Contacts of the helix formed by residues 674 - 680 (chain B) in PDB entry 2XER
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 PRO 674 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621B PRO* 5.1 0.4 - - - +
664B GLY 3.6 4.0 - - - +
665B SER* 1.3 85.1 - - - +
675B HIS* 1.3 62.2 + - + +
677B THR* 4.0 7.9 - - - +
678B ALA* 3.1 24.3 + - - +
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Residues in contact with HIS 675 (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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617B ALA 3.5 16.4 + - - -
618B ARG 3.8 11.5 + - - -
621B PRO* 3.0 41.7 - - + +
658B GLN 3.6 11.6 + - - -
659B LEU 2.8 30.2 + - - -
660B MET 4.1 0.2 - - - -
661B ASN* 3.8 32.7 + - + +
665B SER* 4.2 0.4 - - - -
674B PRO* 1.3 81.7 - - + +
676B LEU* 1.3 63.3 - - - +
678B ALA* 3.3 9.4 + - - +
679B VAL* 3.2 18.5 - - + +
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Residues in contact with LEU 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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660B MET* 3.3 46.9 - - + +
662B LEU 3.8 8.1 - - - +
663B PRO* 3.7 17.7 - - + -
664B GLY 4.3 1.1 - - - +
665B SER* 3.1 9.4 + - - +
675B HIS* 1.3 78.3 - - - +
677B THR* 1.3 65.6 + - - +
678B ALA 3.1 1.8 - - - -
679B VAL* 3.1 22.8 + - + +
680B LEU* 3.0 40.0 + - + +
689B LEU* 5.2 2.0 - - + -
724B GLU* 3.6 36.8 - - + +
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Residues in contact with THR 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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664B GLY* 4.6 7.6 + - - -
665B SER 3.1 15.6 + - - -
674B PRO* 4.1 7.5 - - - +
676B LEU* 1.3 77.4 - - - +
678B ALA* 1.3 61.5 + - - +
680B LEU* 4.1 6.7 - - - +
681B GLN* 3.2 50.7 + - + +
728B ILE* 4.9 13.2 - - + +
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Residues in contact with ALA 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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621B PRO* 4.0 27.1 - - + +
624B ILE* 3.3 20.6 - - + +
674B PRO 3.1 19.2 + - - +
675B HIS 3.3 7.9 - - - +
676B LEU 3.1 0.4 - - - -
677B THR* 1.3 78.4 - - - +
679B VAL* 1.3 58.9 + - - +
681B GLN* 4.1 5.2 - - - +
682B ASN* 3.4 13.0 + - - +
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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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620B LEU* 4.0 30.3 - - + -
621B PRO* 4.8 1.1 - - + -
624B ILE* 4.1 8.1 - - + -
659B LEU* 4.0 26.5 - - + +
660B MET* 5.5 0.4 - - + -
675B HIS* 3.2 21.8 - - + +
676B LEU* 3.1 29.9 + - + +
678B ALA* 1.3 76.9 - - + +
680B LEU* 1.3 73.2 + - + +
681B GLN 3.3 0.4 - - - -
682B ASN* 3.3 5.5 + - - +
685B GLY* 3.2 8.0 - - - +
686B LEU* 2.9 27.9 + - - -
689B LEU* 4.9 5.2 - - + -
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Residues in contact with LEU 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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676B LEU* 3.0 36.2 + - + +
677B THR* 4.2 5.8 - - - +
679B VAL* 1.3 82.4 - - + +
681B GLN* 1.3 59.0 + - - +
682B ASN 3.2 0.7 - - - -
686B LEU* 4.0 19.8 - - + +
689B LEU* 3.6 31.6 - - + -
724B GLU* 4.6 16.4 - - + +
725B LEU* 4.1 19.5 - - + -
728B ILE* 4.6 26.5 - - + -
732B ALA 4.5 0.2 - - - -
733B LEU* 3.9 12.7 - - + +
734B ALA* 3.1 24.1 + - - +
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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