Contacts of the helix formed by residues 879 - 889 (chain C) in PDB entry 1P3F
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 ILE 879 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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875C LYS* 5.9 6.3 - - + -
877C ARG* 3.4 17.9 - - + +
878C ILE* 1.3 87.2 - - - +
880C PRO* 1.3 77.3 - - + +
881C ARG* 3.8 21.3 - - + +
882C HIS* 2.9 34.7 + - + +
883C LEU* 3.4 6.1 + - - +
1252D SER* 3.9 15.0 - - - +
1255D ALA* 4.2 4.0 - - - -
279J A 5.8 5.6 - - - +
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Residues in contact with PRO 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879C ILE* 1.3 90.3 - - + +
881C ARG* 1.3 55.0 + - - +
883C LEU* 2.7 32.7 + - + +
884C GLN* 2.9 12.1 + - - +
902C ILE* 4.2 1.4 - - - +
903C ALA 3.7 22.2 - - - +
904C GLN* 3.7 18.4 - - + +
905C GLY* 4.5 1.3 - - - -
1252D SER* 4.2 8.3 - - - +
1254D LYS* 4.0 14.4 - - + -
1255D ALA* 4.0 13.9 - - - +
1258D ILE* 3.7 20.9 - - + -
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Residues in contact with ARG 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873C ASN* 5.6 1.8 - - - +
879C ILE* 3.1 19.6 + - + +
880C PRO* 1.3 76.8 - - - +
882C HIS* 1.3 64.0 - - + +
884C GLN* 3.3 3.2 + - - +
885C LEU* 2.9 59.4 + - + +
904C GLN 3.7 4.7 + - - +
905C GLY 3.1 26.0 + - - -
906C GLY* 3.4 2.8 - - - -
907C VAL 2.4 49.3 + - - +
909C PRO* 4.0 9.1 - - - +
655E GLN 3.8 14.2 + - - -
656E LYS* 4.1 15.6 + - - +
657E SER* 4.7 0.4 + - - +
658E THR* 3.7 21.0 - - + +
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Residues in contact with HIS 882 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866C ALA* 3.9 17.2 - - - +
869C ALA* 4.0 8.0 - - + +
870C ALA* 3.7 29.2 - - + +
873C ASN* 3.9 19.6 + - - +
875C LYS* 4.1 18.3 - - + +
877C ARG 3.3 21.8 - - - -
878C ILE* 3.1 16.9 - - + -
879C ILE* 2.9 43.8 + - + +
881C ARG* 1.3 79.4 - - + +
883C LEU* 1.3 61.3 + - - +
885C LEU* 3.7 2.0 - - - +
886C ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862C ILE* 4.5 13.7 - - + +
863C LEU* 4.9 4.5 - - + -
866C ALA* 3.8 21.1 - - + -
878C ILE* 4.2 8.5 - - + -
879C ILE 3.4 7.8 + - - +
880C PRO* 2.7 14.9 + - + +
882C HIS* 1.3 73.7 - - - +
884C GLN* 1.3 57.1 + - - +
886C ALA* 3.3 4.3 + - - +
887C VAL* 2.8 36.7 + - - +
902C ILE* 4.4 10.8 - - + -
1251D ILE* 5.5 0.4 - - + -
1255D ALA* 3.8 27.8 - - + +
1258D ILE* 3.5 32.8 - - + -
1259D MET* 4.0 24.2 - - + -
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Residues in contact with GLN 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880C PRO 2.9 9.6 + - - +
881C ARG* 3.5 11.7 - - - +
883C LEU* 1.3 79.0 - - - +
885C LEU* 1.3 66.2 + - + +
887C VAL* 3.2 1.0 + - - +
888C ARG* 2.8 66.5 + - + +
902C ILE* 3.6 27.7 + - + +
905C GLY* 3.4 27.1 - - - +
906C GLY 2.9 25.5 + - - +
907C VAL* 4.2 8.0 - - - +
908C LEU* 5.6 0.4 - - + -
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Residues in contact with LEU 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869C ALA* 4.2 11.7 - - + -
873C ASN* 4.1 21.8 - - - +
881C ARG* 2.9 64.5 + - + +
882C HIS* 3.7 7.6 - - - +
884C GLN* 1.3 74.1 - - + +
886C ALA* 1.3 66.5 + - - +
889C ASN* 2.9 39.8 + - - +
908C LEU* 3.7 25.4 - - + -
909C PRO* 5.1 2.9 - - + -
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Residues in contact with ALA 886 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862C ILE* 4.1 10.5 - - + +
865C LEU* 3.8 21.0 - - + +
866C ALA* 3.5 28.3 - - + +
869C ALA* 4.8 1.5 - - - +
882C HIS 2.9 19.1 + - - +
883C LEU* 3.4 6.1 - - - +
885C LEU* 1.3 79.6 - - - +
887C VAL* 1.3 64.8 + - - +
889C ASN* 3.5 5.2 + - - +
890C ASP* 3.5 15.2 + - - +
893C LEU* 5.2 0.7 - - - -
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Residues in contact with VAL 887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862C ILE* 3.7 29.2 - - + -
883C LEU 2.8 22.0 + - - +
884C GLN 3.6 3.4 - - - +
886C ALA* 1.3 72.8 - - - +
888C ARG* 1.3 95.3 + - - +
889C ASN 2.8 2.1 + - - -
890C ASP* 2.9 22.3 + - - +
893C LEU* 4.1 15.9 - - + +
894C ASN* 3.4 5.4 + - - +
897C LEU* 3.6 29.2 - - + -
902C ILE* 4.2 9.2 - - + -
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Residues in contact with ARG 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884C GLN* 2.8 54.4 + - + +
887C VAL* 1.3 88.9 - - - +
889C ASN* 1.3 60.6 + - - +
890C ASP 3.3 0.9 + - - -
894C ASN* 2.7 51.5 + - - +
897C LEU* 3.1 24.0 + - - +
898C GLY* 4.1 4.4 - - - -
900C VAL* 3.1 27.5 + - - +
901C THR* 5.2 0.2 - - - +
902C ILE* 4.5 6.5 - - - +
908C LEU* 3.7 35.5 - - + +
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Residues in contact with ASN 889 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885C LEU* 2.9 35.0 + - - +
886C ALA* 4.3 2.9 - - - +
887C VAL 2.8 0.2 + - - -
888C ARG* 1.3 80.7 - - - +
890C ASP* 1.3 57.1 + - - +
891C GLU 4.1 1.3 + - - -
908C LEU* 3.6 27.1 - - - +
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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