Contacts of the strand formed by residues 845 - 854 (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 GLY 845 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ARG* 5.7 5.1 - - - -
795C GLU* 3.6 4.3 - - - +
796C VAL* 2.9 30.8 + - - +
844C SER* 1.3 80.9 - - - +
846C LYS* 1.3 63.9 + - - -
873C VAL* 3.9 2.2 - - - -
874C ALA 3.3 8.3 - - - -
875C GLN* 4.7 4.3 - - - -
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Residues in contact with LYS 846 (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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60A LEU 5.0 0.6 + - - -
61A HIS* 4.0 20.6 - - + +
62A GLU* 4.3 7.6 + - + +
63A PHE* 4.6 18.2 - - + -
153A ARG* 3.8 32.4 - - - +
159A ILE 6.1 0.2 - - - -
161A ARG 4.0 7.4 + - - -
162A ILE* 3.4 43.2 - - - +
163A PRO* 4.0 5.2 - - - +
793C GLY 4.3 11.0 - - - +
794C ALA 3.6 9.4 - - - +
795C GLU* 4.5 4.9 - - - -
845C GLY* 1.3 77.5 - - - +
847C VAL* 1.3 65.7 + - - +
848C ILE* 3.3 6.9 + - + +
873C VAL* 4.0 1.8 - - - -
874C ALA 2.8 35.3 + - - -
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Residues in contact with VAL 847 (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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61A HIS* 4.0 0.7 - - - -
790C VAL* 3.8 17.7 - - + -
791C ARG 4.3 7.0 - - - +
792C ILE* 3.8 0.5 - - - -
793C GLY* 2.8 31.5 + - - -
794C ALA 2.9 17.5 + - - +
796C VAL* 3.7 32.3 - - + -
846C LYS* 1.3 68.4 - - - +
848C ILE* 1.3 62.1 + - - +
849C GLY 4.0 1.8 - - - +
850C ILE* 3.6 31.2 - - + -
871C VAL* 3.7 18.6 - - + -
872C TYR 3.5 7.0 - - - +
873C VAL* 4.0 8.3 - - + +
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Residues in contact with ILE 848 (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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61A HIS* 3.8 31.4 + - + +
63A PHE* 3.6 25.8 - - + +
675C PHE* 4.6 15.5 - - + +
752C ILE* 4.1 29.6 - - + -
792C ILE* 4.4 4.4 - - - +
846C LYS 3.5 14.4 - - - +
847C VAL* 1.3 73.5 - - - +
849C GLY* 1.3 57.2 + - - +
872C TYR* 2.8 26.2 + - + +
874C ALA* 3.6 26.5 - - + -
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Residues in contact with GLY 849 (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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792C ILE* 4.6 8.2 - - - +
847C VAL* 3.5 4.2 + - - +
848C ILE* 1.3 81.8 - - - +
850C ILE* 1.3 70.6 + - - +
871C VAL* 3.7 0.5 - - - -
872C TYR* 3.0 40.8 + - - +
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Residues in contact with ILE 850 (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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787C ARG* 4.2 8.1 - - - +
789C ILE* 3.8 21.3 - - + -
790C VAL* 3.3 30.7 - - + +
792C ILE* 3.5 35.1 - - + +
847C VAL* 3.6 19.1 - - + -
849C GLY* 1.3 78.3 - - - +
851C ARG* 1.3 64.1 + - - +
852C VAL* 3.6 27.4 + - + +
869C VAL* 4.5 2.0 - - + -
870C ARG 3.5 5.2 - - - +
871C VAL* 4.4 5.6 - - + -
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Residues in contact with ARG 851 (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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124C ASP* 2.7 40.6 + - - +
125C LYS* 4.5 12.1 - - - +
849C GLY 4.3 0.4 - - - -
850C ILE* 1.3 75.4 - - - +
852C VAL* 1.3 73.9 + - - +
853C PHE* 3.3 46.6 - - + -
868C LEU 3.8 3.1 - - - +
870C ARG* 3.1 39.3 + - + +
872C TYR* 4.4 17.7 - - + +
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Residues in contact with VAL 852 (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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787C ARG* 3.7 28.0 - - - +
789C ILE* 5.0 3.8 - - + -
850C ILE* 3.6 27.2 + - + +
851C ARG* 1.3 83.6 + - - +
853C PHE* 1.3 74.2 + - - +
854C SER* 4.2 17.2 + - - +
857C ASP* 6.1 0.2 - - - +
859C ASP* 4.5 3.6 - - - +
867C GLU* 5.1 8.7 - - + +
868C LEU 3.8 6.3 - - - +
869C VAL* 4.6 15.0 - - + -
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Residues in contact with PHE 853 (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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124C ASP 4.0 14.4 - - - -
125C LYS* 5.1 11.2 - - + -
851C ARG* 3.3 60.1 - - + -
852C VAL* 1.3 78.1 - - - +
854C SER* 1.3 61.3 + - - +
859C ASP* 4.1 24.7 - - + -
861C LEU* 4.3 13.2 - - + +
866C ASN 3.7 1.7 - - - +
867C GLU* 3.5 1.7 - - - -
868C LEU* 2.8 67.4 + - + +
870C ARG* 4.4 21.5 - - + -
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Residues in contact with SER 854 (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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852C VAL* 4.1 9.9 + - - +
853C PHE* 1.3 74.1 - - - +
855C ARG* 1.3 63.2 + - - +
856C GLU* 3.9 11.2 + - - -
857C ASP* 3.3 36.4 + - - -
859C ASP* 3.3 27.5 + - - +
861C LEU* 4.7 0.7 - - - -
866C ASN 3.5 3.6 - - - -
867C GLU* 3.3 30.3 + - - +
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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