Contacts of the helix formed by residues 506 - 514 (chain B) in PDB entry 2ETM
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 GLU 506 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B 7PY 4.1 18.3 + - - +
504B LEU 4.3 0.5 - - - +
505B GLY* 1.3 73.3 - - - -
507B LEU* 1.3 61.6 + - - +
508B ARG* 3.3 37.0 + - + +
509B SER* 3.6 17.5 + - - +
510B PHE* 3.1 29.2 + - - +
550B ARG* 3.4 37.1 - - - +
552B VAL 3.7 6.1 - - - +
553B LEU* 3.8 8.7 - - + +
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Residues in contact with LEU 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B GLY 3.8 0.4 + - - -
506B GLU* 1.3 71.7 - - - +
508B ARG* 1.3 60.1 + - - +
510B PHE* 3.5 4.2 - - + +
511B LEU* 2.9 60.6 + - + +
526B TYR* 4.7 7.6 - - + -
530B LEU* 4.7 1.3 - - + -
549B ALA* 3.6 14.6 - - + +
552B VAL* 2.9 47.6 + - + +
554B VAL* 3.8 23.1 - - + +
560B VAL* 4.3 13.5 - - + -
615B ILE* 3.9 31.6 - - + -
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Residues in contact with ARG 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLU* 3.3 24.2 + - - +
507B LEU* 1.3 73.6 - - - +
509B SER* 1.3 68.9 + - - +
511B LEU* 3.0 4.0 + - - +
512B GLN* 2.8 45.9 + - - +
549B ALA* 3.4 23.6 - - - -
550B ARG* 3.4 22.8 - - - +
588B TRP* 6.0 0.2 - - - -
614B GLU* 3.7 14.0 + - - -
619B GLY* 3.1 34.7 + - - -
621B LYS* 3.5 45.6 - - - +
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Residues in contact with SER 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B 7PY 5.8 4.9 - - - -
506B GLU* 3.6 24.6 + - - +
508B ARG* 1.3 75.5 - - - +
510B PHE* 1.3 66.5 + - - +
512B GLN* 2.9 15.5 + - - +
513B VAL* 2.8 35.3 + - - +
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Residues in contact with PHE 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B LEU* 3.9 21.7 + - + +
506B GLU 3.1 16.7 + - - +
507B LEU* 3.5 7.0 - - + +
509B SER* 1.3 78.0 - - - +
511B LEU* 1.3 71.2 + - + +
513B VAL* 3.7 4.0 + - - -
514B ARG* 3.0 72.0 + - + +
518B LEU* 4.0 15.7 - - + -
526B TYR* 3.8 22.4 - + - -
554B VAL* 3.7 38.6 - - + -
557B ASN* 3.3 26.5 - - - -
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 2.9 49.3 + - + +
508B ARG* 3.0 3.8 + - - +
510B PHE* 1.3 79.5 - - + +
512B GLN* 1.3 66.2 + - - +
514B ARG 3.1 2.8 + - - -
515B LYS* 2.9 25.5 + - - +
518B LEU* 3.6 26.5 - - + -
523B LEU* 3.9 13.9 - - + -
526B TYR* 4.4 6.3 - - + -
549B ALA* 5.5 1.3 - - + -
614B GLU 4.8 0.2 - - - -
615B ILE* 3.7 29.6 - - + +
618B HIS* 3.6 16.8 + - - +
619B GLY* 3.6 20.4 - - - +
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Residues in contact with GLN 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A CYS* 5.4 1.6 - - - +
437A HIS* 5.8 1.0 + - - -
508B ARG* 2.8 54.1 + - - +
509B SER* 3.1 11.4 + - - +
511B LEU* 1.3 72.4 - - - +
513B VAL* 1.3 67.5 + - + +
515B LYS* 2.6 36.0 + - - +
516B TYR* 5.7 0.2 - - - -
618B HIS 3.5 14.8 - - - +
619B GLY 3.5 17.2 + - - +
620B VAL* 5.6 0.4 - - - +
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Residues in contact with VAL 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A ARG* 3.5 40.7 - - + +
427A CYS* 3.5 37.8 + - + +
509B SER* 2.8 29.9 + - - +
510B PHE* 4.0 5.2 - - - +
512B GLN* 1.3 75.6 - - + +
514B ARG* 1.3 72.7 + - - +
515B LYS 3.5 1.9 + - - -
516B TYR* 4.9 2.4 + - - -
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Residues in contact with ARG 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG* 3.4 34.7 - - - +
504B LEU* 4.9 11.9 - - - +
510B PHE* 3.0 55.2 + - + +
511B LEU 3.1 6.3 + - - -
513B VAL* 1.3 92.8 - - - +
515B LYS* 1.3 56.5 + - - +
516B TYR 2.7 13.0 + - - -
517B SER* 2.8 29.2 + - - -
518B LEU* 3.1 32.6 + - + +
557B ASN* 3.8 20.0 + - - +
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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