Contacts of the strand formed by residues 73 - 80 (chain V) in PDB entry 5OOM
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 GLN 73 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61V THR* 5.8 2.7 - - - -
62V VAL 2.9 14.6 - - - +
63V GLU* 3.6 27.3 + - + -
71V GLY 3.9 6.7 + - - +
72V LYS* 1.3 75.7 - - - +
74V GLY* 1.3 60.1 + - - +
91V LEU* 4.0 2.5 - - - -
123V VAL* 4.1 14.4 - - + +
128V ARG* 3.3 40.6 + - - +
256d TYR* 2.7 32.9 + - - +
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Residues in contact with GLY 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61V THR* 3.1 10.3 - - - -
62V VAL* 2.9 29.1 + - - -
64V ILE* 5.8 0.2 - - - +
72V LYS 3.9 0.4 + - - -
73V GLN* 1.3 75.9 - - - +
75V LYS* 1.3 59.7 + - - +
88V VAL* 3.7 18.7 - - - +
89V GLY 5.0 2.9 - - - -
91V LEU* 3.6 12.3 - - - +
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Residues in contact with LYS 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59V GLY* 3.6 36.8 - - - +
60V ASP 3.4 5.2 - - - +
61V THR* 4.8 10.1 - - + -
62V VAL* 4.8 0.2 - - - -
74V GLY* 1.3 75.1 - - - +
76V VAL* 1.3 69.7 + - - +
77V VAL* 3.3 7.0 + - + +
88V VAL* 3.7 5.7 - - - +
89V GLY* 2.9 30.0 + - - +
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Residues in contact with VAL 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56V LEU* 5.2 3.6 - - + -
57V PHE 3.5 22.4 - - - +
58V CYS* 3.5 2.6 - - - -
59V GLY* 2.7 28.5 + - - +
60V ASP* 2.9 18.9 + - + +
62V VAL* 3.8 21.8 - - + -
75V LYS* 1.3 73.9 - - - +
77V VAL* 1.3 61.9 + - - +
78V GLN 3.9 5.8 - - - +
79V VAL* 3.7 25.1 - - + -
86V VAL* 3.7 32.5 - - + -
87V VAL 3.7 3.8 - - - +
88V VAL* 4.5 1.1 - - - +
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Residues in contact with VAL 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58V CYS* 3.5 18.8 - - - +
75V LYS* 3.6 9.6 - - + +
76V VAL* 1.3 76.1 - - - +
78V GLN* 1.3 62.1 + - - +
87V VAL 2.9 11.2 + - - +
89V GLY* 3.6 27.6 - - - -
73d ASP* 4.6 12.2 - - - +
74d ARG* 3.7 41.7 - - + -
77d HIS* 3.7 20.6 - - + +
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Residues in contact with GLN 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804A A 5.8 0.7 + - - -
23V MET 4.2 11.7 + - - +
24V SER 5.7 0.2 + - - -
25V PRO* 5.6 7.3 - - - +
58V CYS* 4.1 2.2 - - - -
76V VAL* 3.9 1.8 - - - +
77V VAL* 1.3 79.2 - - - +
79V VAL* 1.3 71.6 + - - +
80V ILE* 3.7 31.3 - - + +
86V VAL* 3.9 0.7 - - - -
87V VAL* 3.0 39.1 + - + +
73d ASP* 6.3 3.4 - - + -
74d ARG* 3.2 41.2 + - + +
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Residues in contact with VAL 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V TRP* 3.7 36.3 - - + +
56V LEU 3.9 14.8 - - - +
57V PHE* 4.5 0.7 - - - -
58V CYS* 3.7 25.2 - - - +
76V VAL* 3.7 21.8 - - + -
78V GLN* 1.3 79.1 + - - +
80V ILE* 1.3 61.8 + - - +
81V ARG* 3.5 17.9 + - + +
85V TRP 3.7 6.7 - - - +
86V VAL* 5.0 1.3 - - + -
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Residues in contact with ILE 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V TYR* 4.7 10.1 - - + -
22V GLY 3.7 22.4 - - - +
23V MET* 3.8 20.4 - - - -
78V GLN* 3.7 33.5 + - + +
79V VAL* 1.3 69.4 - - - +
81V ARG* 1.3 62.6 + - - +
82V GLN* 3.4 15.9 + - - +
83V ARG* 3.5 7.0 + - + +
85V TRP* 3.0 65.1 + - + +
87V VAL* 4.5 7.0 - - + -
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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