Contacts of the helix formed by residues 689 - 696 (chain D) in PDB entry 4PE5
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 689 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486D HIS* 5.6 1.3 - - - -
487D GLY 5.4 0.2 - - - -
519D ARG* 4.3 2.9 - - - -
686D VAL* 3.8 13.2 + - - -
687D PRO 3.2 5.4 - - - -
688D ASN* 1.3 81.0 - - - +
690D SER* 1.3 61.9 + - - -
691D THR 3.2 2.2 - - - -
692D GLU* 3.3 5.9 + - - +
693D ARG* 3.0 27.9 + - - +
907D GLU* 3.2 18.6 - - - -
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Residues in contact with SER 690 (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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514D THR* 3.3 33.3 + - - +
516D ASN* 4.4 11.0 + - - +
519D ARG* 3.8 13.4 - - - +
534D ILE* 5.6 0.4 - - - +
689D GLY* 1.3 72.4 - - - -
691D THR* 1.3 63.6 + - - +
693D ARG* 3.4 6.6 + - - +
694D ASN* 2.9 30.9 + - - +
732D ASP* 5.3 0.5 + - - -
907D GLU* 2.9 31.7 + - - -
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Residues in contact with THR 691 (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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533D GLY 4.8 0.9 - - - +
534D ILE* 3.8 39.5 - - + +
685D THR* 2.9 28.0 + - - -
686D VAL* 4.7 0.9 - - - +
689D GLY 4.6 0.7 - - - -
690D SER* 1.3 81.4 + - - +
692D GLU* 1.3 56.7 + - - +
694D ASN* 3.8 1.0 - - - +
695D ILE* 2.9 31.9 + - - +
730D ILE* 4.0 5.1 + - - -
731D TYR* 3.8 21.1 - - - -
732D ASP* 4.0 2.9 - - - +
907D GLU* 3.3 27.1 + - - +
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Residues in contact with GLU 692 (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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685D THR* 4.2 15.0 - - + -
686D VAL 3.7 13.5 - - - +
687D PRO* 3.9 12.0 - - - +
688D ASN* 2.4 37.9 + - - +
689D GLY 3.3 6.1 + - - +
690D SER 3.3 0.2 - - - -
691D THR* 1.3 81.0 + - - +
693D ARG* 1.3 59.7 + - - +
695D ILE* 4.1 3.3 - - - +
696D ARG* 3.0 30.3 + - - +
703D HIS* 3.2 35.3 + - + +
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Residues in contact with ARG 693 (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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781A GLU* 4.8 1.2 - - - +
516D ASN* 5.2 8.7 - - - +
518D GLU* 6.2 2.9 - - + -
519D ARG* 6.2 0.2 - - - +
689D GLY 3.0 16.8 + - - +
690D SER* 3.8 7.0 - - - +
692D GLU* 1.3 76.4 - - - +
694D ASN* 1.3 59.4 + - - +
696D ARG* 4.2 4.5 - - - +
697D ASN* 3.7 19.6 + - - +
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Residues in contact with ASN 694 (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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781A GLU* 3.9 29.4 - - + +
534D ILE* 3.7 24.0 - - + -
690D SER 2.9 17.9 + - - +
693D ARG* 1.3 77.7 - - - +
695D ILE* 1.3 62.6 + - - +
696D ARG 3.4 0.4 - - - -
697D ASN* 3.4 3.0 + - - +
698D ASN* 3.2 25.6 + - - +
758D ALA* 5.3 2.2 - - + -
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Residues in contact with ILE 695 (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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534D ILE* 4.8 4.4 - - + +
685D THR* 6.1 2.2 - - + -
691D THR 2.9 20.0 + - - +
692D GLU* 4.1 4.9 - - - +
694D ASN* 1.3 73.1 - - - +
696D ARG* 1.3 55.7 + - - +
697D ASN 3.1 4.7 - - - -
698D ASN* 4.4 2.5 - - - +
699D TYR* 2.6 42.8 + - + +
702D MET* 4.9 12.1 - - + -
703D HIS* 4.8 6.1 - - + +
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Residues in contact with ARG 696 (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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692D GLU 3.0 18.2 + - - +
693D ARG* 4.6 4.9 - - - +
695D ILE* 1.3 77.2 - - - +
697D ASN* 1.3 58.2 + - - +
698D ASN 3.5 0.2 - - - -
699D TYR 4.3 2.5 - - - -
700D ALA* 4.7 10.3 + - - +
703D HIS* 3.7 37.4 - - + +
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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