Contacts of the strand formed by residues 432 - 437 (chain E) in PDB entry 6M17
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 432 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E PHE* 4.6 10.8 - - + -
378E LYS 3.2 6.7 - - - +
379E CYS* 2.0 48.5 - - - -
380E TYR* 4.8 0.7 - - - +
382E VAL* 4.4 2.2 - - - -
387E LEU* 4.2 9.9 - - - -
429E PHE* 4.6 1.8 - - - -
431E GLY* 1.3 77.8 - - - -
433E VAL* 1.3 66.5 + - - +
434E ILE* 4.2 2.2 - - + +
511E VAL 4.2 0.3 - - - +
512E VAL* 3.7 2.1 - - - +
513E LEU* 2.9 42.7 + - + +
515E PHE* 4.2 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 433 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376E THR* 3.6 12.1 - - + +
377E PHE* 3.4 4.0 + - - -
378E LYS* 2.8 35.6 + - + +
380E TYR* 4.3 13.0 - - + +
407E VAL* 5.4 5.4 - - + +
410E ILE* 4.0 37.2 - - + +
425E LEU* 4.5 3.1 - - + -
429E PHE* 4.3 16.2 - - + -
432E CYS* 1.3 76.8 - - - +
434E ILE* 1.3 66.7 + - - +
510E VAL* 4.4 12.3 - - + -
511E VAL 3.9 2.7 - - - -
512E VAL* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 434 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E PHE* 3.9 23.3 - - + -
368E LEU* 4.5 4.0 - - + -
374E PHE* 3.6 42.4 - - + -
376E THR 3.2 6.7 - - - +
377E PHE* 3.4 29.8 - - + -
432E CYS 4.8 0.7 - - - -
433E VAL* 1.3 81.5 - - - +
435E ALA* 1.3 67.4 + - - +
436E TRP* 4.6 3.7 - - + -
509E ARG 4.2 0.2 - - - +
510E VAL* 3.5 4.1 - - - +
511E VAL* 2.9 40.7 + - + +
513E LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 435 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374E PHE* 3.8 1.5 - - - -
375E SER* 2.9 23.3 + - - -
376E THR* 2.9 25.5 + - + +
407E VAL* 3.7 31.9 - - + -
433E VAL* 5.4 0.4 - - + -
434E ILE* 1.3 79.5 - - - +
436E TRP* 1.3 64.5 + - - +
508E TYR* 4.9 5.6 - - + -
509E ARG 3.3 10.1 - - - +
510E VAL* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 436 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E PHE* 4.2 32.5 - + - -
347E PHE* 3.7 32.3 - + - -
373E SER* 3.7 27.1 - - - +
374E PHE* 3.9 27.4 - + - -
375E SER* 4.1 6.3 - - - +
434E ILE* 4.6 6.7 - - + -
435E ALA* 1.3 81.7 - - - +
437E ASN* 1.3 77.1 + - - +
438E SER* 4.8 2.4 - - - -
441E LEU* 5.9 2.8 - - - +
508E TYR* 3.6 6.4 - - - -
509E ARG* 2.9 58.9 + - + +
511E VAL* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 437 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375E SER* 4.8 4.6 - - - -
436E TRP* 1.3 88.6 - - - +
438E SER* 1.3 77.7 + - - +
439E ASN* 2.6 22.0 + - - +
440E ASN* 5.6 0.2 - - - +
503E VAL* 4.8 4.6 - - - +
506E GLN* 3.3 22.2 + - - +
507E PRO 3.7 1.5 - - - +
508E TYR* 3.4 45.4 + - + +
----------------------------------------------------------
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