Contacts of the helix formed by residues 829 - 845 (chain A) in PDB entry 1Y1V
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 VAL 829 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A ILE* 3.1 25.3 + - + +
826A ASP* 4.7 4.7 - - - -
828A ALA* 1.3 82.9 - - + +
830A LYS* 1.3 67.2 + - - +
831A THR 3.0 1.6 - - - -
832A ALA* 2.8 22.6 + - - +
833A GLU* 3.3 5.3 + - - +
1081A LEU* 6.1 0.2 - - + -
1082A ASN* 5.2 10.5 - - - +
506B GLY 4.7 11.0 - - - +
507B LYS* 3.2 52.4 + - + +
508B LEU 5.2 2.7 - - - +
510B LYS* 5.4 3.6 - - - +
512B ARG* 4.7 5.4 - - - +
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Residues in contact with LYS 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826A ASP* 2.7 25.6 + - - +
827A THR* 3.7 20.4 + - - +
829A VAL* 1.3 77.6 - - - +
831A THR* 1.3 59.1 + - - +
833A GLU* 3.1 4.9 + - - +
834A THR* 2.6 49.3 + - - +
1077A THR* 3.7 16.6 - - - +
1078A GLN* 4.9 1.3 - - - +
1079A MET 3.4 19.5 + - - +
1080A THR* 4.9 3.8 - - - +
1081A LEU* 3.4 30.2 - - + +
1098A VAL* 5.6 0.4 - - - +
285S GLN 4.7 0.2 + - - -
286S THR* 2.8 45.6 + - - +
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Residues in contact with THR 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827A THR* 3.0 25.3 + - - +
828A ALA* 3.9 11.0 - - - +
830A LYS* 1.3 85.7 - - - +
832A ALA* 1.3 65.7 + - + +
833A GLU 3.7 0.2 + - - -
834A THR* 4.1 7.2 - - - +
835A GLY* 3.7 14.4 + - - -
531B GLN 6.0 2.5 - - - +
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Residues in contact with ALA 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A ALA 4.3 7.4 - - - +
829A VAL 2.8 16.3 + - - +
831A THR* 1.3 86.2 - - + +
833A GLU* 1.3 57.9 + - - +
835A GLY* 4.8 0.7 - - - -
836A TYR* 4.3 10.6 + - - +
507B LYS* 3.4 25.4 - - - +
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Residues in contact with GLU 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A VAL* 3.3 3.6 + - - +
830A LYS* 3.1 5.8 + - - +
832A ALA* 1.3 77.0 - - - +
834A THR* 1.3 72.1 + - - +
835A GLY 3.2 2.0 - - - -
836A TYR* 3.1 21.7 + - + +
837A ILE* 3.1 17.5 + - + +
840A ARG* 6.2 1.1 - - - +
1081A LEU* 5.8 1.9 - - - +
1098A VAL* 5.0 17.0 - - + +
1099A PRO* 5.7 2.4 - - - +
1102A LYS* 3.5 43.2 + - + +
507B LYS* 2.7 30.0 + - - +
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Residues in contact with THR 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830A LYS* 2.6 42.8 + - - +
831A THR* 4.1 7.0 - - - -
833A GLU* 1.3 74.3 - - - +
835A GLY* 1.3 69.1 - - - +
837A ILE* 2.9 20.3 + - - +
838A GLN* 3.1 10.5 + - + +
1076A ALA* 4.4 5.4 + - + +
1077A THR* 3.1 56.8 + - + +
1081A LEU* 5.2 2.8 - - - +
1098A VAL* 5.3 5.7 - - - +
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Residues in contact with GLY 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831A THR 3.7 10.6 + - - -
832A ALA 4.8 1.3 - - - -
833A GLU 3.2 0.8 - - - -
834A THR* 1.3 84.7 - - - +
836A TYR* 1.3 62.8 + - - +
838A GLN* 3.2 8.0 - - - +
839A ARG* 3.0 21.7 + - - +
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Residues in contact with TYR 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A ALA 4.3 8.4 + - - +
833A GLU* 3.1 20.5 + - + +
835A GLY* 1.3 73.5 - - - +
837A ILE* 1.3 64.5 + - - +
839A ARG* 3.2 10.6 + - + +
840A ARG* 2.8 69.5 + - + +
1106A ASN* 5.7 0.7 - - - -
1385A THR* 3.8 16.2 - - + +
1386A ARG* 4.8 3.8 + - - -
1402A PHE* 4.5 6.5 - + - -
1403A GLU* 2.9 42.1 + - + -
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Residues in contact with ILE 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A GLU* 3.1 14.5 + - + +
834A THR* 2.9 15.3 + - - +
836A TYR* 1.3 76.0 - - - +
838A GLN* 1.3 69.6 + - - +
840A ARG* 2.9 38.8 + - - +
841A LEU* 3.1 26.8 + - + +
1076A ALA* 4.4 17.5 - - + +
1079A MET* 5.3 0.9 - - + -
1098A VAL* 4.5 20.4 - - + -
1101A LEU* 4.0 27.8 - - + -
1102A LYS* 4.7 8.7 - - + +
1105A LEU* 4.0 18.8 - - + -
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Residues in contact with GLN 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A LEU* 3.8 33.0 - - + +
834A THR* 3.1 7.5 + - + +
835A GLY* 3.2 14.6 - - - +
837A ILE* 1.3 82.8 - - - +
839A ARG* 1.3 64.4 + - - +
841A LEU* 3.8 4.0 - - - +
842A VAL* 2.9 45.2 + - - +
1070A GLN* 4.2 17.0 + - - +
1073A GLY* 4.0 31.2 - - - +
1076A ALA* 5.6 0.8 - - + +
1077A THR* 4.0 10.3 - - - +
1133B MET* 4.5 14.1 - - + +
1136B ASP* 5.5 1.4 - - - +
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Residues in contact with ARG 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 2.5 54.8 - - - +
835A GLY 3.0 11.9 + - - +
836A TYR* 3.6 13.2 - - + +
837A ILE 2.9 1.0 + - - -
838A GLN* 1.3 83.2 + - - +
840A ARG* 1.3 55.7 + - + +
842A VAL* 2.9 9.9 + - + +
843A LYS* 2.6 46.9 + - + +
1401A SER 2.9 28.7 + - - -
1402A PHE* 3.5 32.7 - - + +
1403A GLU* 5.7 0.4 - - - +
1132B GLU* 3.8 21.2 + - - -
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Residues in contact with ARG 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A GLU* 6.2 0.6 - - - +
836A TYR* 2.8 65.0 - - + +
837A ILE* 2.9 37.2 + - - +
839A ARG* 1.3 70.7 - - + +
841A LEU* 1.3 68.3 + - + +
843A LYS* 3.0 6.4 + - - +
844A ALA* 2.7 24.8 + - - +
1102A LYS* 5.1 5.9 - - - +
1105A LEU* 4.2 16.4 - - - +
1106A ASN* 3.2 37.8 + - - +
1384A VAL* 3.5 29.3 + - + +
1385A THR* 3.2 13.5 + - - -
1389A PHE* 4.2 2.6 - - + -
1402A PHE* 4.4 15.3 - - + -
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Residues in contact with LEU 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A ILE* 3.1 25.7 + - + +
838A GLN 3.8 5.4 - - - +
840A ARG* 1.3 76.8 - - + +
842A VAL* 1.3 55.8 + - - +
844A ALA* 2.8 28.4 + - - +
845A LEU* 3.0 15.4 - - + +
1069A ALA* 3.8 15.7 - - + +
1072A ILE* 3.7 20.0 - - + -
1073A GLY* 3.4 36.6 - - - +
1076A ALA* 5.2 0.2 - - + -
1101A LEU* 6.5 0.4 - - + -
1105A LEU* 3.7 32.8 - - + -
1371A LEU* 4.2 22.0 - - + -
1384A VAL* 4.2 7.9 - - + -
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Residues in contact with VAL 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838A GLN* 2.9 39.3 - - - +
839A ARG* 3.0 12.6 - - + +
841A LEU* 1.3 76.1 - - + +
843A LYS* 1.3 62.1 + - + +
844A ALA 3.0 5.3 + - - -
845A LEU 3.5 1.0 + - - -
846A GLU* 3.2 23.9 + - - +
1066A VAL* 4.9 10.1 - - + +
1069A ALA* 3.4 24.0 - - + -
1070A GLN* 4.3 8.3 - - + +
1135B ARG* 5.0 2.2 - - - +
1136B ASP* 3.3 41.1 - - + +
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Residues in contact with LYS 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A MET* 3.3 29.5 - - - +
839A ARG* 2.6 37.5 + - + +
840A ARG* 3.4 7.0 - - - +
842A VAL* 1.3 74.5 - - + +
844A ALA* 1.3 58.2 + - - +
846A GLU* 3.2 45.6 + - - +
1389A PHE* 3.5 15.1 - - + -
1398A MET* 4.6 2.8 - - - +
1401A SER* 3.1 33.9 + - - -
1402A PHE* 4.1 23.6 - - + -
1425A SER* 3.3 3.0 + - - -
1132B GLU* 4.5 7.2 + - - +
1135B ARG* 3.5 11.3 - - - +
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Residues in contact with ALA 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840A ARG 2.7 10.3 + - - +
841A LEU* 2.8 13.7 + - - +
843A LYS* 1.3 80.6 - - - +
845A LEU* 1.3 70.9 + - + +
846A GLU 3.5 1.6 + - - -
847A ASP* 4.0 7.6 - - - +
848A ILE* 4.3 2.9 - - - +
1371A LEU* 6.1 0.4 - - + -
1374A VAL* 4.7 7.6 - - + +
1384A VAL* 4.1 15.9 - - + -
1389A PHE* 3.6 31.0 - - + +
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Residues in contact with LEU 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A LEU* 3.0 16.9 + - + +
842A VAL 3.5 2.2 + - - -
844A ALA* 1.3 92.7 - - + +
846A GLU* 1.3 70.8 + - - +
847A ASP* 3.5 3.4 - - - -
848A ILE* 3.2 15.6 + - + -
1065A GLY* 2.8 35.9 - - - +
1066A VAL 4.0 0.2 - - - -
1068A ALA* 4.4 6.7 - - + -
1069A ALA* 3.5 35.0 - - + +
1370A LEU* 5.5 1.1 - - + -
1371A LEU* 4.7 26.2 - - + +
1374A VAL* 3.7 32.5 - - + -
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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