Contacts of the helix formed by residues 75 - 85 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.0 3.0 + - - +
74A SER* 1.3 80.9 + - - +
76A GLY* 1.3 64.4 + - - +
77A GLN 3.4 2.4 + - - -
78A ALA* 3.0 25.0 + - - +
79A ALA 3.1 9.7 + - - -
197A LLP 3.3 14.8 + - - -
206A LEU* 4.8 4.5 - - - -
207A GLY* 3.5 10.1 - - - +
208A GLY* 3.3 11.8 - - - -
48B ARG* 4.3 5.8 - - - -
229B GLY* 2.8 29.8 + - - -
231B VAL* 4.7 4.0 - - - -
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 1.3 71.2 - - - +
77A GLN* 1.3 63.1 + - - +
79A ALA* 3.0 5.2 + - - +
80A ALA* 2.9 22.8 + - - +
192A LEU* 4.3 2.5 - - - +
193A TYR 3.7 21.8 - - - -
194A SER* 3.8 4.5 - - - -
197A LLP 2.9 34.2 + - - -
207A GLY 3.2 4.0 + - - -
208A GLY* 3.8 0.7 - - - -
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 3.2 8.0 - - - +
76A GLY* 1.3 73.2 - - - +
78A ALA* 1.3 52.7 + - - +
80A ALA* 3.3 5.0 + - - +
81A ALA* 2.7 36.0 + - - +
100A TYR* 3.1 26.7 - - - -
102A GLY* 2.8 39.5 + - - -
103A THR* 3.7 2.1 + - - -
106A LEU* 3.5 11.7 - - - +
197A LLP 2.9 13.4 + - - +
48B ARG* 3.3 31.9 - - - +
226B THR 3.9 0.4 - - - +
227B THR* 2.9 33.5 + - - +
228B ALA 3.5 1.8 - - - -
229B GLY* 3.9 7.9 - - - -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.9 10.1 - - + -
74A SER* 3.8 19.3 - - - +
75A SER* 3.0 23.0 + - - +
77A GLN* 1.3 74.2 - - - +
79A ALA* 1.3 61.5 + - - +
81A ALA* 3.7 1.5 - - - +
82A THR* 2.9 33.6 + - - -
230A ASN* 3.5 20.6 + - + +
228B ALA 3.2 14.5 + - - +
229B GLY 3.8 1.1 - - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.7 29.0 - - + -
75A SER 3.1 7.2 + - - +
76A GLY 3.0 10.0 + - - +
78A ALA* 1.3 75.8 - - - +
80A ALA* 1.3 62.4 + - - +
82A THR* 3.2 5.4 + - - -
83A LEU* 3.2 18.9 + - - +
192A LEU* 3.6 18.4 - - + -
193A TYR 4.2 0.7 - - - +
209A ALA 3.7 20.4 - - - +
210A LEU* 3.7 10.2 - - + +
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLY 2.9 12.5 + - - +
77A GLN* 3.6 10.3 - - - +
79A ALA* 1.3 75.0 - - - +
81A ALA* 1.3 58.1 + - - +
83A LEU* 3.3 2.8 + - - -
84A LEU* 2.9 29.5 + - - +
103A THR* 4.9 6.5 - - + +
106A LEU* 3.7 15.7 - - + -
141A TRP* 3.7 34.3 - - + -
192A LEU* 3.7 11.3 - - + +
197A LLP 6.2 2.7 - - + -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLN 2.7 21.3 + - - +
78A ALA* 3.7 4.9 - - - +
79A ALA 3.3 0.2 - - - -
80A ALA* 1.3 73.7 - - - +
82A THR* 1.3 62.1 + - - +
84A LEU* 3.5 5.7 + - - +
85A SER* 3.1 23.0 + - - -
106A LEU* 3.6 26.7 - - + +
224A TYR* 4.3 11.0 + - - +
230A ASN* 5.2 2.9 - - - +
228B ALA* 4.1 16.8 - - + +
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.1 33.7 - - + -
78A ALA 2.9 20.8 + - - -
79A ALA 3.5 5.6 - - - -
80A ALA 3.2 0.2 - - - -
81A ALA* 1.3 77.2 - - - +
83A LEU* 1.3 61.7 + - - +
85A SER* 2.5 23.7 + - - -
86A LEU* 3.9 6.0 + - + +
210A LEU* 4.4 0.7 - - + -
221A VAL* 4.0 30.7 - - + +
224A TYR* 3.4 23.4 - - + -
230A ASN* 3.1 11.8 + - - -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA 3.2 10.2 + - - +
80A ALA* 3.3 7.2 + - - +
82A THR* 1.3 80.6 - - - +
84A LEU* 1.3 62.7 + - - +
86A LEU* 3.3 22.4 + - + +
87A VAL* 4.4 5.0 + - - +
139A LEU* 4.5 12.6 - - + +
141A TRP* 4.3 9.0 - - + -
168A ARG* 4.1 26.2 + - - +
170A VAL* 3.5 45.1 - - + -
190A VAL* 4.1 19.5 - - + -
192A LEU* 5.6 0.2 - - + -
210A LEU* 4.4 14.3 - - + +
217A LEU* 4.4 14.1 - - + -
221A VAL* 5.3 1.1 - - + -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ALA 2.9 17.9 + - - +
81A ALA* 3.8 7.4 - - - +
82A THR 3.2 0.2 - - - -
83A LEU* 1.3 73.7 - - - +
85A SER* 1.3 55.9 + - - +
86A LEU 3.0 5.6 - - - -
87A VAL* 3.0 41.7 + - + +
93A VAL* 3.9 17.5 - - + -
106A LEU* 3.2 45.5 - - + +
107A PHE* 4.0 15.3 - - + +
110A ALA* 3.6 20.3 - - + +
115A VAL* 5.0 0.8 - - + +
139A LEU* 4.6 6.1 - - + -
141A TRP* 4.5 9.6 - - + -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ALA 3.1 14.0 + - - -
82A THR 2.5 21.4 + - - -
84A LEU* 1.3 75.7 - - - +
86A LEU* 1.3 69.9 + - - +
87A VAL 3.2 7.4 + - - +
88A ARG* 6.0 0.2 - - - +
224A TYR* 3.6 37.0 - - - -
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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