Contacts of the strand formed by residues 110 - 118 (chain C) in PDB entry 1SNF
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 ARG 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C SER* 5.0 10.5 + - - -
20C ALA* 5.5 8.9 - - - +
28C ASP* 2.9 33.2 + - + +
29C LEU 3.3 8.5 - - - +
30C TYR* 3.7 40.4 + - + -
64C ARG* 3.5 40.7 + - - +
67C LEU* 4.0 12.8 - - - +
108C GLY 3.7 0.4 + - - +
109C ASP* 1.3 72.0 - - - +
111C ILE* 1.3 58.3 - - - +
112C ALA 3.8 0.9 - - - -
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Residues in contact with ILE 111 (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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29C LEU 2.9 14.5 + - - +
30C TYR 4.0 9.2 - - - +
31C SER* 3.7 27.8 - - - -
45C VAL* 4.1 16.2 - - + -
47C THR* 4.5 4.7 - - + -
63C PRO* 5.0 0.7 - - - +
64C ARG* 4.1 11.4 + - - +
67C LEU* 5.3 1.6 - - + -
73C LEU* 4.8 12.0 - - + +
75C ILE* 4.6 2.9 - - - +
92C VAL* 4.0 29.8 - - + +
94C LEU* 4.1 26.8 - - + +
105C VAL* 3.8 20.4 - - + -
109C ASP* 3.7 13.7 - - + +
110C ARG* 1.3 76.4 - - - +
112C ALA* 1.3 66.5 + - + +
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Residues in contact with ALA 112 (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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28C ASP* 3.4 8.1 - - - +
29C LEU* 2.9 28.9 + - + +
61C VAL* 3.9 22.9 - - + -
62C HIS 3.5 13.2 - - - +
64C ARG* 3.8 12.5 - - - +
75C ILE* 4.1 7.9 - - + -
92C VAL* 4.3 13.0 - - + -
110C ARG 3.8 0.6 - - - -
111C ILE* 1.3 84.4 - - + +
113C GLN* 1.3 63.0 + - - +
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Residues in contact with GLN 113 (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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81A THR* 3.6 27.0 + - - +
83A ASP* 5.1 2.3 - - - +
1170A UMP 3.2 39.5 + - - -
26C GLY* 4.1 16.3 + - - -
27C VAL 3.3 7.9 - - - +
28C ASP* 3.8 16.4 - - - +
29C LEU* 4.5 2.2 - - - +
60C LEU 3.5 0.9 - - - +
61C VAL* 3.5 4.4 - - - +
62C HIS* 2.9 47.8 + - + +
63C PRO 3.5 14.8 + - - -
64C ARG* 4.4 4.4 - - + +
112C ALA* 1.3 77.0 - - - +
114C LEU* 1.3 58.7 + - - +
115C LEU* 3.8 7.4 - - + -
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Residues in contact with LEU 114 (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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124A LEU* 6.3 0.2 - - + -
5C LEU* 4.1 26.5 - - + -
7C ILE* 6.1 1.6 - - + -
19C ARG* 5.1 1.2 + - - -
25C ALA 4.1 0.5 - - - +
26C GLY* 3.2 2.6 - - - -
27C VAL* 2.7 51.8 + - + +
29C LEU* 4.1 17.2 - - + +
51C VAL* 4.4 9.0 - - + -
53C VAL* 6.2 0.7 - - + -
59C GLY* 4.4 7.4 - - - -
60C LEU 3.3 21.8 - - - +
61C VAL* 4.2 13.0 - - + +
82C ILE* 4.7 2.5 - - + -
90C ILE* 4.3 22.4 - - + -
113C GLN* 1.3 72.8 - - - +
115C LEU* 1.3 71.5 + - - +
116C VAL* 5.0 2.3 - - + +
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Residues in contact with LEU 115 (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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58A VAL* 4.5 10.1 - - + -
60A LEU* 4.8 1.3 - - + -
81A THR* 4.3 5.2 - - + -
119A VAL* 4.3 11.2 - - + -
3174B TRS 5.1 1.6 - - - +
25C ALA* 3.7 35.0 - - + +
26C GLY* 4.1 7.0 - - - +
59C GLY* 3.4 4.5 - - - -
60C LEU* 2.9 43.8 + - + +
62C HIS* 3.7 40.4 - - + +
113C GLN* 3.8 22.4 - - + -
114C LEU* 1.3 79.4 - - - +
116C VAL* 1.3 65.5 + - - +
117C GLN* 5.2 6.7 - - + -
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Residues in contact with VAL 116 (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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119A VAL* 3.7 3.4 - - - +
120A GLU* 3.0 31.9 + - + +
122A VAL* 3.8 40.4 - - + +
5C LEU* 4.2 22.0 - - + -
25C ALA 4.9 0.4 + - - -
53C VAL* 4.7 5.8 - - + -
54C PRO* 5.0 3.4 - - + -
57C MET* 3.8 34.1 - - + -
58C VAL 3.3 12.1 - - - +
59C GLY* 5.0 4.3 - - - -
114C LEU* 5.0 5.6 - - + +
115C LEU* 1.3 77.3 - - - +
117C GLN* 1.3 66.0 + - - +
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Residues in contact with GLN 117 (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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58A VAL* 4.0 13.1 - - - +
60A LEU* 4.5 1.4 - - - +
117A GLN* 3.0 26.1 + - - +
118A ARG 3.1 27.2 + - - +
119A VAL* 4.4 7.2 - - + -
120A GLU* 4.4 5.6 - - - +
117B GLN* 3.1 19.6 + - - +
3174B TRS 2.7 26.8 + - - -
57C MET* 3.2 8.9 - - - +
58C VAL* 2.9 31.2 + - + +
60C LEU* 3.0 21.2 - - + +
115C LEU* 4.3 6.2 - - + -
116C VAL* 1.3 78.8 - - - +
118C ARG* 1.3 64.1 + - - +
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Residues in contact with ARG 118 (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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118A ARG 5.5 0.8 + - - -
120A GLU* 3.0 38.2 + - + +
117B GLN* 3.0 27.0 + - - +
118B ARG 5.7 0.3 + - - -
3C THR* 4.5 3.2 + - - -
56C GLY* 3.5 12.0 + - - +
57C MET* 3.9 22.3 - - + +
117C GLN* 1.3 74.1 - - - +
119C VAL* 1.3 59.3 + - - +
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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