Contacts of the strand formed by residues 508 - 516 (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 TYR 508 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375E SER* 4.2 19.1 + - - -
401E VAL* 3.4 4.5 - - - +
402E ILE* 2.9 33.9 + - + +
403E ARG 3.9 11.2 - - - +
404E GLY* 3.5 22.0 - - - -
407E VAL* 4.2 19.3 - - + -
435E ALA* 4.9 3.8 - - + -
436E TRP* 3.6 10.3 - - - +
437E ASN* 3.4 49.3 + - + +
503E VAL* 3.8 19.5 - - + +
504E GLY 5.2 0.4 - - - -
506E GLN* 3.3 18.4 - - + -
507E PRO* 1.3 76.3 - - - +
509E ARG* 1.3 64.8 + - - +
510E VAL* 4.0 1.7 + - + -
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Residues in contact with ARG 509 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E PHE 5.0 1.2 + - - -
344E ALA 3.3 18.6 + - - -
345E THR 3.8 18.2 + - - -
346E ARG* 4.3 0.4 - - - +
347E PHE* 3.0 57.2 - - + +
400E PHE 3.6 3.1 - - - -
401E VAL* 3.6 16.8 - - + -
435E ALA* 3.3 4.2 - - - +
436E TRP* 2.9 54.1 + - + +
438E SER* 3.8 18.5 + - - +
441E LEU* 4.2 25.8 - - - +
442E ASP* 2.9 31.5 + - - -
507E PRO 4.3 0.6 + - - -
508E TYR* 1.3 73.9 - - - +
510E VAL* 1.3 59.9 - - - +
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Residues in contact with VAL 510 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E PHE* 3.6 1.7 - - - -
398E ASP 4.4 0.2 - - - -
399E SER* 3.4 4.7 - - - -
400E PHE* 3.0 57.2 + - + +
402E ILE* 3.7 35.4 - - + -
407E VAL* 4.7 4.7 - - + -
410E ILE* 4.7 6.5 - - + -
433E VAL* 4.4 11.0 - - + -
434E ILE 3.5 11.7 - - - +
435E ALA* 4.2 11.2 - - + -
508E TYR* 4.2 4.5 - - + +
509E ARG* 1.3 80.5 - - - +
511E VAL* 1.3 68.7 + - - +
512E VAL* 4.3 11.2 - - + -
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Residues in contact with VAL 511 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341E VAL* 3.9 19.3 - - + +
342E PHE* 3.7 31.4 - - + -
347E PHE* 4.3 15.7 - - + -
397E ALA* 4.7 11.2 - - + -
398E ASP 3.2 10.5 - - - +
399E SER* 4.3 6.1 - - - +
433E VAL* 3.9 0.7 - - - -
434E ILE* 2.9 37.5 + - + +
436E TRP* 4.3 9.3 - - + -
510E VAL* 1.3 75.8 - - - +
512E VAL* 1.3 69.3 + - - +
513E LEU* 4.0 12.0 + - + -
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Residues in contact with VAL 512 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396E TYR 3.6 1.2 - - - +
397E ALA* 3.5 2.3 - - - -
398E ASP* 2.9 36.9 + - + +
400E PHE* 4.5 5.8 - - + -
410E ILE* 3.8 28.7 - - + -
423E TYR* 3.7 27.6 - - + +
425E LEU* 4.2 5.2 - - + -
429E PHE* 3.7 28.9 - - + -
432E CYS 3.7 4.7 - - - +
433E VAL* 4.0 8.5 - - + -
464E PHE* 5.4 0.2 - - + -
510E VAL* 4.3 9.0 - - + -
511E VAL* 1.3 75.2 - - - +
513E LEU* 1.3 63.2 + - - +
514E SER* 3.8 2.5 + - - +
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Residues in contact with LEU 513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338E PHE* 4.7 18.2 - - + -
341E VAL* 6.0 0.2 - - + -
342E PHE* 5.5 4.0 - - + -
365E TYR* 4.9 7.6 - - + -
368E LEU* 4.5 14.6 - - + -
377E PHE* 5.8 1.6 - - + -
395E VAL* 3.9 20.4 - - + -
396E TYR 3.3 5.6 - - - +
397E ALA* 4.2 13.7 - - + -
429E PHE* 3.6 4.5 - - - -
431E GLY* 3.0 3.8 - - - -
432E CYS* 2.9 43.0 + - + +
434E ILE* 3.8 25.8 - - + -
511E VAL* 4.0 10.7 + - + -
512E VAL* 1.3 73.7 - - - +
514E SER* 1.3 60.3 + - - +
515E PHE* 4.1 19.3 - - + -
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Residues in contact with SER 514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E ARG* 5.2 1.6 - - - -
395E VAL* 3.6 1.1 - - - +
396E TYR* 2.9 50.9 + - - +
398E ASP* 5.7 0.9 - - - -
429E PHE* 3.9 19.8 - - - -
430E THR* 6.1 0.2 - - - -
431E GLY* 4.1 4.7 - - - +
464E PHE* 4.3 20.2 - - - -
512E VAL* 3.8 3.8 + - - -
513E LEU* 1.3 74.4 - - - +
515E PHE* 1.3 65.6 + - - +
516E GLU* 3.6 4.5 + - - +
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Residues in contact with PHE 515 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E TYR* 3.8 32.5 - + - -
382E VAL* 4.4 2.9 - - + -
387E LEU* 4.0 28.9 - - + -
392E PHE* 3.9 42.0 - + + -
394E ASN 3.6 4.3 - - - +
395E VAL* 3.7 27.6 - - + -
430E THR* 3.8 29.9 + - - +
431E GLY* 3.5 31.0 - - - +
432E CYS* 4.2 8.3 - - - -
513E LEU* 4.5 13.7 - - + -
514E SER* 1.3 74.0 + - - +
516E GLU* 1.3 60.8 + - - +
517E LEU* 4.6 1.2 - - - +
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Residues in contact with GLU 516 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393E THR* 3.7 1.3 - - - +
394E ASN* 2.9 45.9 + - + +
396E TYR* 3.5 31.4 + - + -
514E SER* 3.6 7.8 + - - +
515E PHE* 1.3 74.8 - - - +
517E LEU* 1.3 79.3 + - - +
518E LEU* 4.3 25.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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