Contacts of the helix formed by residues 795 - 804 (chain D) in PDB entry 3IYD
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 TYR 795 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339D ARG* 4.1 25.0 + - - -
792D ASN* 4.0 11.7 + - - +
793D SER 3.2 1.6 - - - -
794D GLY* 1.3 76.7 - - - +
796D LEU* 1.3 65.8 + - - +
798D ARG* 3.2 27.5 + - + +
799D ARG* 3.0 45.1 + - + +
1138D LEU* 3.8 23.6 - - + -
1142D ALA* 5.2 12.6 - - + -
18J A 6.0 4.7 - + - -
19J T 5.4 7.4 - - - -
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Residues in contact with LEU 796 (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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793D SER 4.2 9.5 + - - +
794D GLY 3.2 0.2 - - - -
795D TYR* 1.3 82.4 - - - +
797D THR* 1.3 61.9 + - - +
798D ARG 3.1 0.9 + - - -
799D ARG* 3.5 13.2 + - - +
800D LEU* 3.9 20.8 + - + +
923D ILE* 3.8 34.8 - - + +
924D GLY* 4.5 7.4 - - - +
927D GLY* 5.9 4.5 - - - -
1137D GLY 4.4 5.4 - - - +
1138D LEU* 4.5 15.4 - - + +
1141D VAL* 3.6 35.7 - - + -
1145D PHE* 5.3 1.1 - - + -
1241D TYR* 3.3 26.7 - - - +
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Residues in contact with THR 797 (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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1276C TRP* 6.2 0.9 - - + -
794D GLY* 3.4 13.5 + - - -
795D TYR 3.3 0.2 - - - -
796D LEU* 1.3 72.5 - - - +
798D ARG* 1.3 70.3 + - - +
799D ARG 3.1 6.3 + - - -
800D LEU* 4.1 2.9 - - - +
801D VAL* 3.3 39.9 + - + +
920D ALA* 3.0 38.4 + - + +
921D GLN* 3.9 16.5 - - + +
924D GLY* 3.2 18.2 - - - -
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Residues in contact with ARG 798 (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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1272C GLU* 5.0 3.2 + - - -
1273C MET* 3.2 36.1 - - - +
1276C TRP* 3.1 45.1 - - - +
792D ASN* 5.1 7.1 + - - +
794D GLY* 3.2 20.7 + - - +
795D TYR* 3.2 27.4 - - + +
796D LEU 3.1 0.6 - - - -
797D THR* 1.3 88.7 + - - +
799D ARG* 1.3 66.6 + - - +
801D VAL* 5.7 0.8 - - - +
802D ASP* 3.4 22.7 - - - +
18J A 3.6 48.5 + - + +
19J T 5.5 2.0 - - - -
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Residues in contact with ARG 799 (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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795D TYR* 3.0 54.0 + - + +
796D LEU* 3.5 7.2 + - - +
797D THR 3.1 0.4 - - - -
798D ARG* 1.3 90.3 - - - +
800D LEU* 1.3 68.0 + - + +
801D VAL 3.5 0.7 - - - -
802D ASP* 3.7 6.5 + - - +
803D VAL* 3.4 23.7 - - - +
1142D ALA* 5.4 6.9 - - + +
1145D PHE* 6.6 0.2 - - + -
1146D GLU* 3.0 36.5 + - - +
1148D ARG* 3.9 20.0 - - - +
1309D ILE* 3.9 6.5 - - + +
1310D THR* 2.9 31.2 + - - +
1326D GLN* 6.1 0.4 - - - +
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Residues in contact with LEU 800 (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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796D LEU* 4.0 25.4 - - + +
797D THR 3.9 1.6 + - - +
799D ARG* 1.3 78.1 - - + +
801D VAL* 1.3 62.1 + - - +
803D VAL* 3.0 2.8 + - - +
804D ALA* 2.8 33.5 + - + +
916D GLY 5.3 0.2 - - - +
919D ALA 4.7 0.2 - - - +
920D ALA* 3.6 34.5 - - + +
923D ILE* 4.2 6.5 - - + -
1145D PHE* 3.5 35.7 - - + -
1256D ILE* 3.7 39.3 - - + -
1309D ILE* 4.3 15.7 - - + -
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Residues in contact with VAL 801 (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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1276C TRP* 3.3 42.4 - - + +
1279C GLU* 4.5 8.3 - - - +
797D THR* 3.3 36.5 + - + +
798D ARG* 6.1 0.7 - - - +
799D ARG 3.5 0.4 - - - -
800D LEU* 1.3 77.3 - - - +
802D ASP* 1.3 62.4 + - - +
803D VAL 3.0 5.4 + - - -
804D ALA 4.8 0.7 - - - +
805D GLN* 3.3 24.1 + - + +
916D GLY 4.9 5.2 - - - -
917D VAL* 4.6 21.8 - - + +
920D ALA* 3.8 10.8 - - + -
921D GLN* 5.2 0.9 - - + -
1347D LEU* 6.2 0.9 - - + -
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Residues in contact with ASP 802 (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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1276C TRP* 4.3 13.0 + - - -
798D ARG* 3.4 16.8 + - - +
799D ARG* 3.7 8.4 + - - +
800D LEU 3.2 1.6 - - - -
801D VAL* 1.3 84.6 - - - +
803D VAL* 1.3 66.6 + - + +
805D GLN* 4.4 3.1 - - - +
1313D SER* 4.0 2.6 + - - -
1325D PHE* 3.2 53.9 - - + -
1348D LYS* 5.5 4.0 - - - +
18J A 3.4 26.5 + - - +
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Residues in contact with VAL 803 (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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799D ARG 3.4 13.9 - - - +
800D LEU 3.0 5.1 + - - +
801D VAL 3.0 2.0 + - - -
802D ASP* 1.3 88.5 - - + +
804D ALA* 1.3 61.5 + - + +
805D GLN* 3.0 18.8 + - - -
806D ASP* 3.3 13.3 - - - +
1259D GLN* 4.5 15.6 + - + -
1262D ARG* 4.9 4.1 + - - +
1309D ILE* 3.1 46.0 - - + +
1310D THR* 4.1 8.3 - - + -
1312D ALA* 4.4 7.4 - - + -
1313D SER* 4.0 23.4 + - - +
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Residues in contact with ALA 804 (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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800D LEU 2.8 16.1 + - - +
801D VAL 4.3 1.3 - - - -
803D VAL* 1.3 71.2 - - + +
805D GLN* 1.3 59.7 + - - +
806D ASP 3.0 5.6 - - - -
807D LEU* 3.2 20.5 + - + +
808D VAL* 5.4 0.2 - - - +
916D GLY* 3.4 39.3 - - - +
917D VAL* 4.6 1.3 - - - +
1256D ILE* 4.0 20.2 - - + -
1259D GLN* 4.1 17.5 - - + +
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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