Contacts of the strand formed by residues 865 - 877 (chain C) in PDB entry 5UHF
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 865 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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758C ASP* 3.8 31.6 - - + +
759C ALA 3.2 13.5 - - - +
760C ARG* 5.0 5.2 - - + -
855C ARG* 2.7 30.7 + - - -
861C LEU* 3.3 27.4 - - + +
862C PRO* 3.4 26.7 + - + +
863C ALA 4.5 3.8 - - - +
864C GLY* 1.3 81.9 - - - +
866C ASN* 1.3 65.5 + - - +
867C GLU 4.2 5.4 - - - +
868C LEU* 4.6 5.2 - - + -
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Residues in contact with ASN 866 (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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759C ALA* 2.9 16.6 + - + +
760C ARG 4.2 1.2 + - - -
761C ASP* 3.4 29.7 + - - +
766C ALA* 4.1 8.9 - - - +
767C GLU 4.0 17.4 + - - +
854C SER* 3.5 1.0 - - - -
855C ARG* 2.7 42.5 + - + -
856C GLU 5.6 0.2 - - - -
861C LEU* 3.2 7.1 - - - +
864C GLY 4.2 0.5 - - - +
865C VAL* 1.3 79.8 + - - +
867C GLU* 1.3 65.2 + - + +
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Residues in contact with GLU 867 (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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758C ASP* 3.5 2.4 - - - +
759C ALA* 3.0 29.8 + - + +
769C ILE* 3.7 45.6 + - + +
787C ARG* 5.8 4.5 - - - +
852C VAL* 5.1 7.8 - - + +
853C PHE 3.5 2.5 - - - +
854C SER* 3.3 26.3 + - - +
856C GLU* 5.3 3.8 - - - +
865C VAL* 4.2 1.7 - - - +
866C ASN* 1.3 84.8 - - + +
868C LEU* 1.3 60.2 + - - +
869C VAL* 4.2 2.9 - - + -
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Residues in contact with LEU 868 (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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756C GLU* 3.8 33.4 - - + +
757C ILE 3.2 22.0 - - - +
758C ASP* 3.9 13.0 - - + -
851C ARG 3.8 3.5 - - - +
852C VAL* 3.8 1.5 - - - +
853C PHE* 2.8 57.7 + - + +
861C LEU* 4.2 25.8 - - + -
865C VAL* 4.6 3.1 - - + -
867C GLU* 1.3 74.1 - - - +
869C VAL* 1.3 63.0 + - - +
870C ARG* 5.1 6.7 - - + +
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Residues in contact with VAL 869 (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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755C HIS 4.1 0.2 - - - +
756C GLU* 3.6 5.2 - - - +
757C ILE* 3.0 33.0 + - - +
769C ILE* 3.6 28.7 - - + -
789C ILE* 3.7 34.8 - - + -
803C VAL* 3.6 28.8 - - + +
837C LEU* 5.5 0.3 - - - +
850C ILE* 4.5 7.6 - - + -
851C ARG 4.0 1.8 - - - -
852C VAL* 4.6 11.4 - - + +
867C GLU* 4.9 2.0 - - + -
868C LEU* 1.3 79.9 - - - +
870C ARG* 1.3 67.0 + - - +
871C VAL* 4.2 6.7 + - + -
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Residues in contact with ARG 870 (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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123C LYS 5.2 1.6 + - - -
124C ASP 3.9 17.2 + - - -
125C LYS 5.9 0.2 - - - -
126C ASP* 3.2 38.9 + - - +
754C GLU* 4.1 15.6 + - + -
755C HIS 3.6 5.2 - - - +
756C GLU* 2.4 48.1 + - + +
849C GLY 3.8 0.7 - - - +
850C ILE* 3.5 5.4 - - - +
851C ARG* 3.1 38.2 + - + +
853C PHE* 4.4 19.7 - - + -
868C LEU* 5.1 11.3 - - + +
869C VAL* 1.3 73.7 - - - +
871C VAL* 1.3 63.1 + - - +
872C TYR* 3.5 35.5 + - + -
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Residues in contact with VAL 871 (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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753C GLU 3.8 1.6 - - - +
754C GLU* 4.1 1.0 - - - -
755C HIS* 3.1 36.9 + - + +
789C ILE* 4.5 0.4 - - + -
790C VAL* 3.8 21.1 - - + -
802C LEU* 4.1 26.9 - - + +
803C VAL* 3.8 28.5 - - + -
837C LEU* 5.7 1.1 - - + -
847C VAL* 3.7 25.6 - - + -
849C GLY 3.7 2.2 - - - -
850C ILE* 4.4 6.1 - - + -
869C VAL* 4.2 5.8 - - + -
870C ARG* 1.3 75.0 - - - +
872C TYR* 1.3 63.6 + - - +
873C VAL* 3.9 9.3 + - + -
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Residues in contact with TYR 872 (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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677C ARG* 4.8 11.7 - - + -
752C ILE* 4.4 13.7 - - + -
753C GLU 3.6 6.1 - - - +
754C GLU* 3.2 43.4 + - + -
847C VAL* 3.5 4.2 - - - +
848C ILE* 2.8 41.2 + - + +
849C GLY* 3.0 27.1 + - - +
851C ARG* 4.4 13.5 - - + +
870C ARG* 3.5 39.3 + - + -
871C VAL* 1.3 75.9 - - - +
873C VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 873 (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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751C HIS 3.8 0.9 - - - +
752C ILE* 3.5 3.6 - - - -
753C GLU* 3.0 34.0 + - + +
755C HIS* 4.3 22.2 - - + +
796C VAL* 3.7 30.7 - - + -
802C LEU* 4.7 4.5 - - + -
839C VAL* 6.2 0.9 - - + -
843C GLU* 6.3 1.1 - - + -
844C SER* 3.2 29.4 - - - +
845C GLY 3.9 2.0 - - - -
846C LYS 3.4 9.2 - - - +
847C VAL* 4.0 12.3 - - + -
871C VAL* 4.1 11.4 - - + -
872C TYR* 1.3 77.0 - - - +
874C ALA* 1.3 62.4 + - - +
875C GLN* 4.7 3.0 - - + +
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Residues in contact with ALA 874 (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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63A PHE* 4.1 23.2 - - + -
750C ILE* 4.8 3.6 - - + -
751C HIS 3.4 6.3 - - - +
752C ILE* 4.4 6.7 - - + +
845C GLY* 3.3 4.7 - - - -
846C LYS* 2.8 33.2 + - - +
848C ILE* 3.6 35.0 - - + -
872C TYR 4.1 0.8 + - - -
873C VAL* 1.3 73.9 - - - +
875C GLN* 1.3 62.3 + - - +
876C LYS 4.5 0.2 + - - -
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Residues in contact with GLN 875 (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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63A PHE* 4.9 1.3 - - - -
750C ILE* 3.4 10.0 - - - +
751C HIS* 2.7 41.7 + - + +
753C GLU* 4.3 10.5 - - - +
842C GLY 4.5 4.9 + - - +
843C GLU* 3.4 24.2 + - - +
844C SER* 3.1 39.3 + - - +
845C GLY* 4.7 3.6 - - - -
873C VAL* 4.7 4.1 - - + +
874C ALA* 1.3 76.7 - - - +
876C LYS* 1.3 60.9 + - - +
877C ARG* 3.2 48.6 + - + +
1038C ASP* 5.6 1.9 - - - +
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Residues in contact with LYS 876 (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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62A GLU* 3.2 35.3 + - - +
63A PHE* 4.3 15.8 - - + -
74A THR* 5.7 2.5 - - - +
77A ILE* 5.5 1.8 - - - +
81A LYS* 4.4 13.5 - - - +
165A ASP* 4.7 0.6 + - - -
619C VAL* 4.8 13.8 - - + +
745C ASP* 3.6 29.5 + - - -
748C THR* 4.1 13.4 - - + +
749C SER 3.7 4.9 - - - +
750C ILE* 4.8 3.6 - - + +
875C GLN* 1.3 72.8 - - - +
877C ARG* 1.3 58.0 + - - +
878C LYS* 3.3 21.0 + - - +
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Residues in contact with ARG 877 (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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748C THR* 3.6 3.0 - - - -
749C SER* 3.1 30.1 + - - +
751C HIS* 3.4 40.3 + - + +
753C GLU* 5.5 4.9 + - - +
843C GLU* 5.0 1.8 + - - -
875C GLN* 3.2 47.2 + - + +
876C LYS* 1.3 69.0 - - - +
878C LYS* 1.3 67.4 + - - +
1032C LYS* 3.4 10.6 + - - +
1034C HIS* 5.5 1.0 + - - -
1036C LEU* 3.8 13.9 - - + +
1038C ASP* 4.1 36.3 + - - +
1039C ASP* 3.0 39.4 + - - -
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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