Contacts of the strand formed by residues 53 - 58 (chain C) in PDB entry 6MOL
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 TYR 53 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TRP* 4.1 11.9 - + + -
42C GLU* 2.8 39.8 + - - -
50C PRO 4.1 5.7 + - - +
51C GLY* 4.2 6.3 - - - +
52C GLN* 1.3 104.3 + - + +
54C SER* 1.3 61.5 + - - +
69C LEU* 3.6 27.6 - - + +
81C PHE* 4.1 22.4 - + - -
100C VAL* 4.1 12.8 - - + -
101C THR 3.4 4.5 - - - +
102C ALA* 4.1 20.9 - - + -
108C ARG* 3.6 34.5 - - + -
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Residues in contact with SER 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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36A TRP* 5.6 1.4 - - - -
53C TYR* 1.3 75.5 - - - +
55C PHE* 1.3 60.5 + - - +
56C SER* 4.4 3.8 + - - -
66C LEU* 4.6 18.6 - - - -
69C LEU* 5.5 0.7 - - - -
99C ARG 3.6 1.7 - - - +
100C VAL* 3.5 5.8 - - - -
101C THR* 2.8 50.3 + - - -
102C ALA 4.6 2.2 + - - -
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Residues in contact with PHE 55 (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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26C LEU* 4.5 9.9 - - + -
38C CYS* 3.9 29.6 - - + -
40C TRP* 4.2 12.8 - + - -
53C TYR 4.3 0.6 + - - -
54C SER* 1.3 71.0 - - - +
56C SER* 1.3 66.6 + - - +
57C TYR* 4.4 3.1 - + + -
66C LEU* 3.2 10.4 - - - +
67C CYS* 3.0 53.6 + - + +
69C LEU* 4.0 19.0 - - + +
83C CYS* 3.8 9.0 - - + -
85C LEU* 3.9 16.4 - - + -
98C LEU* 3.8 37.2 - - + -
99C ARG 4.0 1.8 - - - -
100C VAL* 3.7 27.1 - - + +
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TRP* 3.6 25.5 - - - -
54C SER* 4.4 6.2 + - - -
55C PHE* 1.3 80.0 + - - +
57C TYR* 1.3 61.5 + - - +
64C TRP* 3.8 21.5 - - - -
65C LYS 3.3 9.0 - - - -
66C LEU* 3.7 15.1 - - - +
97C GLU 3.9 0.5 - - - +
98C LEU* 3.4 4.5 - - - +
99C ARG* 2.9 41.8 + - - -
101C THR* 4.9 0.2 + - - -
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Residues in contact with TYR 57 (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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55C PHE* 4.4 2.7 - + + -
56C SER* 1.3 74.4 - - - +
58C GLN* 1.3 65.0 + - - +
59C LEU* 5.0 6.3 - - + -
63C PRO 4.3 0.3 - - - +
64C TRP* 3.8 2.4 - - - -
65C LYS* 2.8 64.0 + - + +
66C LEU 4.1 15.6 + - - -
67C CYS* 4.1 20.6 - - + -
85C LEU* 3.9 22.9 - - + -
86C PRO* 3.5 18.8 - - + +
89C ASP* 2.8 40.8 + - + -
96C LEU* 4.0 9.6 - - + -
97C GLU 3.3 5.4 - - - -
98C LEU* 3.6 23.6 - - + -
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Residues in contact with GLN 58 (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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13A ARG* 2.3 42.5 + - - +
35A ILE* 6.1 1.8 - - - +
57C TYR* 1.3 78.7 - - - +
59C LEU* 1.3 76.7 + - - +
61C ASP* 4.5 2.0 - - - +
62C GLU 2.4 38.6 + - - +
63C PRO 3.7 7.0 - - - +
64C TRP* 3.4 47.1 + - + +
95C PRO 4.0 0.7 - - - +
96C LEU* 3.4 9.6 - - - +
97C GLU* 3.1 28.6 + - - +
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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