Contacts of the helix formed by residues 540 - 553 (chain D) in PDB entry 4ZVU
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 TRP 540 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532D TRP* 3.4 47.9 + + + +
534D SER* 4.7 6.0 - - - +
538D GLY 4.5 2.7 - - - -
539D SER* 1.3 72.4 - - - +
541D PHE* 1.3 65.2 + - - +
543D GLN* 3.3 9.8 + - - +
544D ALA* 3.0 24.6 + - - +
569D VAL* 4.2 10.5 - - + -
573D PHE* 3.3 59.8 - + + -
574D GLU 3.9 10.1 - - - -
575D SER* 3.6 35.2 - - - -
585D LYS 4.0 5.4 - - - -
587D GLN* 3.7 38.1 - - + +
1E VAL* 4.1 17.1 - - + +
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Residues in contact with PHE 541 (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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482C PHE* 4.8 3.8 - + + -
483C ILE 4.4 9.2 - - - -
484C GLN* 3.3 23.7 + - + +
522D ALA* 3.5 38.8 - - + -
523D TYR 3.6 12.8 - - - -
524D SER* 3.5 29.6 - - - -
539D SER 3.4 0.2 - - - -
540D TRP* 1.3 80.3 - - - +
542D VAL* 1.3 62.6 + - + +
544D ALA* 3.4 2.1 + - - +
545D LEU* 2.8 49.6 + - + +
562D LEU* 5.1 4.5 - - + -
565D VAL* 3.8 23.3 - - + -
566D ASN* 5.4 0.2 - - - -
569D VAL* 3.9 8.2 - - + +
587D GLN* 4.3 7.2 - - - +
589D PRO* 3.9 16.6 - - + -
591D VAL* 6.5 0.9 - - + -
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Residues in contact with VAL 542 (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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393C ASP* 3.4 39.0 - - + +
396C ALA* 4.8 2.2 - - + -
397C LEU* 3.8 25.4 - - + -
440C ILE* 6.0 0.4 - - + -
442C LEU* 4.1 20.9 - - + -
484C GLN* 4.2 9.2 - - + -
539D SER* 3.1 19.8 + - - +
541D PHE* 1.3 78.3 - - + +
543D GLN* 1.3 67.6 + - - +
545D LEU* 4.2 7.0 - - + -
546D CYS* 2.9 31.4 + - - +
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Residues in contact with GLN 543 (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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392C LYS* 5.1 4.0 - - - +
393C ASP* 5.2 1.1 - - - +
396C ALA* 6.5 0.4 - - - -
534D SER* 4.4 2.2 - - - -
537D ARG* 3.4 47.9 - - - +
538D GLY* 2.7 25.8 + - - -
539D SER 3.0 15.6 + - - +
540D TRP* 3.4 11.8 - - - +
542D VAL* 1.3 79.1 - - - +
544D ALA* 1.3 56.7 + - - +
546D CYS* 4.1 3.0 - - - +
547D SER* 3.0 30.3 + - - -
568D ARG* 4.0 4.0 + - - +
573D PHE* 3.8 29.5 - - + -
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Residues in contact with ALA 544 (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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540D TRP 3.0 16.3 + - - +
541D PHE 3.8 1.8 - - - +
543D GLN* 1.3 74.2 - - - +
545D LEU* 1.3 66.9 + - - +
547D SER* 3.4 0.7 + - - -
548D ILE* 3.0 30.5 + - - +
565D VAL* 4.0 10.3 - - + -
568D ARG* 3.6 34.8 - - + +
569D VAL* 3.7 22.4 - - + -
573D PHE* 4.7 2.0 - - + -
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Residues in contact with LEU 545 (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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397C LEU* 4.2 21.5 - - + -
401C PHE* 4.7 1.8 - - + -
482C PHE* 3.7 33.4 - - + -
541D PHE* 2.8 33.1 + - + +
542D VAL* 3.7 6.7 - - + +
544D ALA* 1.3 77.5 - - - +
546D CYS* 1.3 57.7 + - - +
548D ILE* 3.5 1.2 + - - +
549D LEU* 3.0 55.9 + - + +
561D ILE* 4.7 4.0 - - + -
562D LEU* 4.1 17.9 - - + -
565D VAL* 3.9 24.8 - - + +
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Residues in contact with CYS 546 (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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396C ALA* 3.6 37.7 - - + -
397C LEU* 3.6 29.2 - - - -
400C CYS* 3.6 18.8 - - - -
542D VAL* 2.9 22.0 + - - +
543D GLN* 4.1 2.7 - - - +
545D LEU* 1.3 74.8 - - - +
547D SER* 1.3 60.9 + - - +
549D LEU* 3.3 2.0 + - - -
550D GLU* 2.9 42.4 + - - +
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Residues in contact with SER 547 (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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543D GLN 3.0 19.5 + - - -
544D ALA 3.6 1.7 + - - -
546D CYS* 1.3 78.8 - - - +
548D ILE* 1.3 63.4 + - - +
550D GLU* 3.5 18.4 + - - +
551D GLU* 3.1 28.9 + - - +
568D ARG* 3.4 30.0 + - - -
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Residues in contact with ILE 548 (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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544D ALA 3.0 12.9 + - - +
545D LEU 4.1 2.5 - - - +
547D SER* 1.3 78.9 - - - +
549D LEU* 1.3 60.3 + - - +
551D GLU* 3.3 12.2 + - - +
552D HIS* 2.8 40.4 + - + +
553D GLY 3.8 0.2 + - - -
561D ILE* 4.0 27.1 - - + +
564D ARG* 3.4 50.9 - - + +
565D VAL* 3.4 16.6 - - + +
568D ARG* 4.4 15.5 - - + -
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Residues in contact with LEU 549 (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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397C LEU* 5.9 0.4 - - + -
400C CYS* 4.7 11.7 - - + -
401C PHE* 3.8 34.1 - - + -
404C LEU* 4.4 22.5 - - + +
482C PHE* 5.8 0.9 - - + -
545D LEU* 3.0 40.8 + - + +
546D CYS* 3.8 4.9 - - - +
548D ILE* 1.3 72.7 - - - +
550D GLU* 1.3 63.9 + - - +
553D GLY* 2.8 42.5 + - - +
554D LYS* 5.8 0.5 - - - +
558D ILE* 5.7 1.6 - - + -
561D ILE* 4.0 25.6 - - + -
601D PHE* 4.6 7.6 - - + -
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Residues in contact with GLU 550 (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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396C ALA* 6.0 1.0 - - - +
400C CYS* 3.8 19.2 - - - -
546D CYS* 2.9 34.7 + - - +
547D SER* 3.5 11.0 + - - +
549D LEU* 1.3 77.9 - - - +
551D GLU* 1.3 59.1 + - + +
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Residues in contact with GLU 551 (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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547D SER* 3.1 25.7 + - - +
548D ILE* 3.7 15.3 - - - +
549D LEU 3.2 0.2 - - - -
550D GLU* 1.3 76.6 - - + +
552D HIS* 1.3 87.4 + - + +
553D GLY 3.9 0.2 - - - -
555D ASP* 3.9 5.6 - - - +
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Residues in contact with HIS 552 (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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58A TYR* 5.3 1.4 + - - -
548D ILE* 2.8 23.5 + - + +
551D GLU* 1.3 104.9 + - + +
553D GLY* 1.3 67.4 + - - +
554D LYS 3.2 3.4 - - - -
555D ASP* 2.8 27.6 + - - -
556D LEU* 3.1 47.5 + - + +
561D ILE* 4.1 4.3 - - + +
564D ARG* 3.5 28.5 + - - -
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Residues in contact with GLY 553 (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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404C LEU* 4.0 11.2 - - - -
548D ILE 3.8 0.2 + - - -
549D LEU* 2.8 41.2 + - - -
551D GLU 3.9 0.2 - - - -
552D HIS* 1.3 78.0 - - - +
554D LYS* 1.3 61.3 + - - +
555D ASP 3.8 0.2 + - - -
556D LEU 4.2 7.6 - - - +
561D ILE* 4.3 2.4 - - - +
601D PHE* 3.7 26.0 + - - +
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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