Contacts of the helix formed by residues 674 - 687 (chain B) in PDB entry 1EGI
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 674 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638B THR* 3.8 13.6 - - - +
672B ILE* 3.4 11.8 + - - +
673B ASN* 1.3 83.8 + - - +
675B LYS* 1.3 63.0 + - - +
676B GLU* 3.0 22.0 - - - +
677B GLU* 3.0 45.0 + - - +
678B GLN* 3.3 15.2 + - - +
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Residues in contact with LYS 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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674B ASN* 1.3 72.8 - - - +
676B GLU* 1.3 78.5 + - - +
678B GLN* 3.1 30.5 + - - +
679B GLN* 2.9 35.5 + - + +
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Residues in contact with GLU 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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635B SER* 4.6 9.2 - - - +
636B SER* 5.4 6.3 - - - +
637B ARG* 4.9 22.0 - - + -
638B THR* 5.7 1.9 - - + +
674B ASN* 3.0 24.5 - - - +
675B LYS* 1.3 81.1 + - + +
677B GLU* 1.3 63.1 + - - +
679B GLN* 3.2 9.4 + - - +
680B THR* 3.0 24.8 + - - -
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Residues in contact with GLU 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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635B SER* 3.5 16.6 - - - +
638B THR* 2.9 27.8 + - - +
640B LEU* 3.6 18.5 - - - +
642B PHE* 3.8 18.0 - - + -
671B SER 3.7 4.7 - - - +
672B ILE* 4.5 6.5 - - + -
673B ASN* 3.0 35.0 + - - +
674B ASN* 3.0 29.8 + - - +
676B GLU* 1.3 76.1 - - - +
678B GLN* 1.3 61.6 + - - +
680B THR* 3.3 9.2 + - - -
681B ILE* 3.3 26.6 + - - +
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Residues in contact with GLN 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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672B ILE* 3.8 32.5 - - + +
674B ASN 3.3 5.9 + - - +
675B LYS* 3.1 34.9 + - - +
677B GLU* 1.3 78.0 - - - +
679B GLN* 1.3 59.8 + - - +
681B ILE* 3.2 5.2 + - - +
682B TRP* 3.0 25.2 + - + +
743B THR 4.7 2.6 - - - +
744B MET* 3.9 41.5 + - + +
746B TRP* 4.8 9.5 - - - +
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Residues in contact with GLN 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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675B LYS* 2.9 26.6 + - + +
676B GLU* 3.2 12.3 + - - +
678B GLN* 1.3 77.0 - - - +
680B THR* 1.3 63.7 + - - +
682B TRP* 3.4 20.8 + - - +
683B ARG* 3.0 56.4 + - + +
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Residues in contact with THR 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B GLY* 3.5 37.6 - - - +
634B ALA 3.6 12.4 + - - +
635B SER* 3.6 17.2 - - - -
636B SER 4.8 0.5 + - - -
642B PHE* 4.0 14.6 - - + -
676B GLU 3.0 15.5 + - - -
677B GLU* 3.5 9.4 - - - -
678B GLN 3.3 0.4 - - - -
679B GLN* 1.3 76.1 - - - +
681B ILE* 1.3 62.0 + - - +
683B ARG* 3.4 8.5 + - - +
684B LEU* 3.2 21.5 + - - +
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Residues in contact with ILE 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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642B PHE* 3.7 37.9 - - + -
644B LEU* 4.4 5.8 - - + -
670B ALA* 4.6 3.6 - - + -
672B ILE* 3.9 30.7 - - + -
677B GLU 3.3 12.8 + - - +
678B GLN* 3.2 8.7 + - - +
679B GLN 3.2 0.4 - - - -
680B THR* 1.3 77.1 - - - +
682B TRP* 1.3 60.1 + - - +
684B LEU* 3.0 10.2 + - + +
685B ILE* 2.9 30.5 + - + +
697B LEU* 5.0 0.2 - - + -
738B LEU* 4.1 14.8 - - + -
744B MET* 4.9 2.0 - - - -
758B ILE* 3.8 35.0 - - + -
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Residues in contact with TRP 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 GLN* 3.0 14.2 + - + +
679B GLN* 3.4 35.6 + - - +
681B ILE* 1.3 76.2 - - - +
683B ARG* 1.3 64.5 + - - +
685B ILE* 3.2 12.2 + - + +
686B THR* 3.0 41.0 + - - -
691B TYR* 3.9 22.9 - + - -
740B GLY 3.7 11.0 - - - -
741B ASP* 3.6 21.8 - - - -
742B PRO* 3.6 31.6 - - + -
744B MET* 3.7 34.7 - - + -
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Residues in contact with ARG 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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679B GLN* 3.0 46.3 + - + +
680B THR* 3.7 7.9 - - - +
682B TRP* 1.3 81.5 - - - +
684B LEU* 1.3 66.1 + - + +
686B THR* 3.8 11.3 - - - +
687B ALA* 3.1 24.9 + - - +
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Residues in contact with LEU 684 (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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632B TRP* 5.4 0.4 - - - -
633B GLY* 3.7 24.7 - - - +
642B PHE* 3.2 45.3 - - + +
643B LYS* 3.8 9.2 - - - +
644B LEU* 3.4 21.4 - - + +
680B THR 3.2 17.5 + - - +
681B ILE* 3.0 9.1 + - - +
683B ARG* 1.3 75.5 - - + +
685B ILE* 1.3 68.3 + - - +
687B ALA* 3.3 13.9 + - + +
688B SER* 3.0 17.8 + - - -
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Residues in contact with ILE 685 (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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644B LEU* 3.5 20.0 - - + -
681B ILE* 2.9 17.4 + - + +
682B TRP* 3.2 15.2 + - + +
684B LEU* 1.3 76.7 - - - +
686B THR* 1.3 64.1 + - - +
688B SER* 3.1 6.3 + - - -
689B GLY* 3.9 0.2 - - - -
690B SER* 3.1 50.9 + - - +
691B TYR* 3.9 4.6 - - + +
695B PHE* 4.1 15.3 - - + -
738B LEU* 4.5 8.7 - - + -
740B GLY* 3.6 23.6 - - - +
744B MET* 3.5 35.9 - - + -
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Residues in contact with THR 686 (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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682B TRP* 3.0 40.0 + - - -
683B ARG* 3.9 13.5 - - - +
684B LEU 3.3 0.2 - - - -
685B ILE* 1.3 77.4 - - - +
687B ALA* 1.3 60.1 + - - +
688B SER 2.9 5.5 + - - -
689B GLY* 3.3 9.5 + - - -
691B TYR* 3.1 34.1 + - - +
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Residues in contact with ALA 687 (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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683B ARG 3.1 18.8 + - - +
684B LEU* 3.3 8.0 + - + +
686B THR* 1.3 76.2 - - - +
688B SER* 1.3 57.8 + - - +
689B GLY 3.7 0.2 - - - -
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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