Contacts of the strand formed by residues 381 - 388 (chain C) in PDB entry 3QEL
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 LYS 381 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ASN 3.5 0.3 - - - +
377C LEU* 3.7 7.9 - - - +
378C GLN 3.1 30.3 + - - +
379C ASN 3.8 0.4 - - - -
380C ARG* 1.3 80.3 - - - +
382C LEU* 1.3 67.0 + - - +
383C VAL* 3.7 9.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ILE* 4.1 25.4 - - + +
280C LEU* 3.5 37.0 - - + -
287C ILE* 5.4 2.7 - - + -
291C GLN* 4.4 16.8 - - - +
375C MET* 3.7 25.0 - - + +
376C ASN 4.1 2.0 - - - -
377C LEU* 3.9 35.6 - - + +
381C LYS* 1.3 76.1 - - - +
383C VAL* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C MET* 3.5 4.8 - - - +
376C ASN 2.9 30.8 + - - +
378C GLN* 3.1 34.1 - - + +
381C LYS* 3.8 18.6 - - + +
382C LEU* 1.3 80.9 - - - +
384C GLN* 1.3 67.5 + - - +
385C VAL* 3.3 15.0 + - + +
398C ARG* 4.6 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ILE* 5.8 1.6 - - - +
373C SER* 3.2 27.9 + - - -
374C ILE 3.4 7.0 - - - +
375C MET* 3.8 13.9 - - + +
383C VAL* 1.3 73.1 - - - +
385C VAL* 1.3 56.6 + - - +
386C GLY 3.4 26.3 - - - +
387C ILE* 4.6 7.6 - - - +
396C ASN* 2.8 28.8 + - - +
398C ARG* 4.3 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ILE* 5.4 1.3 - - + -
374C ILE* 2.9 31.3 + - + +
376C ASN* 3.6 24.9 - - + +
378C GLN* 4.4 8.5 - - - +
383C VAL* 3.5 18.4 - - + +
384C GLN* 1.3 72.0 - - - +
386C GLY* 1.3 58.5 + - - +
395C GLN* 3.5 11.6 - - + +
396C ASN* 3.2 28.3 + - - +
398C ARG* 4.3 13.3 - - + +
399C LYS 4.7 0.4 - - - +
400C ILE* 3.8 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C SER* 3.9 0.2 - - - -
374C ILE* 2.9 33.2 + - - -
384C GLN* 3.3 20.3 + - - +
385C VAL* 1.3 84.3 - - - +
387C ILE* 1.3 61.0 + - - -
394C ILE 3.3 13.9 - - - -
395C GLN* 4.1 2.7 - - - -
396C ASN* 4.0 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ILE* 5.1 9.6 - - + -
371C GLN* 5.6 2.9 - - - +
372C TYR 3.3 9.9 - - - +
373C SER* 5.3 0.2 - - - -
374C ILE* 4.0 6.0 - - - +
384C GLN* 4.6 8.5 - - - +
386C GLY* 1.3 74.4 - - - +
388C PHE* 1.3 63.2 + - - +
389C ASN* 3.9 2.9 + - + +
392C TYR 3.8 0.3 - - - +
393C ILE* 3.4 2.9 - - - +
394C ILE* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 4.2 24.7 - - + -
150C VAL* 3.7 32.8 - - + -
153C GLU* 3.6 25.6 - - + -
370C ALA 4.1 4.3 - - - -
371C GLN* 3.4 7.6 - - - +
372C TYR* 2.8 50.2 + + + +
374C ILE* 4.2 3.1 - - + +
387C ILE* 1.3 74.1 - - - +
389C ASN* 1.3 59.6 + - - +
390C GLY* 3.2 34.3 + - - -
391C SER* 3.9 13.9 - - - -
392C TYR 3.6 5.6 - - - -
393C ILE* 3.9 21.8 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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