Contacts of the strand formed by residues 151 - 156 (chain C) in PDB entry 3ALQ
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 151 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.4 17.2 - - + +
120A LEU* 4.2 1.2 - - - -
121A GLY 3.0 43.6 + - - -
15C HIS* 3.3 28.5 - + + +
16C VAL 3.3 13.0 - - - +
17C VAL* 4.5 3.6 - - + -
28C TRP* 3.4 7.1 - - - -
59C TYR* 3.7 15.0 - + - -
60C SER* 2.9 20.1 + - - -
61C GLN* 2.9 54.9 + - + +
119C TYR* 3.4 9.2 - + - -
148C GLY* 3.4 31.4 - - - -
150C VAL* 1.3 79.4 - - - +
152C PHE* 1.3 61.9 + - - +
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Residues in contact with PHE 152 (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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14C ALA 4.0 0.7 - - - +
15C HIS* 3.3 1.3 - - - -
16C VAL* 2.8 49.2 + - + +
28C TRP* 3.7 26.7 - + + -
46C ASN 5.5 0.2 - - - -
47C GLN* 5.4 1.1 - - - -
48C LEU* 3.6 35.6 - - + +
58C ILE* 4.2 10.5 - - + -
59C TYR* 3.3 18.6 - - - -
60C SER* 3.8 7.6 - - - +
80C ILE* 3.8 23.6 - - + -
132C LEU* 3.9 32.1 - - + -
133C SER* 4.2 2.7 - - - -
134C ALA* 3.8 27.4 - - + -
151C TYR* 1.3 77.4 - - - +
153C GLY* 1.3 62.2 + - - +
154C ILE* 4.6 0.7 - - + -
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Residues in contact with GLY 153 (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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14C ALA 2.9 12.3 - - - -
48C LEU* 4.8 0.7 - - - -
58C ILE* 4.0 0.3 - - - +
59C TYR* 2.8 66.1 + - - +
152C PHE* 1.3 77.3 - - - +
154C ILE* 1.3 69.0 + - - +
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Residues in contact with ILE 154 (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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13C VAL* 3.4 1.3 - - - +
14C ALA* 2.8 53.1 + - + +
41C VAL* 3.9 30.3 - - + -
48C LEU* 3.6 21.3 - - + -
50C VAL* 4.6 9.6 - - + -
56C TYR* 3.9 24.5 - - + -
57C LEU 3.2 9.0 - - - +
58C ILE* 3.9 12.3 - - + -
59C TYR* 4.8 1.1 - - - -
132C LEU* 3.7 30.3 - - + -
152C PHE* 4.6 1.1 - - + -
153C GLY* 1.3 80.8 - - - +
155C ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 155 (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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55A LEU* 3.9 17.9 - - + -
123A VAL* 3.6 29.2 - - + -
157A LEU* 3.5 37.0 - - + -
9C SER* 5.5 0.7 - - - +
11C MET* 5.3 4.7 - - + -
12C PRO 3.7 6.7 - - - +
13C VAL* 3.7 23.6 - - + -
56C TYR* 3.4 6.2 - - - -
57C LEU* 3.0 48.8 + - + +
59C TYR* 5.1 0.4 - - + -
154C ILE* 1.3 75.8 - - - +
156C ALA* 1.3 74.2 + - - +
157C LEU* 3.3 4.3 + - + +
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Residues in contact with ALA 156 (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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157A LEU* 6.2 0.2 - - - +
11C MET* 3.6 26.3 - - + +
12C PRO* 3.0 42.5 + - + +
52C SER* 5.7 0.7 - - - +
54C GLY* 6.3 0.4 - - - -
55C LEU 3.8 6.5 - - - +
56C TYR* 3.7 23.2 - - + -
155C ILE* 1.3 74.5 - - - +
157C LEU* 1.3 63.8 + - - +
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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