Contacts of the helix formed by residues 434 - 456 (chain D) in PDB entry 5TWV
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 434 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D TYR* 5.9 5.2 - - + -
380D ALA* 5.8 0.2 - - - -
430D TRP 5.0 0.4 + - - -
431D PHE 4.6 2.9 + - - -
432D PHE 3.3 0.2 - - - -
433D PHE* 1.3 88.2 - - + +
435D CYS* 1.3 59.9 - - - +
436D PRO* 3.5 4.0 - - - -
437D ASN* 3.1 19.8 + - + +
438D LEU* 3.0 25.5 + - - +
596D VAL* 5.2 4.7 - - + +
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Residues in contact with CYS 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D PHE 5.0 3.6 + - - +
432D PHE* 3.4 37.1 + - + +
434D LEU* 1.3 74.1 - - - +
436D PRO* 1.3 69.3 - - + +
438D LEU* 3.3 8.9 + - - +
439D TRP* 2.9 24.8 + - - +
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Residues in contact with PRO 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D LEU* 4.6 6.1 - - - +
302D SER* 4.2 8.3 - - - +
303D SER* 3.8 35.9 - - - +
306D ARG* 4.2 12.7 - - + +
376D SER* 4.5 4.9 - - - +
380D ALA* 5.2 12.8 - - + -
432D PHE* 4.9 8.5 - - + +
434D LEU* 3.9 2.5 - - - -
435D CYS* 1.3 90.1 - - + +
437D ASN* 1.3 60.3 + - - +
439D TRP* 3.6 10.1 - - + +
440D THR* 2.9 31.2 + - - -
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Residues in contact with ASN 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D ARG* 5.6 1.6 - - - -
377D TYR* 4.8 20.4 - - + +
434D LEU* 3.1 26.9 + - + +
436D PRO* 1.3 78.0 - - - +
438D LEU* 1.3 59.4 + - - +
440D THR* 3.7 3.8 - - - -
441D MET* 2.9 30.4 + - - +
592D LEU* 6.1 4.7 - - + -
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Residues in contact with LEU 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D LEU 3.0 11.2 + - - +
435D CYS* 3.6 10.5 - - - +
437D ASN* 1.3 76.0 - - - +
439D TRP* 1.3 62.9 + - - +
441D MET* 3.9 5.9 - - - +
442D PRO* 3.3 21.0 - - - +
593D LEU* 6.4 0.7 - - - +
596D VAL* 3.7 29.8 - - + +
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Residues in contact with TRP 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D SER* 4.4 24.3 - - - -
307D ILE* 6.2 2.9 - - + -
435D CYS 2.9 17.0 + - - +
436D PRO* 3.3 9.8 + - + +
438D LEU* 1.3 77.9 - - - +
440D THR* 1.3 61.1 + - - +
442D PRO* 4.0 6.9 - - - +
443D VAL* 5.0 4.3 + - - +
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Residues in contact with THR 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D SER 5.5 0.4 - - - -
306D ARG* 4.2 28.3 - - - -
307D ILE* 4.7 4.9 - - - -
310D ASP* 4.7 10.7 - - - +
436D PRO 2.9 16.9 + - - -
437D ASN* 3.7 4.3 - - - -
439D TRP* 1.3 79.9 - - - +
441D MET* 1.3 65.0 + - - +
442D PRO 3.6 0.4 - - - -
443D VAL* 3.8 9.3 + - - +
444D GLN* 3.4 20.8 + - - +
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Residues in contact with MET 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437D ASN 2.9 18.1 + - - +
438D LEU* 3.9 7.0 - - - +
439D TRP 3.5 0.2 - - - -
440D THR* 1.3 77.0 - - - +
442D PRO* 1.4 65.8 - - + +
444D GLN* 3.1 7.6 + - - +
445D ILE* 2.9 26.8 + - - +
589D PRO* 4.6 27.8 - - + +
592D LEU* 6.1 1.8 - - + -
593D LEU* 5.1 10.5 - - + +
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Residues in contact with PRO 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D LEU 3.3 17.0 - - - +
439D TRP 4.0 6.7 - - - +
440D THR 3.9 0.9 - - - -
441D MET* 1.4 86.8 - - + +
443D VAL* 1.3 59.7 + - - +
445D ILE* 3.7 9.7 - - + +
446D ILE* 2.9 31.0 + - - +
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Residues in contact with VAL 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ASP* 5.5 7.0 - - + -
439D TRP 5.0 3.3 + - - +
440D THR* 4.1 13.2 - - - +
441D MET 3.2 0.8 - - - -
442D PRO* 1.3 79.9 - - - +
444D GLN* 1.3 58.1 + - - +
446D ILE* 4.1 3.7 - - - +
447D VAL* 2.9 32.7 + - - +
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Residues in contact with GLN 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ASP* 4.9 13.8 - - + +
314D PHE* 5.7 9.6 - - + +
440D THR 3.4 11.2 + - - +
441D MET* 3.1 10.8 + - - +
443D VAL* 1.3 77.4 - - - +
445D ILE* 1.3 59.3 + - - +
447D VAL* 4.7 3.6 - - - -
448D GLY* 2.9 26.3 + - - -
589D PRO* 5.2 11.4 - - + -
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Residues in contact with ILE 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D MET 2.9 15.9 + - - +
442D PRO* 3.9 8.7 - - + +
444D GLN* 1.3 76.1 - - - +
446D ILE* 1.3 58.8 + - - +
448D GLY* 5.2 0.2 - - - -
449D VAL* 2.9 31.2 + - - +
589D PRO* 5.5 9.3 - - + +
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Residues in contact with ILE 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D PRO 2.9 19.8 + - - +
443D VAL* 4.1 4.3 - - - +
445D ILE* 1.3 75.9 - - - +
447D VAL* 1.3 60.0 + - - +
449D VAL* 3.7 4.3 - - - +
450D ILE* 2.9 28.1 + - - +
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Residues in contact with VAL 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D PHE* 5.1 12.3 - - + -
443D VAL 2.9 19.5 + - - +
444D GLN* 4.4 3.1 - - - +
446D ILE* 1.3 75.6 - - - +
448D GLY* 1.3 60.3 + - - +
450D ILE* 3.1 7.8 + - - +
451D LEU* 2.9 28.4 + - - +
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Residues in contact with GLY 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D PHE* 5.7 5.0 - - - +
444D GLN 2.9 18.3 + - - -
445D ILE* 4.2 0.4 - - - -
447D VAL* 1.3 73.2 - - - +
449D VAL* 1.3 59.4 + - - +
451D LEU* 3.6 6.7 + - - +
452D LEU* 2.9 27.0 + - - +
582D LEU* 5.1 10.3 - - - +
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Residues in contact with VAL 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D ILE 2.9 22.3 + - - +
446D ILE* 3.9 5.4 - - - +
448D GLY* 1.3 75.0 - - - +
450D ILE* 1.3 58.3 + - - +
452D LEU* 3.5 8.9 + - - +
453D TYR* 2.9 25.6 + - - +
460D ALA* 4.8 6.4 - - + +
464D ALA* 5.8 8.5 - - + -
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Residues in contact with ILE 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D ILE 2.9 18.4 + - - +
447D VAL* 3.1 9.1 + - - +
449D VAL* 1.3 75.1 - - - +
451D LEU* 1.3 58.9 + - - +
453D TYR* 3.0 10.7 + - - +
454D TYR* 2.9 40.8 + - + -
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Residues in contact with LEU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D VAL 2.9 15.1 + - - +
448D GLY* 4.0 6.7 - - - +
450D ILE* 1.3 73.2 - - - +
452D LEU* 1.3 61.0 + - - +
454D TYR* 3.1 17.5 + - + +
455D ILE* 3.0 23.9 + - - +
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Residues in contact with LEU 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D GLY 2.9 20.0 + - - +
449D VAL* 3.5 10.3 - - - +
451D LEU* 1.3 76.1 - - - +
453D TYR* 1.3 56.5 + - - +
455D ILE* 3.1 9.9 + - - +
456D LEU 2.8 28.4 + - - +
459D SER* 5.7 2.3 - - - -
460D ALA* 4.3 20.3 + - + +
579D SER* 6.5 1.6 - - - -
582D LEU* 5.4 10.5 - - + +
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Residues in contact with TYR 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D VAL 2.9 15.1 + - - +
450D ILE* 3.0 13.2 + - - +
452D LEU* 1.3 72.8 - - - +
454D TYR* 1.3 72.5 + + - +
455D ILE 4.1 0.3 - - - -
456D LEU* 3.3 20.8 + - - +
457D GLY* 4.7 11.0 - - - -
460D ALA* 4.7 6.2 - - + +
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Residues in contact with TYR 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D ILE* 2.9 35.7 + - + -
451D LEU* 3.1 16.4 + - + +
453D TYR* 1.3 82.8 - + - +
455D ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D LEU 3.0 11.8 + - - +
452D LEU* 3.1 12.7 + - - +
453D TYR 4.1 0.2 - - - -
454D TYR* 1.3 79.8 - - - +
456D LEU* 1.3 65.0 + - + +
459D SER* 6.2 2.5 - - - -
575D VAL* 4.9 18.4 - - + -
579D SER* 5.4 8.1 - - - -
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Residues in contact with LEU 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452D LEU 2.8 18.8 + - - +
453D TYR* 3.3 19.3 - - - -
454D TYR 3.7 0.4 - - - -
455D ILE* 1.3 78.9 - - + +
457D GLY* 1.3 62.3 + - - +
458D VAL 4.5 4.5 - - - +
459D SER* 4.7 15.5 - - - +
460D ALA* 4.2 3.2 - - - +
564D SER* 4.8 10.8 - - - +
575D VAL* 6.2 2.5 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
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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