.3 - - - -
392S GLY* 3.1 14.3 + - - -
618S ASP* 5.4 0.2 - - - +
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Residues in contact with LEU 390 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304S ASP 4.5 2.0 - - - +
305S LEU* 4.0 25.4 - - - +
306S LEU* 3.5 28.3 - - + -
354S ARG* 4.3 37.2 + - + +
355S VAL* 5.8 1.9 + - - +
357S SER 4.3 1.6 - - - +
358S SER* 3.6 43.4 - - - +
361S GLN* 4.8 5.8 - - + -
386S LYS 3.9 8.1 - - - +
387S VAL* 3.1 14.1 + - - +
389S HIS* 1.3 83.2 - - + +
391S MET* 1.3 60.8 + - - +
434S LYS* 5.0 1.4 + - - -
618S ASP* 3.4 17.0 - - - +
621S VAL* 4.0 4.0 - - - +
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Residues in contact with MET 391 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358S SER* 5.0 2.2 - - - -
362S LEU* 3.7 21.8 - - + -
387S VAL* 3.1 35.6 + - - +
389S HIS 3.1 1.4 - - - -
390S LEU* 1.3 78.8 - - - +
392S GLY* 1.3 55.9 + - - +
393S ILE* 3.0 26.7 + - + +
398S PHE* 4.3 10.1 - - + -
430S LEU* 4.2 17.0 - - + -
434S LYS* 3.2 33.9 - - + +
613S LEU* 3.3 31.9 - - + -
616S SER* 3.0 21.1 + - - -
621S VAL* 3.7 15.4 - - + +
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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