Contacts of the helix formed by residues 554 - 565 (chain A) in PDB entry 6X70
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 GLY 554 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A ASP* 4.8 5.2 - - - -
553A VAL* 1.3 73.1 - - - +
555A HIS* 1.3 57.3 + - - -
556A SER 3.1 3.3 + - - -
557A THR 3.3 0.7 + - - -
558A LEU* 2.7 37.5 + - - +
10P T 2.8 27.9 + - - -
11P A 4.1 10.8 - - - -
801P MG 4.6 0.2 - - - -
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Residues in contact with HIS 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A ASP* 5.7 1.5 + - - -
554A GLY* 1.3 70.9 - - - -
556A SER* 1.3 77.2 + - - +
558A LEU* 3.4 9.6 - - - +
559A SER* 2.8 38.6 + - - +
9P G 4.9 13.6 + - + -
10P T 3.3 23.3 + - + -
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Residues in contact with SER 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A HIS* 1.3 94.3 - - - +
557A THR* 1.3 67.4 + - - +
559A SER* 3.3 7.1 + - - -
560A ARG* 3.2 35.2 + - - +
9P G 3.5 30.1 + - - -
10P T 3.1 13.9 + - - -
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Residues in contact with THR 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A GLY 3.9 2.3 + - - -
553A VAL* 3.9 26.7 - - + -
556A SER* 1.3 70.4 + - - +
558A LEU* 1.3 67.2 + - - +
560A ARG* 3.1 9.4 + - - +
561A LEU* 2.9 26.3 + - + +
587A VAL* 3.5 25.7 - - + +
591A LEU* 3.6 28.7 - - + +
595A ILE* 4.6 0.9 - - + -
9P G 3.9 3.8 + - - -
10P T 2.6 26.8 + - - -
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Residues in contact with LEU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A LEU* 3.5 34.8 - - + +
548A ASP* 4.3 19.7 - - + +
553A VAL* 3.6 9.7 - - + +
554A GLY 2.7 23.7 + - - +
555A HIS* 3.4 10.8 - - - +
557A THR* 1.3 72.2 - - - +
559A SER* 1.3 67.8 + - - +
561A LEU* 3.1 6.9 + - - +
562A GLU* 3.0 54.3 + - + +
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Residues in contact with SER 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A HIS* 2.8 29.2 + - - +
556A SER* 3.7 7.1 - - - -
558A LEU* 1.3 77.9 - - - +
560A ARG* 1.3 63.2 + - - +
562A GLU* 3.3 14.3 + - - +
563A SER* 3.2 22.2 + - - -
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Residues in contact with ARG 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A SER* 3.2 24.9 + - - +
557A THR* 3.1 9.7 + - - +
559A SER* 1.3 74.1 - - - +
561A LEU* 1.3 63.6 + - - +
563A SER* 3.5 5.2 + - - +
564A THR* 2.6 33.3 + - - -
586A SER* 3.1 34.8 + - - +
587A VAL* 3.9 23.2 + - + +
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A LEU* 4.0 28.7 - - + +
550A LEU* 5.8 0.4 - - + -
553A VAL* 4.2 21.8 - - + -
557A THR* 2.9 18.3 + - + +
558A LEU* 3.5 6.7 - - - +
560A ARG* 1.3 76.2 - - - +
562A GLU* 1.3 58.1 + - - +
565A PHE* 3.0 48.5 + - + +
568A PRO* 3.9 3.1 - - - +
574A LEU* 4.2 13.0 - - + -
583A LEU* 3.6 30.1 - - + -
586A SER* 4.2 2.5 - - - +
587A VAL* 3.8 15.0 - - + -
595A ILE* 4.3 12.8 - - + -
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Residues in contact with GLU 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A LEU* 5.2 1.1 - - + -
558A LEU* 3.0 48.5 + - + +
559A SER* 3.6 12.3 + - - +
561A LEU* 1.3 74.6 - - - +
563A SER* 1.3 66.9 + - - +
566A ASP* 2.9 7.4 + - - -
567A SER* 2.8 50.5 + - - +
568A PRO* 4.1 12.6 - - + +
569A HIS* 5.7 3.2 + - - -
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Residues in contact with SER 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A SER 3.2 12.6 + - - -
560A ARG* 3.9 5.2 - - - -
562A GLU* 1.3 79.5 - - - +
564A THR* 1.3 65.1 + - - +
566A ASP* 3.9 4.9 + - - -
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Residues in contact with THR 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A ARG* 2.6 23.0 + - - +
561A LEU 3.9 2.5 - - - -
563A SER* 1.3 80.4 - - - +
565A PHE* 1.3 81.3 + - + +
566A ASP 3.5 0.7 + - - -
582A ALA* 4.3 10.1 - - + +
586A SER* 2.7 31.0 + - - -
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Residues in contact with PHE 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A LEU* 3.0 44.2 + - + +
564A THR* 1.3 93.6 - - + +
566A ASP* 1.3 69.4 + - - +
567A SER 3.2 2.8 + - - -
568A PRO* 3.3 14.4 - - + +
574A LEU* 3.7 19.7 - - + -
577A ARG* 2.9 37.3 + - + -
578A TYR* 3.7 32.8 - - + -
579A THR 4.4 0.7 - - - -
582A ALA* 4.1 14.4 - - + -
583A LEU* 3.9 31.6 - - + -
586A SER* 4.7 0.7 - - - -
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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
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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