Contacts of the helix formed by residues 75 - 85 (chain C) in PDB entry 4XQ2
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 75 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C PHE* 3.0 3.5 + - - +
74C SER* 1.3 81.9 + - - +
76C GLY* 1.3 64.6 + - - +
77C GLN* 3.4 6.2 + - - +
78C ALA* 2.8 31.2 + - - +
79C ALA 3.1 17.3 + - - -
197C LLP 3.4 15.5 - - - -
206C LEU* 4.9 5.8 - - - -
207C GLY* 3.6 9.2 - - - +
208C GLY* 3.2 14.3 - - - -
48D ARG* 4.2 12.5 - - - -
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Residues in contact with GLY 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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75C SER* 1.3 70.6 - - - +
77C GLN* 1.3 63.5 + - - +
79C ALA* 3.2 4.6 + - - +
80C ALA* 2.9 22.6 + - - +
192C LEU* 4.0 4.2 - - - +
193C TYR 4.0 3.1 - - - -
194C SER* 3.8 11.9 - - - -
197C LLP 2.9 35.2 + - - -
207C GLY 3.3 3.8 + - - -
208C GLY* 3.7 11.2 - - - -
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Residues in contact with GLN 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C SER* 3.6 7.4 - - - +
76C GLY* 1.3 72.8 - - - +
78C ALA* 1.3 56.1 + - - +
80C ALA* 3.3 4.1 + - - +
81C ALA* 2.8 27.6 + - - +
100C TYR* 3.4 15.2 - - - -
102C GLY* 2.7 48.5 + - - -
103C THR* 3.8 2.4 + - - -
106C LEU* 3.4 24.6 - - + +
197C LLP 2.8 27.2 + - - +
48D ARG* 3.4 31.1 - - - +
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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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73C PHE* 3.8 5.8 - - + -
74C SER* 3.4 21.8 - - - +
75C SER* 2.8 27.1 + - - +
77C GLN* 1.3 70.8 - - - +
79C ALA* 1.3 65.4 + - - +
81C ALA* 3.3 5.4 + - - +
82C THR* 2.8 31.0 + - - -
230C ASN* 3.5 22.2 + - + +
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C PHE* 3.6 30.4 - - + -
75C SER 3.1 8.5 + - - +
76C GLY 3.5 8.3 - - - +
78C ALA* 1.3 75.4 - - - +
80C ALA* 1.3 62.2 + - - +
82C THR* 3.3 4.2 + - - -
83C LEU* 3.2 17.8 + - - +
192C LEU* 3.6 17.7 - - + -
208C GLY* 4.1 0.2 - - - -
209C ALA 3.8 19.1 - - - +
210C LEU* 3.7 14.9 - - + +
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLY 2.9 13.4 + - - +
77C GLN* 3.5 11.7 - - - +
79C ALA* 1.3 74.9 - - - +
81C ALA* 1.3 66.2 + - - +
82C THR 3.2 0.2 + - - -
83C LEU* 3.3 2.1 + - - -
84C LEU* 3.0 24.9 + - - +
103C THR* 5.0 5.2 - - - +
106C LEU* 3.6 15.9 - - + -
141C TRP* 3.7 30.8 - - + -
192C LEU* 4.0 11.4 - - + +
197C LLP 6.2 2.0 - - + -
210C LEU* 5.4 0.2 - - - -
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Residues in contact with ALA 81 (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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77C GLN 2.8 20.1 + - - +
78C ALA* 3.7 8.5 - - - +
80C ALA* 1.3 72.6 - - - +
82C THR* 1.3 53.5 + - - +
84C LEU* 3.3 5.0 + - - +
85C SER* 2.8 35.2 + - - -
106C LEU* 3.6 26.9 - - + +
224C TYR* 4.5 13.3 + - + +
230C ASN* 5.3 1.8 - - - +
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Residues in contact with THR 82 (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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73C PHE* 3.0 32.6 - - + -
78C ALA 2.8 20.7 + - - -
79C ALA 3.5 6.1 - - - -
80C ALA 3.2 0.2 - - - -
81C ALA* 1.3 73.8 - - - +
83C LEU* 1.3 65.7 + - - +
85C SER* 2.6 22.2 + - - -
86C LEU* 3.8 6.9 + - + +
210C LEU* 4.3 2.5 - - + -
221C VAL* 4.0 26.9 - - + +
224C TYR* 3.2 27.0 - - + -
230C ASN* 3.1 10.9 + - - -
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Residues in contact with LEU 83 (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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79C ALA 3.2 9.5 + - - +
80C ALA 3.9 6.3 - - - +
82C THR* 1.3 79.0 - - - +
84C LEU* 1.3 62.0 + - - +
86C LEU* 3.1 25.0 + - + +
87C VAL* 4.3 3.8 + - - +
139C LEU* 4.6 12.1 - - + +
141C TRP* 4.4 11.9 - - + -
168C ARG* 4.4 22.8 + - - +
170C VAL* 3.5 43.3 - - + -
190C VAL* 4.0 20.2 - - + -
192C LEU* 5.5 0.4 - - + -
210C LEU* 4.3 14.8 - - + +
217C LEU* 4.4 17.9 - - + -
221C VAL* 5.2 1.3 - - + -
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Residues in contact with LEU 84 (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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80C ALA 3.0 17.2 + - - +
81C ALA* 3.6 5.6 - - - +
83C LEU* 1.3 74.6 - - - +
85C SER* 1.3 60.7 + - - +
86C LEU 3.0 6.6 + - - -
87C VAL* 3.0 28.1 + - + +
93C VAL* 4.1 21.8 - - + -
103C THR* 5.7 0.2 - - + -
106C LEU* 3.8 34.5 - - + +
107C PHE* 3.5 41.3 - - + -
110C ALA* 4.4 16.5 - - + +
115C VAL* 5.4 1.4 - - - +
139C LEU* 4.3 1.3 - - + -
141C TRP* 4.1 15.0 - - + -
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ALA 2.8 14.0 + - - -
82C THR 2.6 19.9 + - - -
84C LEU* 1.3 74.8 - - - +
86C LEU* 1.3 65.7 + - - +
87C VAL 3.2 9.9 + - - +
88C ARG* 5.6 2.4 - - - +
224C TYR* 3.4 38.8 - - - -
109D LEU* 6.1 1.8 - - - -
113D GLN* 4.8 10.0 + - - -
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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