Contacts of the strand formed by residues 892 - 899 (chain C) in PDB entry 5UH6
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 LYS 892 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490C GLU* 4.4 7.9 + - - -
604C ARG* 4.4 15.6 - - - +
607C MET* 4.2 27.7 - - - +
611C MET* 4.0 19.7 - - - -
733C ASP* 4.0 14.4 - - + +
735C ILE* 4.7 4.3 - - - +
884C LYS* 3.9 21.1 - - - +
885C LEU 3.4 8.3 - - - +
886C ALA* 4.0 2.9 - - + -
890C GLY 3.6 1.7 + - - +
891C ASN* 1.3 77.8 - - - +
893C GLY* 1.3 58.9 + - - +
537D ASP* 3.8 32.6 + - + -
2I A 2.8 36.0 + - - +
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Residues in contact with GLY 893 (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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733C ASP 3.3 16.2 - - - -
735C ILE* 3.9 8.6 - - - +
884C LYS* 3.4 4.5 - - - +
885C LEU* 2.6 38.4 + - - +
892C LYS* 1.3 80.5 - - - +
894C VAL* 1.3 61.1 + - - -
536D PHE 3.7 6.5 - - - -
537D ASP* 4.3 4.9 - - - +
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Residues in contact with VAL 894 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733C ASP 3.9 0.2 + - - -
734C ALA* 3.6 3.7 - - + -
735C ILE* 3.0 22.3 + - - -
882C GLY* 3.5 26.2 - - - +
883C ASP 3.2 3.1 - - - -
884C LYS* 3.8 14.8 - - + -
893C GLY* 1.3 76.8 - - - -
895C ILE* 1.3 65.0 + - - +
896C GLY 3.2 0.7 + - - -
429D VAL* 4.3 3.6 - - + -
430D ILE 4.0 15.7 - - - +
431D VAL* 4.4 9.0 - - + -
536D PHE* 3.1 30.9 + - + +
538D GLY* 3.7 28.7 - - - +
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Residues in contact with ILE 895 (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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735C ILE* 3.5 22.2 - - + +
737C LEU* 3.5 31.9 - - + -
879C ILE* 4.3 5.4 - - + -
880C SER 3.6 19.3 - - - +
881C ASP* 3.4 8.0 - - - +
882C GLY 2.9 23.4 + - - -
883C ASP 2.9 19.6 + - - +
885C LEU* 3.6 28.3 - - + -
894C VAL* 1.3 70.4 - - - +
896C GLY* 1.3 66.8 + - - +
897C LYS 4.2 2.2 - - - +
898C ILE* 3.6 31.4 - - + -
431D VAL* 3.8 4.9 - - - +
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Residues in contact with GLY 896 (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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729C HIS* 4.2 16.6 + - - -
734C ALA* 4.4 4.0 - - - -
735C ILE 2.5 17.4 + - - -
881C ASP* 3.2 18.5 - - - +
894C VAL 3.2 5.5 + - - -
895C ILE* 1.3 73.6 - - - +
897C LYS* 1.3 61.0 + - - +
431D VAL* 3.5 26.8 - - - +
432D VAL* 5.0 1.1 - - - +
523D GLN* 5.8 1.2 + - - -
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Residues in contact with LYS 897 (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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729C HIS* 3.5 50.9 + - + +
735C ILE 3.4 3.7 + - - +
736C ILE* 3.3 12.4 - - + +
737C LEU 2.9 23.6 + - - -
881C ASP* 3.8 9.2 - - - +
895C ILE* 4.4 0.7 - - - -
896C GLY* 1.3 81.5 - - - +
898C ILE* 1.3 74.0 + - - +
899C LEU* 4.1 25.0 - - + +
1014C ARG* 5.8 2.2 - - - +
435D GLN* 4.1 19.2 + - - +
523D GLN* 6.0 5.1 - - - +
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Residues in contact with ILE 898 (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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737C LEU* 3.6 26.2 - - + +
738C SER 4.1 4.3 - - - +
739C ASN* 3.6 40.0 - - - +
742C VAL* 4.1 18.4 - - + -
879C ILE* 4.2 2.0 - - + +
880C SER* 4.2 21.5 - - - -
881C ASP* 3.7 10.0 + - - +
895C ILE* 3.6 23.1 - - + -
897C LYS* 1.3 82.2 - - - +
899C LEU* 1.3 61.4 + - - +
900C PRO* 4.2 2.9 - - - +
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Residues in contact with LEU 899 (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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726C TRP* 3.4 39.9 - - + -
729C HIS* 5.6 1.1 - - + +
736C ILE* 3.6 24.9 - - + -
737C LEU 3.1 6.1 + - - -
739C ASN* 3.1 24.9 + - - +
897C LYS* 4.1 22.0 - - + +
898C ILE* 1.3 72.4 - - - +
900C PRO* 1.3 76.6 - - + +
903C ASP* 3.9 13.7 - - + +
904C MET* 3.6 24.0 - - + +
916C ILE* 4.7 0.9 - - + -
1014C ARG* 3.8 25.8 - - - +
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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