Contacts of the helix formed by residues 434 - 456 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377H TYR* 5.9 4.9 - - + -
430H TRP 5.0 0.2 + - - -
431H PHE 4.6 2.9 + - - -
433H PHE* 1.3 89.3 - - + +
435H CYS* 1.3 60.3 + - - +
436H PRO* 3.5 4.3 - - - -
437H ASN* 3.1 19.4 + - + +
438H LEU* 3.0 25.6 + - - +
596H VAL* 5.2 5.1 - - + +
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Residues in contact with CYS 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431H PHE 5.0 2.9 + - - +
432H PHE* 3.4 37.2 + - + +
434H LEU* 1.3 74.1 - - - +
436H PRO* 1.3 69.2 - - + +
438H LEU* 3.3 8.7 + - - +
439H TRP* 2.9 25.1 + - - +
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Residues in contact with PRO 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H LEU* 4.6 6.1 - - - +
302H SER* 4.2 7.6 - - - +
303H SER* 3.8 36.8 - - - +
306H ARG* 4.2 12.5 - - + +
376H SER* 4.5 5.8 - - - +
380H ALA* 5.2 13.0 - - + -
432H PHE* 4.9 7.6 - - + +
434H LEU* 3.9 2.7 - - - -
435H CYS* 1.3 91.1 - - + +
437H ASN* 1.3 59.4 + - - +
439H TRP* 3.5 10.5 - - + +
440H THR* 2.9 30.7 + - - -
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Residues in contact with ASN 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ARG* 5.6 2.0 - - - -
377H TYR* 4.8 19.9 - - + +
434H LEU* 3.1 27.7 + - + +
436H PRO* 1.3 77.2 - - - +
438H LEU* 1.3 58.9 + - - +
440H THR* 3.5 3.3 + - - -
441H MET* 2.9 30.0 + - - +
592H LEU* 6.1 4.7 - - + -
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Residues in contact with LEU 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434H LEU 3.0 10.0 + - - +
435H CYS* 3.6 10.8 - - - +
436H PRO 3.3 0.2 - - - -
437H ASN* 1.3 75.5 - - - +
439H TRP* 1.3 63.1 + - - +
441H MET* 3.9 5.8 - - - +
442H PRO* 3.3 20.4 - - - +
592H LEU 5.9 0.4 - - - -
593H LEU* 6.4 0.7 - - - +
596H VAL* 3.7 30.2 - - + +
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Residues in contact with TRP 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H SER* 4.4 24.3 - - - -
307H ILE* 6.2 3.1 - - + -
435H CYS 2.9 16.5 + - - +
436H PRO* 3.3 10.7 + - + +
438H LEU* 1.3 78.1 - - - +
440H THR* 1.3 61.8 + - - +
442H PRO* 4.0 7.1 - - - +
443H VAL* 5.0 4.3 + - - +
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Residues in contact with THR 440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H SER 5.5 0.7 - - - -
306H ARG* 4.2 27.4 - - - -
307H ILE* 4.7 4.9 - - - -
310H ASP* 4.7 9.5 - - - +
436H PRO 2.9 16.1 + - - -
437H ASN* 3.7 3.4 - - - -
439H TRP* 1.3 78.7 - - - +
441H MET* 1.3 63.5 + - - +
442H PRO 3.6 0.7 - - - -
443H VAL* 3.8 9.5 + - - +
444H GLN* 3.4 21.0 + - - +
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Residues in contact with MET 441 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437H ASN 2.9 17.7 + - - +
438H LEU* 3.9 7.4 - - - +
439H TRP 3.5 0.2 - - - -
440H THR* 1.3 78.5 - - - +
442H PRO* 1.4 65.5 - - + +
444H GLN* 3.1 7.3 + - - +
445H ILE* 2.9 25.9 + - - +
589H PRO* 4.6 27.7 - - + +
592H LEU* 6.1 1.1 - - + -
593H LEU* 5.1 11.0 - - + +
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Residues in contact with PRO 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438H LEU 3.3 17.5 - - - +
439H TRP 4.0 6.5 - - - +
440H THR 3.9 0.9 - - - -
441H MET* 1.4 86.3 - - + +
443H VAL* 1.3 60.4 + - - +
445H ILE* 3.7 9.0 - - + +
446H ILE* 2.9 31.0 + - - +
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Residues in contact with VAL 443 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H ASP* 5.5 7.4 - - + -
439H TRP 5.0 2.9 + - - +
440H THR* 3.8 13.2 + - - +
441H MET 3.2 0.6 - - - -
442H PRO* 1.3 80.5 - - - +
444H GLN* 1.3 58.4 + - - +
446H ILE* 4.1 3.9 - - - +
447H VAL* 2.9 31.9 + - - +
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Residues in contact with GLN 444 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H ASP* 4.9 13.2 - - + +
314H PHE* 5.7 10.2 - - + +
440H THR 3.4 11.0 + - - +
441H MET* 3.1 10.6 + - - +
443H VAL* 1.3 77.4 - - - +
445H ILE* 1.3 59.4 + - - +
447H VAL* 4.7 2.9 - - - -
448H GLY* 2.9 26.9 + - - -
589H PRO* 5.2 11.0 - - + -
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Residues in contact with ILE 445 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441H MET 2.9 16.0 + - - +
442H PRO* 3.9 8.7 - - + +
443H VAL 3.4 0.2 - - - -
444H GLN* 1.3 75.9 - - - +
446H ILE* 1.3 57.6 + - - +
449H VAL* 2.9 32.1 + - - +
589H PRO* 5.5 9.1 - - + +
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Residues in contact with ILE 446 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442H PRO 2.9 18.7 + - - +
443H VAL* 4.1 4.5 - - - +
445H ILE* 1.3 76.7 - - - +
447H VAL* 1.3 59.5 + - - +
449H VAL* 3.7 4.5 - - - +
450H ILE* 2.9 28.2 + - - +
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Residues in contact with VAL 447 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H PHE* 5.1 13.5 - - + -
443H VAL 2.9 19.1 + - - +
444H GLN* 4.4 2.9 - - - +
446H ILE* 1.3 75.8 - - - +
448H GLY* 1.3 60.2 + - - +
450H ILE* 3.1 7.2 + - - +
451H LEU* 2.9 28.1 + - - +
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Residues in contact with GLY 448 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H PHE* 5.7 5.0 - - - +
444H GLN 2.9 17.4 + - - -
445H ILE 4.2 0.2 - - - -
447H VAL* 1.3 73.6 - - - +
449H VAL* 1.3 60.8 + - - +
451H LEU* 3.6 5.6 + - - +
452H LEU* 2.9 27.8 + - - +
582H LEU* 5.1 9.4 - - - +
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Residues in contact with VAL 449 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445H ILE 2.9 22.7 + - - +
446H ILE* 3.9 6.1 - - - +
448H GLY* 1.3 75.1 - - - +
450H ILE* 1.3 59.9 + - - +
452H LEU* 3.5 8.9 + - - +
453H TYR* 2.9 25.5 + - - +
460H ALA* 4.8 6.2 - - + +
464H ALA* 5.8 7.6 - - + -
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Residues in contact with ILE 450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446H ILE 2.9 19.0 + - - +
447H VAL* 3.1 9.6 + - - +
449H VAL* 1.3 76.0 - - - +
451H LEU* 1.3 60.3 + - - +
453H TYR* 3.0 11.1 + - - +
454H TYR* 2.9 39.8 + - + -
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Residues in contact with LEU 451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447H VAL 2.9 15.2 + - - +
448H GLY* 4.0 5.6 - - - +
450H ILE* 1.3 72.3 - - - +
452H LEU* 1.3 61.3 + - - +
454H TYR* 3.1 17.2 + - + +
455H ILE* 3.0 24.6 + - - +
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Residues in contact with LEU 452 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448H GLY 2.9 20.0 + - - +
449H VAL* 3.5 10.5 - - - +
451H LEU* 1.3 77.1 - - - +
453H TYR* 1.3 55.4 + - - +
455H ILE* 3.1 9.5 + - - +
456H LEU 2.8 28.0 + - - +
459H SER* 5.7 2.3 - - - -
460H ALA* 4.3 20.5 + - + +
579H SER* 6.5 1.8 - - - -
582H LEU* 5.4 10.5 - - + +
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Residues in contact with TYR 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449H VAL 2.9 14.4 + - - +
450H ILE* 3.0 15.0 + - - +
452H LEU* 1.3 74.1 - - - +
454H TYR* 1.3 72.0 + + - +
455H ILE 4.1 0.2 - - - -
456H LEU* 3.3 20.6 + - - +
457H GLY* 4.7 11.2 - - - -
460H ALA* 4.9 6.5 - - + -
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Residues in contact with TYR 454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450H ILE* 2.9 34.4 + - + -
451H LEU* 3.1 16.8 + - + +
453H TYR* 1.3 82.2 - + - +
455H ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451H LEU 3.0 11.6 + - - +
452H LEU* 3.1 12.1 + - - +
454H TYR* 1.3 79.7 - - - +
456H LEU* 1.3 65.6 + - + +
459H SER* 6.2 2.5 - - - -
575H VAL* 4.9 17.9 - - + -
579H SER* 5.4 8.5 - - - -
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Residues in contact with LEU 456 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452H LEU 2.8 18.7 + - - +
453H TYR* 3.3 18.5 - - - +
454H TYR 3.7 0.8 - - - -
455H ILE* 1.3 80.0 - - + +
457H GLY* 1.3 62.3 - - - +
458H VAL 4.5 5.2 - - - +
459H SER* 4.7 15.3 - - - +
460H ALA* 4.2 3.0 - - - +
564H SER* 4.8 11.4 - - - +
575H VAL* 6.2 2.7 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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