Contacts of the helix formed by residues 672 - 683 (chain B) in PDB entry 3E0D
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 SER 672 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669B GLN 4.8 0.9 + - - -
670B LEU 3.7 0.6 - - - -
671B GLU* 1.3 76.4 + - - +
673B GLY* 1.3 66.9 + - - +
674B GLY 4.3 1.8 - - - -
675B MET* 3.5 22.1 - - - +
676B THR* 2.9 25.5 + - - -
697B TYR* 5.0 3.4 - - - -
6E T 3.1 41.4 + - - -
7E G 5.7 2.1 + - - -
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Residues in contact with GLY 673 (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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671B GLU 3.6 2.4 + - - -
672B SER* 1.3 73.0 - - - +
674B GLY* 1.3 61.7 + - - +
676B THR* 3.3 7.2 + - - -
677B ALA* 3.3 18.4 + - - +
1078B GLU* 3.9 28.5 - - - +
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Residues in contact with GLY 674 (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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672B SER* 3.3 2.4 - - - -
673B GLY* 1.3 71.7 - - - +
675B MET* 1.3 65.7 + - - +
677B ALA* 3.1 10.4 + - - +
678B THR* 3.0 23.8 + - - -
697B TYR* 3.1 20.4 + - - -
1067B ARG* 5.1 15.5 - - - +
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Residues in contact with MET 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B GLN 4.4 11.7 - - - +
670B LEU* 3.4 34.3 - - + -
672B SER* 3.2 26.6 + - - +
674B GLY* 1.3 74.1 - - - +
676B THR* 1.3 62.9 + - - +
678B THR* 3.1 4.5 + - - -
679B VAL* 3.0 27.4 + - + +
693B LEU* 4.1 23.3 - - - -
694B VAL* 4.4 22.7 - - + +
697B TYR* 3.3 53.1 + - + +
6E T 5.6 3.4 - - - +
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Residues in contact with THR 676 (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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662B GLY* 3.4 20.5 - - - +
664B THR* 2.6 30.7 + - - +
670B LEU 3.8 4.4 + - - -
671B GLU 4.0 6.4 + - - -
672B SER 2.9 18.7 + - - -
673B GLY* 3.5 7.6 - - - +
675B MET* 1.3 77.6 - - - +
677B ALA* 1.3 61.5 + - - +
679B VAL* 3.4 7.6 + - - +
680B ARG* 3.2 33.6 + - - +
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Residues in contact with ALA 677 (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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673B GLY 3.3 8.2 + - - +
674B GLY* 3.1 12.4 + - - +
676B THR* 1.3 77.9 - - - +
678B THR* 1.3 63.6 + - - +
680B ARG* 3.2 29.5 + - - +
681B GLY* 3.0 19.2 + - - -
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Residues in contact with THR 678 (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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674B GLY 3.0 14.3 + - - -
675B MET* 3.1 10.1 + - - -
677B ALA* 1.3 77.0 - - - +
679B VAL* 1.3 56.6 + - - +
681B GLY* 3.1 2.9 + - - +
682B LEU* 2.8 29.9 + - + +
693B LEU* 3.5 28.3 - - + -
697B TYR* 3.4 19.0 - - + -
702B MET* 5.5 0.7 - - - -
705B ILE* 3.9 29.5 - - + +
709B ILE* 5.2 3.4 - - + +
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Residues in contact with VAL 679 (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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659B LEU* 3.4 30.7 - - + +
660B SER* 4.2 0.2 - - - -
664B THR* 4.7 8.5 - - + -
670B LEU* 4.5 15.3 - - + -
675B MET* 3.0 28.2 + - + +
676B THR* 3.8 7.2 - - - +
678B THR* 1.3 74.8 - - - +
680B ARG* 1.3 57.6 + - - +
682B LEU* 4.4 1.3 - - - +
683B LYS* 2.9 27.7 + - - -
684B PRO* 3.5 25.4 - - + +
690B ILE* 6.3 0.7 - - + -
693B LEU* 3.5 25.6 - - + -
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Residues in contact with ARG 680 (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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659B LEU 4.2 0.8 + - - -
660B SER 3.4 13.7 - - - +
661B ARG 3.4 25.7 + - - +
662B GLY* 3.5 15.8 + - - -
676B THR* 3.2 24.1 + - - +
677B ALA* 3.2 32.8 + - - +
679B VAL* 1.3 77.9 - - - +
681B GLY* 1.3 61.6 + - - +
683B LYS* 3.4 27.6 - - - +
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Residues in contact with GLY 681 (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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677B ALA 3.0 13.3 + - - -
678B THR* 3.1 4.9 + - - -
680B ARG* 1.3 77.5 - - - +
682B LEU* 1.3 63.8 + - - +
683B LYS* 4.0 3.1 - - - +
709B ILE* 4.6 14.9 - - - +
713B HIS* 3.6 16.1 + - - -
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Residues in contact with LEU 682 (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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678B THR* 2.8 20.6 + - + +
679B VAL* 4.0 2.9 - - - +
681B GLY* 1.3 74.4 - - - +
683B LYS* 1.3 68.8 + - - +
684B PRO* 4.3 12.8 - - + -
689B ASP* 4.2 18.8 - - + +
693B LEU* 3.8 41.7 - - + +
705B ILE* 6.1 1.3 - - + -
708B TYR* 3.7 35.7 - - + -
709B ILE* 4.6 16.7 - - + +
712B HIS* 3.8 21.8 - - + +
713B HIS* 3.6 14.4 - - - -
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Residues in contact with LYS 683 (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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660B SER* 2.9 47.8 + - - +
661B ARG* 4.2 7.7 - - - +
679B VAL 2.9 11.7 + - - -
680B ARG* 3.4 21.6 + - - +
681B GLY 4.0 4.7 - - - +
682B LEU* 1.3 81.2 - - - +
684B PRO* 1.3 70.6 - - - +
685B ARG* 3.6 14.4 + - - +
712B HIS* 4.4 4.5 + - - -
713B HIS* 4.9 7.9 - - + -
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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