Contacts of the strand formed by residues 403 - 414 (chain B) in PDB entry 3GV8
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 LEU 403 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 3.3 9.3 - - + -
310B LYS* 3.5 6.8 - - - -
311B CYS* 2.9 44.2 + - + +
346B ILE* 3.8 42.4 - - + -
347B ARG 3.4 5.4 - - - +
348B ARG* 4.0 15.5 - - + +
391B PHE* 3.8 30.3 - - + -
395B VAL* 4.6 4.5 - - + -
401B PHE* 4.1 19.1 - - + -
402B HIS* 1.3 79.4 - - - +
404B THR* 1.3 63.9 + - - +
405B LEU 4.4 2.0 - - - +
406B LEU* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B SER* 3.4 1.4 - - - -
308B PHE* 3.1 34.4 + - - +
309B LYS* 3.5 21.8 - - - +
347B ARG* 2.7 59.2 + - - +
348B ARG 4.2 3.5 + - - -
349B TYR* 3.9 15.9 - - - +
402B HIS* 3.8 10.5 - - + -
403B LEU* 1.3 77.3 - - - +
405B LEU* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLU* 3.9 19.1 - - - +
306B ASP 3.5 13.0 - - - +
307B SER* 4.5 9.9 - - - -
308B PHE* 3.5 7.6 - - - -
345B ILE* 4.4 8.1 - - + +
346B ILE* 3.4 7.3 - - - +
347B ARG* 3.2 52.4 + - + +
357B ARG* 3.9 41.1 - - - +
403B LEU* 4.4 2.4 - - - +
404B THR* 1.3 80.3 - - - +
406B LEU* 1.3 79.3 + - - +
407B SER* 4.1 12.8 - - - +
839T A 5.7 0.7 - - - -
840T T 6.1 1.1 - - + -
841T G 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLU* 3.6 0.3 - - - -
306B ASP* 2.9 34.2 + - + +
308B PHE* 3.6 24.3 - - + -
311B CYS* 4.6 3.1 - - - -
317B ALA* 4.3 19.1 - - + +
320B LYS* 3.8 25.6 - - + -
321B ILE* 3.9 12.1 - - + -
324B LEU* 3.5 16.5 - - + +
344B LEU* 3.9 25.4 - - + -
345B ILE 3.5 1.6 - - - -
346B ILE* 3.9 19.7 - - + -
391B PHE* 4.5 3.8 - - + -
403B LEU* 4.3 11.7 - - + -
405B LEU* 1.3 78.5 - - - +
407B SER* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER* 4.4 6.2 + - - -
304B GLU 3.3 12.0 + - - -
305B GLU* 3.4 23.7 + - - +
324B LEU* 4.1 0.7 - - - -
344B LEU* 3.5 6.8 - - - +
345B ILE* 2.8 59.8 + - - +
357B ARG* 5.8 0.7 - - - -
405B LEU* 4.1 7.0 - - - -
406B LEU* 1.3 76.9 - - - +
408B VAL* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER* 3.3 3.6 - - - -
304B GLU 3.1 30.3 + - - -
321B ILE* 4.4 15.0 - - + +
324B LEU* 4.2 23.3 - - + +
325B LEU* 4.4 6.7 - - + +
328B LEU* 3.6 23.8 - - + +
342B VAL* 4.0 12.3 - - + -
343B ARG 3.5 8.1 - - - +
344B LEU* 4.0 17.3 - - + -
387B LEU* 3.9 25.6 - - + -
407B SER* 1.3 80.8 - - - +
409B CYS* 1.3 62.6 + - - +
410B PHE* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B SER* 3.9 18.8 - - - -
302B PHE 3.8 6.1 - - - -
303B SER* 3.7 13.5 - - - -
342B VAL* 3.4 6.9 - - - +
343B ARG* 2.9 60.3 + - + +
345B ILE* 4.2 8.0 - - + +
408B VAL* 1.3 76.9 - - - +
410B PHE* 1.3 80.4 + - - +
411B CYS* 4.0 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B SER* 3.3 4.0 - - - -
302B PHE* 2.9 47.4 + + + +
325B LEU* 3.8 22.0 - - + -
328B LEU* 3.7 34.3 - - + +
329B LEU* 4.0 15.9 - - + -
332B VAL* 3.7 29.8 - - + -
339B PRO* 3.6 17.0 - - + -
341B THR 3.6 1.1 - - - -
342B VAL* 3.7 17.0 - - + -
364B ILE* 3.9 22.0 - - + -
371B LYS* 5.9 2.0 - - - -
383B MET* 3.7 25.8 - - + -
408B VAL* 4.4 1.1 - - + -
409B CYS* 1.3 74.3 - - - +
411B CYS* 1.3 59.1 + - - +
413B LEU* 4.0 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLN 4.0 10.1 - - - +
301B SER* 4.3 8.5 - - - -
339B PRO* 3.5 0.7 - - - +
340B HIS 3.1 5.0 + - - -
341B THR* 2.9 48.5 + - - +
343B ARG* 4.7 18.4 - - - -
361B GLN* 5.7 2.5 - - - -
409B CYS* 4.3 11.0 - - - -
410B PHE* 1.3 75.4 - - - +
412B ASN* 1.3 71.3 + - + +
413B LEU* 3.3 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLN 4.0 4.6 + - - -
340B HIS* 3.1 36.5 + - - +
341B THR* 3.3 26.4 + - - +
411B CYS* 1.3 79.7 - - + +
413B LEU* 1.3 65.1 + - - +
414B LYS* 3.6 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO* 3.5 12.8 - - + +
300B GLN* 4.0 13.5 + - - +
302B PHE* 4.0 23.1 - - + -
337B ARG* 3.1 49.2 + - + +
338B LYS 3.4 8.3 - - - +
339B PRO* 3.8 18.8 - - + -
410B PHE 4.0 5.6 - - - +
411B CYS* 3.3 29.2 - - - +
412B ASN* 1.3 80.7 - - - +
414B LYS* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ARG* 3.4 37.5 - - - +
338B LYS 3.0 12.0 + - - -
340B HIS* 3.6 31.2 - - + +
412B ASN* 3.6 1.5 + - - +
413B LEU* 1.3 73.6 - - - +
----------------------------------------------------------
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