Contacts of the helix formed by residues 549 - 563 (chain D) in PDB entry 6T8O
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 ASN 549 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542D MET* 3.6 11.1 - - - +
547D VAL* 4.1 4.5 - - - +
548D ARG* 1.3 82.8 - - + +
550D LEU* 1.3 65.2 + - - +
551D ALA* 4.2 11.4 - - - +
552D GLY* 3.5 16.5 + - - -
553D PHE* 3.4 14.7 + - - +
621D ALA* 3.4 25.6 - - + +
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Residues in contact with LEU 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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538D ARG* 4.6 3.4 - - - +
542D MET* 4.4 7.4 - - + -
549D ASN* 1.3 75.6 - - - +
551D ALA* 1.3 60.2 + - - +
553D PHE* 3.2 21.8 + - + +
554D ASN* 2.9 48.3 + - - +
587D LEU* 4.0 23.3 - - + +
588D PRO 4.1 13.0 - - - +
589D THR* 3.8 22.7 - - - +
621D ALA 3.1 13.5 + - - +
622D ALA 3.9 10.8 - - - +
623D GLY* 3.9 21.8 - - - +
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Residues in contact with ALA 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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549D ASN* 3.4 11.4 + - - +
550D LEU* 1.3 78.8 - - - +
552D GLY* 1.3 56.9 + - - +
554D ASN* 3.3 8.5 + - - +
555D ARG* 2.9 31.5 + - - +
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Residues in contact with GLY 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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547D VAL* 3.5 20.1 - - - +
549D ASN* 3.5 10.1 + - - -
550D LEU 3.4 0.4 - - - -
551D ALA* 1.3 79.4 - - - +
553D PHE* 1.3 56.4 + - - +
555D ARG* 3.3 28.2 + - - +
556D LYS* 2.9 32.2 + - - +
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Residues in contact with PHE 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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541D LEU* 3.6 29.4 - - + -
542D MET* 4.6 14.1 - - + -
545D MET* 3.7 35.0 - - + -
547D VAL* 3.7 9.0 - - + +
549D ASN 3.4 14.2 + - - +
550D LEU* 3.2 25.7 + - + +
552D GLY* 1.3 77.5 - - - +
554D ASN* 1.3 62.9 + - - +
556D LYS* 3.3 5.9 + - + +
557D VAL* 2.9 31.7 + - + +
584D LEU* 4.3 13.0 - - + -
585D SER 4.1 17.0 - - - -
587D LEU* 3.6 31.2 - - + -
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Residues in contact with ASN 554 (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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550D LEU* 2.9 39.2 + - - +
551D ALA* 3.3 7.8 + - - +
553D PHE* 1.3 80.3 - - - +
555D ARG* 1.3 61.3 + - - +
557D VAL* 3.4 5.9 - - + +
558D LYS* 2.9 29.5 + - - +
586D THR* 3.4 19.8 - - + +
587D LEU* 3.1 36.0 + - - +
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Residues in contact with ARG 555 (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 VAL* 5.0 4.9 - - - +
551D ALA* 2.9 14.5 + - - +
552D GLY* 3.4 31.6 + - - +
554D ASN* 1.3 77.0 - - - +
556D LYS* 1.3 61.9 + - + +
558D LYS* 3.3 11.1 + - + +
559D ASP* 2.9 48.7 + - - +
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Residues in contact with LYS 556 (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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545D MET* 4.9 20.9 - - + -
547D VAL* 3.7 25.6 - - + -
552D GLY 2.9 18.7 + - - +
553D PHE* 3.6 9.0 - - + +
555D ARG* 1.3 83.5 - - + +
557D VAL* 1.3 57.6 + - - +
559D ASP* 3.3 10.4 + - + +
560D ALA* 2.9 29.3 + - - +
567D LEU* 5.2 12.9 - - + +
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Residues in contact with VAL 557 (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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545D MET* 5.9 2.2 - - + +
553D PHE* 2.9 22.9 + - + +
554D ASN* 3.4 18.4 - - - +
556D LYS* 1.3 73.5 - - - +
558D LYS* 1.3 63.1 + - - +
560D ALA* 4.0 7.6 - - + -
561D GLU* 3.4 32.1 + - + +
567D LEU* 5.6 2.0 - - + +
584D LEU* 4.1 19.1 - - + -
585D SER* 3.4 42.6 - - - +
586D THR* 3.8 17.5 - - + -
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Residues in contact with LYS 558 (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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554D ASN 2.9 18.8 + - - +
555D ARG* 3.5 10.8 - - + +
557D VAL* 1.3 76.5 - - - +
559D ASP* 1.3 64.2 + - - +
560D ALA 3.2 0.2 - - - -
561D GLU* 3.2 8.0 + - - +
562D GLU* 2.9 56.2 + - + +
586D THR* 5.7 4.3 - - + -
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Residues in contact with ASP 559 (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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555D ARG* 2.9 36.0 + - - +
556D LYS* 3.9 11.4 - - + +
558D LYS* 1.3 80.7 - - - +
560D ALA* 1.3 62.4 + - - +
562D GLU* 3.8 19.0 - - - +
563D ALA* 3.1 27.9 + - - +
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Residues in contact with ALA 560 (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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556D LYS 2.9 16.8 + - - +
557D VAL* 4.3 9.2 - - + +
558D LYS 3.2 0.2 - - - -
559D ASP* 1.3 78.9 - - - +
561D GLU* 1.3 62.1 + - + +
562D GLU 3.5 0.3 + - - -
563D ALA* 3.7 7.3 + - - +
565D THR 2.9 27.0 - - - +
566D PRO* 3.7 4.0 - - + -
567D LEU* 3.6 42.4 - - + +
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Residues in contact with GLU 561 (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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557D VAL* 3.4 24.0 + - + +
558D LYS* 3.2 7.2 + - - +
560D ALA* 1.3 74.1 - - + +
562D GLU* 1.3 65.2 + - + +
564D GLY 4.7 5.6 + - - +
566D PRO* 4.1 23.0 - - + +
584D LEU 4.6 4.5 - - - +
585D SER* 4.5 17.8 - - - -
586D THR* 5.2 8.2 + - - +
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Residues in contact with GLU 562 (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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558D LYS* 2.9 49.4 + - + +
559D ASP* 3.8 16.0 - - - +
560D ALA 3.3 0.2 - - - -
561D GLU* 1.3 80.4 - - + +
563D ALA* 1.3 52.5 + - + +
564D GLY* 2.7 16.7 + - - -
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Residues in contact with ALA 563 (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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559D ASP 3.1 16.5 + - - +
560D ALA* 3.7 2.6 + - - +
561D GLU 3.6 0.2 - - - -
562D GLU* 1.3 73.9 - - + +
564D GLY* 1.3 52.7 + - - +
565D THR* 2.7 22.3 + - - +
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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