Contacts of the strand formed by residues 48 - 54 (chain C) in PDB entry 5HJD
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 48 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C LEU* 5.4 0.7 - - + -
44C ILE* 2.8 30.0 + - + +
45C GLN* 3.4 15.8 - - - +
47C PHE* 1.3 104.5 - - + +
49C GLU* 1.3 64.2 + - - +
50C LYS 3.6 13.7 - - - +
51C VAL* 3.8 24.7 - - + -
71C TYR* 3.8 22.4 + - + +
87C VAL* 3.8 17.3 - - + -
88C TYR 3.4 7.4 - - - +
89C PHE* 5.0 0.2 - - + -
90C LYS* 3.6 5.9 + - - -
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Residues in contact with GLU 49 (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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48C VAL* 1.3 75.8 - - - +
50C LYS* 1.3 78.4 + - + +
67C LYS* 3.2 23.8 - - + +
71C TYR* 5.0 0.5 - - - -
88C TYR* 2.9 21.5 + - - +
89C PHE 4.3 13.1 - - - +
90C LYS* 3.5 28.5 - - + +
96C ARG* 4.8 10.2 + - - -
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Residues in contact with LYS 50 (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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48C VAL* 3.6 3.9 - - - -
49C GLU* 1.3 96.9 + - + +
51C VAL* 1.3 66.3 + - - +
52C VAL* 4.5 8.3 - - + -
65C VAL* 4.4 15.7 - - + +
66C CYS 3.4 12.8 - - - +
67C LYS* 3.9 16.6 - - + +
71C TYR* 4.7 1.3 - - - -
88C TYR* 2.9 71.6 + - + +
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Residues in contact with VAL 51 (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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36C VAL* 4.3 13.2 - - + -
44C ILE* 5.5 0.4 - - + -
48C VAL* 3.8 13.5 - - + -
50C LYS* 1.3 76.8 - - - +
52C VAL* 1.3 63.4 + - - +
53C PHE* 3.8 22.3 + - + -
65C VAL 3.9 0.5 - - - -
66C CYS* 2.7 35.7 + - - +
71C TYR* 3.5 33.4 - - + -
85C ILE* 3.7 26.7 - - + -
86C GLU 3.5 4.9 - - - +
87C VAL* 4.3 16.2 - - + -
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Residues in contact with VAL 52 (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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50C LYS* 4.5 8.1 - - + -
51C VAL* 1.3 76.9 - - - +
53C PHE* 1.3 64.5 + - - +
54C HIS* 3.5 33.5 - - + +
63C LYS* 4.2 12.6 - - + +
64C ARG 3.5 10.1 - - - +
65C VAL* 3.8 30.7 - - + -
85C ILE* 3.5 4.0 - - - -
86C GLU* 2.8 38.2 + - + +
88C TYR* 3.9 26.0 - - + +
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Residues in contact with PHE 53 (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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34C VAL* 3.9 26.5 - - + -
35C PHE* 4.2 3.1 - - - -
36C VAL* 4.2 9.9 - - + -
51C VAL* 3.8 25.6 - - + -
52C VAL* 1.3 72.7 - - - +
54C HIS* 1.3 61.3 + - - +
55C LEU* 3.6 6.6 + - + -
62C PRO 3.5 3.6 - - - +
63C LYS* 4.0 0.9 - - - -
64C ARG* 2.9 40.2 + - + +
66C CYS* 3.9 14.1 - - + -
71C TYR 3.2 36.1 - - - -
72C LYS* 4.1 3.6 - - - -
73C VAL* 3.5 27.1 - - + -
83C LEU* 4.0 8.1 - - + -
84C PRO 4.0 2.7 - - - -
85C ILE* 4.0 29.8 - - + +
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Residues in contact with HIS 54 (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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52C VAL* 3.5 29.2 - - + +
53C PHE* 1.3 69.6 - - - +
55C LEU* 1.3 67.2 + - - +
62C PRO 4.2 3.1 - - - -
63C LYS* 4.0 28.0 - - + +
81C PHE* 4.6 0.2 - - - -
82C ILE 4.7 0.2 - - - +
83C LEU* 3.6 9.8 - - - +
84C PRO* 2.9 67.2 + - + +
86C GLU* 3.2 33.0 + - + +
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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