Contacts of the strand formed by residues 441 - 447 (chain B) in PDB entry 3GEB
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 CYS 441 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLU* 5.1 2.2 - - - -
269B ARG* 3.3 37.9 - - - +
271B PHE* 3.8 14.6 - - + -
435B ILE* 3.0 21.4 - - + +
436B ASN* 4.5 2.9 - - - +
438B ARG* 3.3 41.0 + - + +
439B PRO 3.6 0.8 + - - +
440B ASN* 1.3 85.1 - - - +
442B VAL* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLU* 5.3 4.0 + - - +
269B ARG 3.5 4.0 + - - -
270B VAL* 3.7 33.2 - - + -
271B PHE* 3.0 31.2 + - - +
435B ILE* 3.9 2.0 - - - -
436B ASN* 6.0 0.7 - - - +
441B CYS* 1.3 74.9 - - - +
443B ASN* 1.3 70.2 + - - +
444B VAL* 4.1 7.9 - - + -
468B PRO* 5.5 4.3 - - + -
471B ASN* 3.2 23.6 - - - +
491B PHE* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE 3.7 2.5 - - - -
273B TRP* 3.1 19.2 + - - +
432B LEU* 3.1 41.7 + - + +
435B ILE* 3.3 27.2 - - - +
436B ASN* 3.9 12.9 + - - +
442B VAL* 1.3 77.1 - - - +
444B VAL* 1.3 62.6 + - - +
466B VAL* 4.4 12.8 + - - +
467B PHE* 3.8 22.6 - - + -
468B PRO* 4.6 2.5 - - + +
471B ASN* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 3.3 29.8 - - + -
271B PHE 2.9 11.5 + - - +
272B VAL* 4.4 4.7 - - + -
273B TRP* 2.9 31.2 + - - +
442B VAL* 4.1 1.8 - - + -
443B ASN* 1.3 78.2 - - - +
445B LEU* 1.3 65.7 + - - +
446B VAL* 4.7 0.4 - - + -
467B PHE* 3.8 1.6 - - - -
471B ASN* 3.4 23.3 - - + +
473B TYR* 3.9 14.6 - - + -
487B ILE* 3.4 32.8 - - + -
490B ARG* 5.4 0.4 - - - +
491B PHE* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TRP* 3.6 32.3 - - + +
274B ASP 3.9 13.7 - - - +
275B LEU* 4.1 25.6 - - + +
279B ILE* 4.0 9.4 - - + -
444B VAL* 1.3 76.1 - - - +
446B VAL* 1.3 62.4 + - - +
447B THR* 4.9 6.7 - - + -
458B VAL* 4.2 20.4 - - + -
467B PHE* 3.6 24.0 - - + -
471B ASN 2.7 13.7 + - - +
472B ILE* 3.5 17.0 - - + -
473B TYR* 2.6 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL* 3.4 27.8 - - + -
273B TRP 3.0 13.4 + - - +
274B ASP* 3.7 6.2 - - - +
275B LEU 4.2 0.2 + - - -
445B LEU* 1.3 75.0 - - - +
447B THR* 1.3 61.9 + - - +
473B TYR* 3.4 4.3 - - + +
475B ALA* 4.0 8.5 - - + -
480B LYS* 2.9 46.1 + - + +
483B CYS* 3.6 27.4 - - + -
484B PHE* 3.6 13.9 - - + -
487B ILE* 3.5 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ASP* 5.2 1.9 + - - -
275B LEU* 3.8 28.7 + - + +
445B LEU* 4.9 8.3 - - + -
446B VAL* 1.3 77.3 - - - +
448B THR* 1.3 64.3 + - - +
449B THR* 3.2 30.8 + - - +
454B ALA* 3.9 20.4 - - + -
472B ILE* 5.1 4.3 - - + -
473B TYR 3.0 15.0 + - - +
474B SER* 3.4 3.5 - - - -
475B ALA* 2.9 27.4 + - - -
480B LYS* 4.9 3.1 - - - +
----------------------------------------------------------
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