Contacts of the strand formed by residues 382 - 388 (chain D) in PDB entry 3U1K
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 382 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380D LEU* 3.1 7.8 - - - +
381D HIS* 1.3 81.3 - - - +
383D SER* 1.3 64.4 + - - -
396D THR* 3.4 3.3 - - - -
397D VAL* 2.8 29.4 + - - +
494D ALA* 4.0 3.8 - - - -
497D ASP* 3.3 12.3 - - - -
498D SER* 3.8 15.0 - - - -
601D LYS* 4.8 1.3 - - - -
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Residues in contact with SER 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D VAL* 3.2 6.4 - - - +
375D ASP* 3.1 20.3 + - - -
376D MET* 3.4 34.6 + - - +
377D PHE 4.1 4.5 + - - -
380D LEU* 3.9 22.9 - - - +
382D GLY* 1.3 75.8 - - - -
384D ALA* 1.3 62.8 + - - +
394D LEU* 5.3 1.6 - - - -
395D CYS 3.2 13.0 - - - -
396D THR* 4.5 1.8 - - - -
494D ALA* 3.9 7.4 - - - +
497D ASP* 2.9 11.9 + - - +
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Residues in contact with ALA 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D GLU 3.1 15.0 - - - +
374D VAL* 3.9 1.8 - - + -
376D MET* 3.9 6.7 - - - -
383D SER* 1.3 78.2 - - - +
385D LEU* 1.3 61.1 + - - +
386D PHE 4.1 0.2 - - - -
393D VAL 3.9 0.5 - - - +
394D LEU* 3.6 4.0 - - - +
395D CYS* 2.9 32.6 + - - +
490D GLY* 3.7 15.7 - - - +
493D LEU* 3.6 32.8 - - + -
494D ALA 3.7 2.9 - - - +
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Residues in contact with LEU 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LYS* 5.4 0.7 - - + +
63B LEU* 4.0 25.8 - - + -
371D SER 4.0 0.2 - - - +
372D CYS* 3.1 8.8 - - - +
373D GLU* 2.9 56.1 + - + +
376D MET* 3.8 9.7 - - - -
384D ALA* 1.3 75.2 - - - +
386D PHE* 1.3 61.2 + - - +
387D GLN* 5.2 4.3 - - + +
392D GLN* 3.6 33.7 - - + +
393D VAL 3.4 19.3 - - - +
394D LEU* 4.1 14.6 - - + -
477D LEU* 4.6 1.3 - - + -
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Residues in contact with PHE 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D VAL* 4.1 21.5 - - + -
371D SER 3.8 0.9 - - - -
372D CYS* 4.3 5.8 - - + -
384D ALA 4.1 0.6 - - - -
385D LEU* 1.3 75.0 - - - +
387D GLN* 1.3 63.4 + - - +
388D ARG* 3.7 34.8 - - + -
391D THR 3.9 1.0 - - - +
392D GLN* 3.6 1.4 - - - -
393D VAL* 2.9 38.0 + - - +
486D ALA* 3.7 33.4 - - + +
489D CYS* 3.5 36.3 - - + -
490D GLY* 4.0 11.0 - - - -
493D LEU* 4.0 16.6 - - + -
585D ILE* 4.0 11.7 - - + -
589D MET* 4.0 16.8 - - + -
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Residues in contact with GLN 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ARG* 3.2 14.1 + - - +
369D ASN 5.4 0.9 - - - +
370D VAL* 3.1 7.1 - - - +
371D SER* 2.8 54.3 + - - +
385D LEU* 4.1 6.2 - - + +
386D PHE* 1.3 77.9 - - - +
388D ARG* 1.3 60.9 + - - +
389D GLY 3.0 24.3 + - - +
390D GLN* 3.8 3.8 - - - +
391D THR 3.3 16.7 + - - -
392D GLN* 2.9 31.8 + - - +
478D GLU* 3.1 21.4 + - - -
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Residues in contact with ARG 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D LEU* 4.8 1.6 - - - -
368D ARG* 3.0 33.4 - - + +
369D ASN 3.5 3.4 - - - -
370D VAL* 4.2 19.1 - - + -
386D PHE* 3.7 19.9 - - + -
387D GLN* 1.3 74.7 - - - +
389D GLY* 1.3 65.8 + - - +
390D GLN 3.3 0.3 + - - -
391D THR* 2.9 32.5 + - + +
481D GLY 3.6 3.4 + - - -
482D SER* 2.8 39.7 + - - -
485D MET* 4.0 4.4 - - - +
486D ALA* 3.5 20.9 - - - +
489D CYS* 5.5 0.4 - - - -
508D GLY 4.3 4.4 + - - -
509D VAL* 5.3 1.9 - - - +
532D ASP* 3.1 32.1 + - - +
585D ILE* 4.5 17.7 - - - +
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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