Contacts of the helix formed by residues 675 - 685 (chain D) in PDB entry 3BWE
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 675 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D PO4 3.6 17.3 - - - -
613D GLY 3.7 10.5 - - - -
615D GLU* 4.0 8.0 - - - +
618D GLU* 4.1 0.4 + - - -
647D SER* 4.9 0.4 - - - -
674D GLY* 1.3 72.5 - - - -
676D ASN* 1.3 70.7 + - - +
677D LEU 3.4 2.2 - - - -
678D GLY 3.2 2.1 + - - -
679D ALA* 3.0 22.3 + - - +
706D CYS* 3.9 12.9 - - - -
707D ALA* 4.3 4.8 - - - +
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Residues in contact with ASN 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B GLU* 5.5 3.1 - - + +
379B ALA* 3.4 43.5 + - - +
380B GLN* 4.2 9.5 - - + +
383B ALA* 4.8 8.1 - - - +
1D PO4 2.8 30.5 + - - +
675D GLY* 1.3 74.3 - - - +
677D LEU* 1.3 65.4 + - - +
679D ALA* 4.2 1.9 - - - +
680D GLN* 3.3 29.6 + - - +
707D ALA* 4.9 6.4 - - - +
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Residues in contact with LEU 677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B GLU* 3.8 36.6 + - + +
1D PO4 4.8 0.2 + - - -
612D LYS* 3.7 37.0 - - + +
613D GLY* 3.8 12.0 + - - -
675D GLY 3.4 0.2 - - - -
676D ASN* 1.3 82.6 + - - +
678D GLY* 1.3 57.6 + - - +
680D GLN* 3.1 21.2 + - - +
681D ASN* 2.9 51.1 + - - +
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Residues in contact with GLY 678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611D ALA* 4.4 5.8 - - - -
612D LYS 3.6 12.6 - - - -
613D GLY 3.2 21.4 + - - -
614D ALA* 3.9 9.4 - - - -
673D PRO 5.4 0.7 - - - -
674D GLY 4.2 2.2 - - - -
675D GLY 3.2 3.7 + - - -
677D LEU* 1.3 76.7 - - - +
679D ALA* 1.3 56.6 + - - +
681D ASN* 3.3 1.7 + - - +
682D LEU* 2.9 37.5 + - - +
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Residues in contact with ALA 679 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673D PRO 4.9 1.6 - - - +
674D GLY 4.4 2.2 + - - -
675D GLY 3.0 15.1 + - - +
676D ASN 4.3 1.6 - - - +
678D GLY* 1.3 71.4 - - - +
680D GLN* 1.3 59.8 + - - +
682D LEU* 3.5 11.8 - - - +
683D SER* 2.8 36.1 + - - -
707D ALA* 3.4 36.6 - - + +
708D GLY* 4.1 8.7 - - - +
710D THR* 3.6 9.6 - - - +
711D ALA* 4.3 0.4 - - - +
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Residues in contact with GLN 680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676D ASN* 3.3 23.3 + - - +
677D LEU* 3.1 25.1 + - - +
679D ALA* 1.3 80.2 - - - +
681D ASN* 1.3 64.7 + - - +
683D SER* 3.2 5.7 + - - -
684D GLU* 3.1 50.5 + - + +
732D LYS* 5.9 8.3 - - - +
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Residues in contact with ASN 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611D ALA* 3.9 3.4 - - + -
612D LYS* 2.9 40.0 + - - +
638D LEU* 3.7 21.2 - - + +
677D LEU* 2.9 32.7 + - - +
678D GLY 3.7 4.0 - - - +
680D GLN* 1.3 77.3 - - - +
682D LEU* 1.3 63.0 + - - +
684D GLU* 3.3 15.2 + - - +
685D SER* 3.1 22.5 + - - -
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Residues in contact with LEU 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D ILE* 4.4 17.9 - - + +
611D ALA* 3.3 26.7 - - + +
638D LEU* 4.6 3.1 - - + -
672D LEU* 3.6 43.3 - - + -
673D PRO* 4.2 15.0 - - + +
678D GLY 2.9 26.4 + - - +
679D ALA* 3.5 11.4 - - - +
680D GLN 3.2 0.2 - - - -
681D ASN* 1.3 77.0 - - - +
683D SER* 1.3 60.2 + - - +
685D SER* 3.0 18.9 + - - -
688D VAL* 3.7 15.3 - - + +
708D GLY 5.0 0.9 - - - +
711D ALA* 3.8 9.6 - - + -
715D HIS* 2.9 18.5 + - - -
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Residues in contact with SER 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679D ALA 2.8 25.1 + - - -
680D GLN* 3.5 8.2 - - - -
682D LEU* 1.3 72.8 - - - +
684D GLU* 1.3 61.1 + - - +
710D THR* 3.6 5.9 + - - -
711D ALA* 3.0 24.5 + - - +
714D ALA* 3.4 22.4 - - - +
715D HIS* 2.8 25.9 + - - -
732D LYS* 5.2 6.5 + - - -
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Residues in contact with GLU 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680D GLN* 3.1 42.2 + - + +
681D ASN* 3.7 14.0 - - - +
682D LEU 3.2 0.2 - - - -
683D SER* 1.3 79.2 - - - +
685D SER* 1.3 65.0 + - - +
686D ALA* 3.3 3.8 + - - +
715D HIS* 4.7 0.2 - - - -
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Residues in contact with SER 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638D LEU* 3.5 17.9 - - - +
681D ASN 3.1 10.6 + - - -
682D LEU 3.0 13.6 + - - -
684D GLU* 1.3 77.3 - - - +
686D ALA* 1.3 60.8 + - - +
687D ALA* 3.2 8.0 + - - +
688D VAL* 2.9 34.1 + - - +
689D LYS* 3.2 4.9 + - - +
715D HIS* 3.2 23.1 - - - -
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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