Contacts of the strand formed by residues 457 - 467 (chain C) in PDB entry 4P3N
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 ARG 457 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C GLY 3.3 5.3 + - - +
342C SER* 3.8 27.3 - - - +
343C CYS 5.5 4.2 + - - +
345C PHE* 5.8 2.2 - - - -
353C TYR* 3.3 14.8 + - - -
439C VAL* 3.4 22.1 - - + +
440C LEU 3.4 3.6 - - - -
441C HIS* 3.3 34.9 - - + +
455C VAL* 3.4 14.1 - - - +
456C ARG* 1.3 82.0 - - - +
458C PHE* 1.3 68.5 + - - +
459C GLN* 3.2 25.0 - - - +
598C GLU* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 458 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C VAL* 3.7 2.3 - - - +
440C LEU* 2.9 51.8 + - + +
442C ARG* 3.6 51.4 - - + -
455C VAL* 3.9 22.0 - - + -
457C ARG* 1.3 86.1 - - - +
459C GLN* 1.3 68.9 + - - +
460C GLN* 3.5 36.6 - - + -
596C SER* 3.9 22.9 - - - -
598C GLU* 3.2 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C TYR* 3.4 31.4 + - + +
357C ILE* 3.9 11.4 - - - +
437C PHE* 3.4 25.4 - - + +
438C GLY 4.1 4.0 - - - -
439C VAL* 3.4 20.4 - - + +
457C ARG* 3.2 28.5 - - - +
458C PHE* 1.3 83.2 - - - +
460C GLN* 1.3 63.1 + - - +
597C VAL* 2.9 34.9 + - + +
598C GLU* 3.3 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 460 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C MET* 6.0 0.9 - - - +
412C ASN* 5.3 0.9 - - - +
436C ASP 3.6 9.9 - - - +
437C PHE* 3.7 16.0 - - - -
438C GLY 4.5 4.9 + - - -
440C LEU* 3.5 15.4 - - + +
442C ARG* 3.8 20.4 - - - +
458C PHE* 3.5 29.4 - - + -
459C GLN* 1.3 75.6 - - - +
461C ASP* 1.3 61.7 + - - +
462C ASP* 3.4 37.2 + - + +
592C ALA* 5.3 6.8 - - + +
595C GLY* 3.2 18.8 - - - +
596C SER* 5.1 0.4 - - - +
597C VAL* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ILE* 4.0 23.0 - - + +
364C TYR* 4.0 6.8 + - - +
437C PHE* 4.0 22.9 - - + -
459C GLN 4.0 0.4 + - - -
460C GLN* 1.3 71.3 - - - +
462C ASP* 1.3 59.1 + - - +
591C ARG* 3.7 2.6 + - - -
592C ALA* 3.2 18.7 - - - +
593C ILE* 3.3 16.5 + - - +
594C LEU* 3.0 43.5 + - + +
595C GLY 2.9 18.5 + - - +
597C VAL* 5.3 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C TYR* 4.1 2.9 + - - -
412C ASN* 3.2 28.0 + - - +
413C CYS* 4.7 3.2 - - - -
416C HIS* 4.8 0.5 - - - -
434C LEU 4.0 0.5 - - - +
435C ALA* 3.3 2.9 - - - +
436C ASP* 2.7 47.2 + - - +
460C GLN* 3.4 27.2 - - + +
461C ASP* 1.3 74.5 - - - +
463C ALA* 1.3 68.6 + - - +
464C HIS* 3.5 28.8 + - - -
590C HIS* 5.3 1.9 - - - +
591C ARG 3.5 11.6 + - - +
592C ALA* 4.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 463 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C TYR* 4.1 4.3 - - - +
369C PHE* 3.5 24.7 - - + -
434C LEU 3.3 6.5 - - - +
435C ALA* 4.2 2.2 - - - -
462C ASP* 1.3 77.5 + - - +
464C HIS* 1.3 64.2 + - - +
589C VAL 3.4 1.2 - - - +
590C HIS* 3.8 0.9 - - - -
591C ARG* 2.9 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 464 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ASN 4.2 0.4 - - - -
413C CYS* 2.9 49.7 - - + +
416C HIS* 3.0 27.5 + + + +
432C LEU 3.6 1.9 - - - +
433C ARG* 3.3 3.6 - - - +
434C LEU 2.9 34.0 + - - +
462C ASP* 3.5 23.8 + - - -
463C ALA* 1.3 73.6 - - - +
465C ILE* 1.3 61.6 + - - +
466C PHE* 4.1 21.9 - + + -
588C ILE* 4.2 9.2 - - + -
589C VAL 3.2 4.3 - - - +
590C HIS* 3.0 37.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C PHE* 4.3 21.8 - - + -
431C PRO* 4.2 7.4 - - + -
432C LEU 3.7 1.3 - - - -
433C ARG* 4.0 15.5 - - + +
464C HIS* 1.3 76.8 - - - +
466C PHE* 1.3 66.1 - - - +
467C CYS* 3.9 6.1 - - - -
475C GLU* 3.3 43.3 - - + +
479C CYS* 3.8 28.0 - - - -
587C VAL 3.3 6.4 - - - +
588C ILE* 3.6 2.6 - - - +
589C VAL* 2.9 49.7 + - + +
591C ARG* 4.7 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 466 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C HIS* 4.0 24.9 - - + -
417C CYS* 4.7 1.1 - - - -
420C PHE* 3.5 52.7 - + + -
430C LEU* 3.3 10.2 - - + +
431C PRO* 3.3 1.4 - - - +
432C LEU* 2.9 55.2 + - + +
434C LEU* 4.2 19.1 - - + -
464C HIS* 4.1 26.7 - + + -
465C ILE* 1.3 72.9 - - - +
467C CYS* 1.3 61.0 + - - +
573C LEU* 4.0 7.4 - - + -
586C PRO* 4.6 6.3 - - + -
587C VAL 3.9 2.7 - - - -
588C ILE* 3.9 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 467 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LEU* 3.9 9.0 - - - -
431C PRO* 4.2 11.7 - - + -
465C ILE* 4.5 6.7 - - + -
466C PHE* 1.3 76.2 - - - +
468C ALA* 1.3 67.1 + - - +
471C GLN* 3.2 23.3 - - + +
472C ILE* 3.5 34.1 - - - -
475C GLU* 4.6 6.3 - - + -
586C PRO* 3.4 4.1 - - - +
587C VAL 2.9 35.6 + - - -
589C VAL* 4.4 9.9 - - - -
----------------------------------------------------------
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