Contacts of the strand formed by residues 837 - 842 (chain C) in PDB entry 4YOC
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 LEU 837 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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819C TYR* 3.8 6.2 + - - -
823C ALA 4.0 6.5 - - - +
826C VAL* 3.9 12.1 - - + -
827C ALA* 3.7 41.3 - - + +
830C LEU* 4.4 3.8 - - + -
832C THR* 4.3 9.6 - - + -
833C ASP 4.3 0.7 - - - +
834C PRO 3.4 14.9 - - - +
835C MET 3.1 2.8 + - - -
836C LEU* 1.3 86.6 - - - +
838C GLN* 1.3 59.8 + - - +
839C PHE* 4.0 17.2 - - + -
878C TYR* 4.0 26.2 - - + -
879C GLN 3.6 5.4 - - - +
880C GLN* 4.1 17.9 - - + -
881C LEU* 4.0 3.6 - - - -
885C ILE* 3.4 19.6 - - - +
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Residues in contact with GLN 838 (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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837C LEU* 1.3 74.1 - - - +
839C PHE* 1.3 71.4 + - - +
840C PHE* 3.4 18.5 - - + -
852C PRO* 4.1 16.5 - - + +
853C LEU 4.5 7.4 + - - +
878C TYR* 3.1 5.9 - - - +
879C GLN* 2.9 64.8 + - + -
881C LEU* 3.9 20.3 - - + +
885C ILE* 4.1 15.0 - - + +
888C PHE* 3.4 24.9 - - - -
889C GLU* 5.2 6.7 - - - +
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Residues in contact with PHE 839 (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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798C PHE* 4.4 4.5 - + - -
819C TYR* 3.4 26.3 + + + -
822C VAL* 4.4 10.5 - - + -
823C ALA* 3.8 39.5 - - + -
826C VAL* 4.0 29.4 - - + -
834C PRO 5.3 0.2 - - - -
837C LEU* 4.0 23.1 - - + -
838C GLN* 1.3 79.4 - - - +
840C PHE* 1.3 64.2 + - - +
852C PRO* 3.4 4.2 - - - +
853C LEU* 2.8 49.3 + - + -
876C LEU* 3.5 22.7 - - + -
877C TYR 3.5 5.6 - - - -
878C TYR* 3.9 13.0 - - + -
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Residues in contact with PHE 840 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801C LYS* 3.5 39.3 - - + -
838C GLN* 3.4 40.6 - - - -
839C PHE* 1.3 76.0 - - - +
841C LYS* 1.3 68.2 + - - +
842C SER 3.8 0.2 + - - -
849C PRO* 3.9 13.0 - - + -
850C GLY 3.5 18.2 - - - +
851C ASN 3.5 2.2 - - - -
852C PRO* 3.7 26.9 - - + -
853C LEU* 4.9 0.7 - - - -
876C LEU* 3.8 7.1 - - - +
877C TYR* 2.9 47.3 + - + +
878C TYR* 4.0 9.9 - - - -
879C GLN* 3.9 12.6 - - + -
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Residues in contact with LYS 841 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1391A GLU* 3.2 37.2 + - - +
1403A ALA* 4.7 8.5 + - - +
839C PHE 4.3 0.2 - - - -
840C PHE* 1.3 74.7 - - - +
842C SER* 1.3 60.9 + - - +
849C PRO* 3.6 0.9 - - - +
850C GLY* 2.5 34.7 + - - -
851C ASN* 3.0 19.4 + - - +
853C LEU* 4.5 7.5 - - + +
863C ASP 3.9 15.2 + - - -
864C LEU* 3.9 35.9 - - + +
866C GLN* 5.3 6.3 - - - +
867C PHE* 3.5 36.0 - - + -
876C LEU* 4.5 8.1 - - - -
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Residues in contact with SER 842 (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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1405A TYR* 5.1 1.9 - - - +
840C PHE 3.8 0.8 + - - -
841C LYS* 1.3 83.1 - - - +
843C GLN* 1.3 66.8 + - - +
844C GLY* 3.0 16.7 + - - -
846C ARG 4.1 3.1 + - - -
847C ASP* 5.1 2.4 + - - -
848C GLY 3.6 9.8 + - - -
850C GLY* 3.9 2.6 - - - -
864C LEU 5.1 0.6 + - - -
867C PHE* 3.0 18.5 - - - -
868C PHE* 3.4 34.3 - - - -
875C LYS* 3.9 11.4 + - - +
876C LEU* 5.0 1.4 - - - +
877C TYR* 4.1 13.6 + - - -
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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