Contacts of the strand formed by residues 999 - 1006 (chain C) in PDB entry 4OQB
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 999 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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839C ILE* 3.1 36.1 - - + +
840C GLU* 4.9 2.9 - - - +
841C ARG* 4.2 22.9 - - + -
844C GLU* 3.2 24.2 + - - +
872C ILE* 4.3 15.9 - - + +
873C LEU* 5.7 3.8 - - + -
877C LEU* 3.8 31.2 - - + +
897C PHE* 5.3 1.3 - - + -
920C LEU* 4.1 30.3 - - + -
921C LEU 4.8 0.4 - - - +
922C GLY* 3.9 11.4 - - - +
997C VAL* 4.0 10.1 - - + -
998C ASN* 1.3 75.0 - - - +
1000C LYS* 1.3 60.6 + - - +
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Residues in contact with LYS1000 (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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838C LYS* 3.6 31.2 - - - +
839C ILE* 2.8 34.9 + - - +
840C GLU* 5.9 1.4 + - - -
845C CYS* 6.2 0.4 - - - -
852C LYS* 5.1 3.6 - - - +
859C LEU* 4.0 15.5 - - + -
921C LEU 2.8 15.6 + - - +
923C GLU* 2.9 30.7 + - + -
964C LEU* 5.6 3.1 - - + -
965C ASP* 4.9 14.8 - - - -
967C VAL* 5.3 5.8 - - + -
998C ASN* 3.2 26.9 + - - +
999C LEU* 1.3 74.6 - - - +
1001C TYR* 1.3 78.7 + - + +
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Residues in contact with TYR1001 (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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804C VAL* 4.7 1.6 - - + -
810C GLU* 3.0 28.7 + - + +
814C ILE* 3.8 27.8 - - + -
836C ILE* 4.7 4.3 - - + -
837C PHE 3.3 7.2 - - - +
838C LYS* 4.1 33.2 + - + -
839C ILE* 3.7 6.7 - - - +
859C LEU* 4.6 7.9 - - + -
920C LEU* 3.6 2.6 - - - -
921C LEU* 2.8 58.0 + - + +
964C LEU* 3.6 33.4 - - + +
965C ASP* 4.1 7.4 + - - -
1000C LYS* 1.3 97.5 - - + +
1002C LEU* 1.3 59.8 + - - +
1003C LEU* 4.1 11.4 - - + -
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Residues in contact with LEU1002 (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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672C LEU* 4.1 32.3 - - + -
676C ILE* 6.3 1.1 - - + -
836C ILE* 4.0 0.2 - - - -
837C PHE* 2.7 48.6 + - + +
839C ILE* 3.6 25.9 - - + +
869C PHE* 3.6 31.6 - - + -
873C LEU* 4.3 14.4 - - + -
918C LEU* 3.9 11.7 - - + -
919C ILE 3.6 4.5 - - - +
920C LEU* 3.7 14.1 - - + -
1001C TYR* 1.3 72.8 - - - +
1003C LEU* 1.3 83.6 + - - +
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Residues in contact with LEU1003 (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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814C ILE* 3.4 24.9 - - + -
818C VAL* 3.7 11.7 - - + -
833C VAL* 4.5 6.7 - - + -
835C ASP 3.7 5.2 - - - +
836C ILE* 3.7 18.2 - - + -
837C PHE* 5.2 1.1 - - - -
861C TRP* 3.5 24.2 - - + -
918C LEU* 3.3 3.6 - - - +
919C ILE* 2.9 27.8 + - + +
921C LEU* 3.7 28.5 - - + -
1001C TYR* 4.1 11.4 - - + -
1002C LEU* 1.3 94.7 - - - +
1004C LYS* 1.3 60.5 + - - +
1005C LEU* 3.5 16.4 - - + -
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Residues in contact with LYS1004 (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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668C PRO* 4.0 10.9 + - - +
671C ASP* 3.7 34.1 + - - +
672C LEU* 4.1 6.0 - - - +
675C MET* 4.1 27.8 - - + +
833C VAL* 3.8 2.9 - - - +
834C ILE* 2.9 53.9 + - + +
835C ASP* 3.3 25.7 + - + +
837C PHE* 4.3 16.2 - - + -
916C ILE* 4.6 6.3 - - + -
917C GLY 3.6 4.0 - - - +
918C LEU* 3.9 15.7 - - + -
1003C LEU* 1.3 74.9 - - - +
1005C LEU* 1.3 61.6 + - - +
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Residues in contact with LEU1005 (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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818C VAL* 4.9 9.2 - - + -
831C LEU* 3.3 40.4 - - + -
832C GLU 3.7 4.7 - - - +
833C VAL* 4.9 9.4 - - + -
834C ILE* 4.5 4.0 - - - -
901C VAL* 4.3 14.1 - - + -
905C ALA* 5.1 2.2 - - + -
916C ILE* 3.5 2.6 - - - -
917C GLY 2.8 39.0 + - - +
918C LEU 4.7 0.2 - - - -
919C ILE* 3.3 39.5 - - + -
1003C LEU* 3.5 24.2 - - + +
1004C LYS* 1.3 75.2 - - - +
1006C LYS* 1.3 60.7 + - - +
1007C PHE* 3.6 11.2 - - + -
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Residues in contact with LYS1006 (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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830C ASP 3.6 3.8 - - - +
831C LEU* 3.6 2.4 - - - +
832C GLU* 3.0 57.7 + - + +
834C ILE* 3.9 21.9 - - + +
915C PRO* 4.1 24.2 - - + -
916C ILE* 4.7 2.2 - - + +
1005C LEU* 1.3 72.3 - - - +
1007C PHE* 1.3 68.2 + - - +
1008C ASN* 3.9 26.3 + - - +
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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