Contacts of the strand formed by residues 73 - 80 (chain C) in PDB entry 6S1M
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 SER 73 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 6.1 0.2 - - - -
448B GLN* 3.3 34.9 + - - +
449B PRO* 3.8 7.7 - - - +
66C SER* 4.7 8.1 - - - -
67C LEU 3.4 7.9 - - - -
68C ILE* 4.0 11.0 - - - -
71C GLY 3.8 1.4 + - - -
72C HIS* 1.3 71.3 - - - +
74C CYS* 1.3 60.0 + - - +
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Residues in contact with CYS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B GLN* 3.6 4.4 + - - -
449B PRO* 3.8 25.1 - - + +
450B ILE* 5.9 0.2 - - - -
451B SER* 5.8 5.2 - - - +
66C SER* 3.5 6.6 + - - -
67C LEU* 2.9 51.9 + - - +
69C GLN* 4.2 24.7 - - - +
72C HIS* 3.6 11.6 + - + -
73C SER* 1.3 75.3 - - - +
75C HIS* 1.3 68.5 + - - +
76C LYS* 4.4 11.2 - - - -
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Residues in contact with HIS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE* 3.4 39.4 - + + -
3B SER* 3.8 17.1 + - - -
6B ALA* 4.9 4.7 - - + -
231B GLU* 3.9 16.3 + - - -
448B GLN* 3.6 13.9 - - - +
449B PRO 3.5 9.5 + - - +
450B ILE* 3.8 15.4 - - + +
451B SER 3.3 24.9 + - - +
64C SER* 3.0 24.7 + - - -
65C GLY* 3.3 26.0 + - - -
66C SER* 4.4 0.2 - - - +
74C CYS* 1.3 78.1 - - - +
76C LYS* 1.3 61.9 + - - +
77C VAL* 4.3 6.1 - - + +
96C ALA* 4.9 0.8 - - - +
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Residues in contact with LYS 76 (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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451B SER* 4.0 24.7 - - - +
453B SER* 4.1 19.5 - - - +
63C VAL 4.1 0.9 - - - +
64C SER* 3.4 3.1 - - - -
65C GLY 2.9 36.1 + - - +
66C SER 5.0 0.2 - - - -
67C LEU* 4.0 26.7 - - + +
69C GLN* 4.4 16.9 - - - +
74C CYS* 4.1 11.8 - - - -
75C HIS* 1.3 72.8 - - - +
77C VAL* 1.3 65.4 + - - +
78C ALA* 4.3 6.5 - - + -
92C LEU* 4.9 12.5 - - + +
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 5.2 7.6 - - + +
221B VAL* 5.1 7.6 - - + -
226B LEU* 5.0 8.7 - - + -
231B GLU* 5.2 3.8 - - - +
450B ILE* 5.3 3.8 - - + -
451B SER 3.5 13.0 + - - +
452B PHE* 3.9 24.2 - - + -
453B SER* 3.3 25.8 + - - -
62C LEU* 4.5 21.5 - - + -
63C VAL 3.7 3.1 - - - -
64C SER* 3.3 28.0 - - - +
75C HIS* 4.3 13.0 - - + +
76C LYS* 1.3 76.9 - - - +
78C ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 78 (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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217B LEU* 5.8 0.4 - - - -
453B SER* 3.4 18.2 - - - +
62C LEU* 3.4 6.2 - - - +
63C VAL 2.9 37.6 + - - +
76C LYS* 5.1 7.0 - - + -
77C VAL* 1.3 77.5 - - - +
79C VAL* 1.3 64.3 + - - +
80C VAL* 3.6 15.1 - - + +
88C VAL* 5.2 8.7 - - + -
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Residues in contact with VAL 79 (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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213B LEU* 5.4 7.2 - - + -
217B LEU* 3.8 27.4 - - + -
453B SER 3.8 5.7 + - - +
454B GLY* 4.3 7.8 - - - -
455B PHE* 3.1 42.1 + - + +
60C THR* 4.9 4.7 - - - -
61C TYR 3.5 11.2 - - - +
62C LEU* 3.7 24.0 - - + -
78C ALA* 1.3 71.4 - - - +
80C VAL* 1.3 63.9 + - - +
101C TYR* 4.2 30.1 - - + -
111C SER* 5.8 0.2 - - - +
114C LEU* 5.1 5.4 - - + -
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Residues in contact with VAL 80 (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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455B PHE* 4.7 4.9 - - + -
60C THR* 3.4 8.1 - - - -
61C TYR* 2.9 34.7 + - + +
63C VAL* 3.9 24.2 - - + +
78C ALA* 3.6 26.7 - - + +
79C VAL* 1.3 78.7 - - - +
81C ARG* 1.3 70.5 + - - +
84C LYS* 4.1 31.0 - - + +
85C LEU* 4.5 7.4 - - + -
88C VAL* 4.4 15.7 - - + -
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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