Contacts of the helix formed by residues 673 - 682 (chain D) in PDB entry 4PC0
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 673 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672D LEU* 1.3 73.4 - - - +
674D SER* 1.3 57.5 + - - +
675D SER* 4.0 8.6 + - - -
676D GLU* 3.0 31.4 + - - +
677D THR* 2.7 34.4 + - - -
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Residues in contact with SER 674 (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 SER* 1.3 74.5 - - - +
675D SER* 1.3 62.5 + - - +
677D THR* 4.1 4.6 - - - -
678D LYS* 3.1 26.9 + - - +
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Residues in contact with SER 675 (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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358B ASP* 5.2 3.1 + - - +
673D SER* 3.2 9.1 - - - -
674D SER* 1.3 79.7 - - - +
676D GLU* 1.3 59.3 + - - +
678D LYS* 3.8 5.9 - - - +
679D ARG* 3.0 53.2 + - - +
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Residues in contact with GLU 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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672D LEU* 3.7 28.3 - - + +
673D SER* 3.0 26.3 + - - +
675D SER* 1.3 78.6 - - - +
677D THR* 1.3 59.6 + - - +
679D ARG* 3.3 25.0 + - - +
680D ALA* 2.9 29.6 + - - +
689D ALA 5.4 4.5 - - - +
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Residues in contact with THR 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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30B PHE 5.5 4.3 - - - +
31B LEU* 4.2 4.8 - - + +
407B ASN* 3.5 39.9 + - - +
408B ILE* 3.9 20.8 - - + +
672D LEU* 3.6 21.6 + - + +
673D SER 2.7 22.8 + - - -
674D SER* 4.1 4.9 - - - -
676D GLU* 1.3 73.2 - - - +
678D LYS* 1.3 64.8 + - - +
680D ALA* 3.4 5.7 + - - +
681D ALA* 3.1 22.7 + - - +
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Residues in contact with LYS 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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349B LYS* 5.7 9.0 - - - +
354B GLN* 3.0 30.7 + - - +
358B ASP* 4.5 19.2 + - - +
364B PRO* 4.8 9.5 + - - +
366B LEU 5.5 0.4 - - - -
367B LEU 5.8 1.3 - - - +
408B ILE* 5.9 2.9 - - - +
674D SER 3.1 18.9 + - - +
675D SER* 3.8 5.6 - - - +
677D THR* 1.3 76.8 - - - +
679D ARG* 1.3 65.4 + - - +
681D ALA* 3.1 17.2 + - - +
682D ARG* 3.2 45.0 + - - +
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Residues in contact with ARG 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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355B SER* 4.9 2.2 + - - -
357B GLU* 4.6 12.3 - - - +
358B ASP* 3.2 29.1 + - - +
361B ASP* 4.5 4.0 - - - +
675D SER* 3.0 36.5 + - - +
676D GLU* 3.5 26.6 + - - +
677D THR 3.3 0.4 - - - -
678D LYS* 1.3 79.1 - - - +
680D ALA* 1.3 61.7 + - - +
682D ARG* 3.4 3.3 + - - +
683D ARG* 3.2 80.1 + - - +
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Residues in contact with ALA 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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30B PHE* 6.0 0.2 - - + -
31B LEU* 3.5 28.0 - - + +
672D LEU* 5.3 3.4 - - + -
676D GLU 2.9 17.0 + - - +
677D THR* 3.8 4.7 - - - +
678D LYS 3.2 0.2 - - - -
679D ARG* 1.3 76.3 - - - +
681D ALA* 1.3 63.3 + - - +
682D ARG 3.3 0.5 + - - -
683D ARG* 3.3 22.1 + - - +
684D PRO* 4.0 0.7 - - - +
688D ILE* 3.8 32.1 - - + -
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Residues in contact with ALA 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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31B LEU* 3.5 11.6 - - + +
367B LEU 3.6 18.8 - - - +
368B PHE* 3.7 16.8 - - + -
369B ILE* 2.9 35.2 + - - +
408B ILE* 4.1 11.0 - - + -
677D THR 3.1 14.6 + - - +
678D LYS* 3.1 12.5 + - - +
680D ALA* 1.3 77.2 - - - +
682D ARG* 1.3 56.7 + - - +
683D ARG 3.6 0.2 - - - -
684D PRO* 4.9 0.6 - - - +
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Residues in contact with ARG 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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354B GLN* 3.1 12.9 + - - -
358B ASP* 2.9 31.3 + - - +
361B ASP* 3.8 25.6 + - + +
362B GLY 3.1 17.8 + - - +
363B PRO 3.0 20.2 + - - -
364B PRO* 4.4 1.0 - - - +
366B LEU* 2.9 47.1 + - + +
367B LEU 4.3 7.9 - - - +
369B ILE* 3.6 18.6 - - + +
678D LYS* 3.2 47.4 + - - +
679D ARG* 3.4 3.6 + - - +
680D ALA 3.2 0.2 - - - -
681D ALA* 1.3 79.0 - - - +
683D ARG* 1.3 63.6 + - - +
684D PRO* 3.5 11.2 - - - +
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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