Contacts of the strand formed by residues 324 - 334 (chain C) in PDB entry 6IWQ
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 ILE 324 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C PRO* 3.3 39.7 - - + +
318C ILE* 3.6 21.7 - - - +
320C LYS* 5.6 1.8 - - + -
321C ASP* 3.1 34.0 + - + +
322C ARG 4.3 1.9 - - - +
323C THR* 1.3 80.8 - - - +
325C CYS* 1.3 68.7 + - - +
326C THR* 4.1 2.9 - - - +
394C ILE* 4.3 5.6 - - - +
429C LYS* 3.5 27.1 - - + +
431C LEU* 3.8 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C THR 3.8 0.4 + - - -
324C ILE* 1.3 74.6 - - - +
326C THR* 1.3 62.5 + - - +
387C MET* 3.8 28.9 - - - -
392C PHE* 3.9 10.8 - - - -
393C ALA 3.3 17.3 - - - -
394C ILE* 3.5 22.7 - - + -
423C ILE* 3.7 20.6 - - + -
429C LYS 2.8 10.1 + - - +
430C LEU* 3.3 8.9 - - + +
431C LEU* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C LEU* 3.2 48.3 + - + +
317C PRO* 3.3 20.4 - - - +
318C ILE* 3.9 6.9 - - - +
324C ILE* 4.1 2.1 - - - +
325C CYS* 1.3 74.9 + - - +
327C VAL* 1.3 64.6 + - - +
328C PRO* 4.5 0.3 - - - +
392C PHE* 3.3 4.9 - - - +
393C ALA* 2.7 44.6 + - - +
431C LEU* 3.4 4.4 + - - +
433C VAL* 3.3 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C LEU* 4.1 3.8 - - - -
326C THR* 1.3 76.9 - - - +
328C PRO* 1.3 77.6 - - + +
330C ILE* 4.9 8.7 - - + -
387C MET* 3.7 21.8 - - + -
388C ALA* 5.4 2.2 - - + +
389C GLY 6.1 0.2 - - - +
391C LEU 3.4 17.5 - - - +
392C PHE* 4.1 8.1 - - + -
430C LEU* 3.5 29.8 - - + -
431C LEU 2.8 6.4 + - - +
432C PHE* 3.5 27.8 - - + -
433C VAL* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU* 5.8 1.3 - - + -
314C LEU* 3.5 26.2 - - + -
327C VAL* 1.3 105.4 - - + +
329C LEU* 1.3 64.6 + - - +
330C ILE* 3.4 6.6 + - + +
391C LEU* 3.7 27.1 - - + +
392C PHE* 4.4 2.5 - - - -
432C PHE* 5.6 1.4 - - - -
433C VAL 4.1 2.2 - - - +
436C SER* 3.2 21.3 - - - +
438C VAL* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C PRO* 1.3 73.8 - - - +
330C ILE* 1.3 61.7 + - - +
331C ASP* 3.8 1.7 + - - +
350C GLY 4.7 6.5 - - - +
351C TYR* 3.7 27.8 - - + -
382C TYR* 3.9 18.8 - - + +
432C PHE* 4.2 21.8 - - + -
433C VAL 3.7 6.3 + - - +
434C PRO* 3.7 19.3 - - + +
436C SER 3.0 10.1 + - - +
437C ARG* 3.4 42.5 - - + +
438C VAL 3.1 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C VAL* 4.9 5.4 - - + -
328C PRO* 3.5 15.3 - - + +
329C LEU* 1.3 72.3 - - - +
331C ASP* 1.3 64.3 + - - +
343C GLN* 3.1 35.7 + - - +
364C ARG* 5.6 0.3 + - - -
388C ALA* 4.2 24.9 - - + -
390C GLY 5.6 1.1 - - - +
391C LEU* 3.9 39.5 - - + +
438C VAL* 3.3 9.0 - - - +
440C HIS* 3.9 26.5 - - + -
442C TYR* 4.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C LEU* 2.9 30.1 - - + +
329C LEU* 4.5 5.2 - - - +
330C ILE* 1.3 80.5 + - - +
332C VAL* 1.3 61.8 + - - +
340C ILE* 4.0 9.0 - - + -
341C ILE 3.4 7.6 - - - +
342C PRO* 3.6 10.5 - - - +
343C GLN 4.4 0.5 + - - -
437C ARG* 2.9 43.5 + - - +
438C VAL 2.7 13.2 + - - +
439C GLY* 3.2 3.2 - - - +
440C HIS* 2.8 29.5 + - - +
442C TYR* 4.1 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ASP* 1.3 73.7 - - - +
333C ILE* 1.3 68.1 + - - +
334C ASN* 5.5 1.1 - - - -
339C GLU 3.7 0.9 - - - +
340C ILE* 3.3 2.7 - - - -
341C ILE* 2.6 57.5 + - + +
342C PRO 4.2 2.9 - - - +
343C GLN* 3.8 32.1 - - + +
440C HIS 3.8 2.0 - - - -
442C TYR* 3.4 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ARG* 4.3 2.9 - - - +
305C GLU* 3.6 31.6 - - + +
332C VAL* 1.3 80.5 - - - +
334C ASN* 1.3 68.0 + - - +
338C TYR* 3.9 26.9 - - + +
339C GLU 3.4 9.6 - - - +
340C ILE* 3.9 15.7 - - + -
439C GLY* 3.6 26.9 - - - +
440C HIS 2.9 20.2 + - - +
441C ILE* 3.4 21.6 - - + -
442C TYR* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A PRO* 4.8 10.3 - - - +
633A HIS* 6.0 2.0 + - - -
332C VAL* 4.1 2.1 + - - -
333C ILE* 1.3 72.5 - - - +
335C GLY* 1.3 64.8 + - - +
336C ASN* 2.6 32.8 + - - +
337C THR* 3.5 24.5 + - + +
338C TYR* 2.9 40.3 + - - +
339C GLU* 3.1 15.9 + - + +
341C ILE* 4.7 13.1 - - + +
441C ILE* 4.3 0.2 - - - -
442C TYR* 6.0 0.4 - - - -
444C LEU* 4.5 4.0 - - - +
----------------------------------------------------------
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