Contacts of the helix formed by residues 100 - 113 (chain D) 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 TYR 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C TYR* 5.8 0.2 - - - -
48C ARG* 2.9 25.0 + - - -
77D GLN* 3.3 19.3 - - - -
99D VAL* 1.3 76.2 - - - +
101D ALA* 1.3 73.9 + - + +
102D GLY* 3.4 23.7 - - - -
103D THR* 3.1 20.2 + - - +
104D ASP 3.0 15.9 + - - -
143D GLU* 2.8 21.8 + - - +
147D ASN* 6.3 2.5 - - - -
197D LLP 3.3 55.1 - + + +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL 3.6 3.0 + - - -
100D TYR* 1.3 78.0 - - + +
102D GLY* 1.3 55.5 + - - +
104D ASP* 2.8 10.6 + - + +
105D GLY* 2.4 36.0 + - - -
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Residues in contact with GLY 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ARG* 5.8 1.3 - - - -
227C THR* 5.8 0.4 - - - -
77D GLN* 2.8 40.4 + - - -
100D TYR* 3.3 19.0 - - - -
101D ALA* 1.3 77.5 - - - +
103D THR* 1.3 55.4 + - - +
105D GLY* 3.3 3.2 + - - -
106D LEU* 2.9 20.6 + - - +
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Residues in contact with THR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D GLN* 3.6 3.7 + - - -
80D ALA* 5.0 3.5 - - + +
84D LEU* 5.1 1.6 - - + -
99D VAL* 3.6 7.7 - - + +
100D TYR* 3.1 27.5 + - - +
102D GLY* 1.3 73.7 - - - +
104D ASP* 1.3 53.6 + - - +
106D LEU* 3.1 9.2 + - - +
107D PHE* 2.5 67.8 + - + -
141D TRP* 3.4 36.2 + - + +
172D ASP* 4.6 5.9 + - - -
192D LEU* 5.6 0.2 - - - +
197D LLP 4.8 1.9 + - - -
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Residues in contact with ASP 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ASP* 4.8 4.7 - - - +
99D VAL* 4.2 8.3 - - + +
100D TYR 3.0 9.9 + - - +
101D ALA* 2.8 16.1 + - + +
103D THR* 1.3 69.1 - - - +
105D GLY* 1.3 56.5 + - - +
107D PHE* 3.4 13.6 - - + +
108D ASP* 2.6 52.8 + - - +
119D TYR* 3.0 42.2 + - - -
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Residues in contact with GLY 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C THR* 3.6 18.9 - - - +
101D ALA 2.4 23.7 + - - -
102D GLY* 3.5 4.3 - - - -
103D THR 3.2 0.2 - - - -
104D ASP* 1.3 68.6 - - - +
106D LEU* 1.3 60.6 + - - +
108D ASP* 3.2 10.6 + - - +
109D LEU* 3.1 18.0 + - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C THR* 3.3 30.1 - - + +
228C ALA* 4.2 1.3 - - - -
77D GLN* 3.3 40.4 - - - +
80D ALA* 3.6 15.9 - - + -
81D ALA* 3.4 31.6 - - + +
84D LEU* 3.7 14.7 - - + +
102D GLY 2.9 8.8 + - - +
103D THR* 3.5 7.4 - - - +
105D GLY* 1.3 72.6 - - - +
107D PHE* 1.3 66.6 + - - +
109D LEU* 3.0 20.8 + - + +
110D ALA* 2.9 22.7 + - - +
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Residues in contact with PHE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 3.5 30.5 - - + -
93D VAL* 4.3 9.9 - - + -
95D SER* 3.5 36.6 - - - -
99D VAL* 3.8 10.3 - - + -
103D THR* 2.5 44.2 + - + +
104D ASP* 3.1 29.6 + - - +
106D LEU* 1.3 73.2 - - - +
108D ASP* 1.3 51.0 + - - +
110D ALA* 3.2 3.5 + - + -
111D ALA 2.5 31.5 + - - -
117D VAL* 3.1 41.8 - - + +
119D TYR* 4.4 1.6 - + - -
141D TRP* 3.8 14.4 - + + -
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Residues in contact with ASP 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ASP* 2.6 38.2 + - - +
105D GLY* 3.6 8.3 - - - +
106D LEU 3.2 0.2 - - - -
107D PHE* 1.3 71.3 - - - +
109D LEU* 1.3 55.1 + - - +
111D ALA* 3.3 13.1 - - + +
112D ARG* 2.6 58.0 + - - +
117D VAL* 5.7 0.9 - - - +
119D TYR* 4.8 3.5 + - - -
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C SER* 6.1 1.6 - - - -
224C TYR* 4.3 31.2 - - + -
227C THR* 4.0 12.3 - - + -
228C ALA* 5.2 1.3 - - + +
105D GLY 3.1 9.9 + - - +
106D LEU* 3.0 36.9 + - + +
108D ASP* 1.3 75.8 - - - +
110D ALA* 1.3 50.9 - - - +
112D ARG* 2.8 18.4 + - + +
113D GLN* 2.5 50.8 + - + +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 5.1 19.1 - - + +
87D VAL* 6.2 0.2 - - + -
93D VAL* 5.8 0.4 - - + -
106D LEU 2.9 11.5 + - - +
107D PHE* 3.7 8.3 - - - +
109D LEU* 1.3 71.9 - - - +
111D ALA* 1.3 64.3 + - - +
113D GLN* 3.2 11.6 + - - +
115D VAL* 2.7 58.6 + - + +
117D VAL* 4.8 2.9 - - + -
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PHE 2.5 18.9 + - - +
108D ASP* 3.3 22.0 - - - +
109D LEU 3.2 0.2 - - - -
110D ALA* 1.3 73.9 - - - +
112D ARG* 1.3 59.9 + - - +
114D GLY* 4.1 4.5 + - - -
115D VAL 3.7 12.1 - - - +
117D VAL* 4.2 11.4 - - + +
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG* 4.8 28.6 + - - +
89C PRO* 5.0 7.4 - - - +
108D ASP* 2.6 43.8 + - - +
109D LEU* 3.2 19.9 - - + +
111D ALA* 1.3 76.3 - - - +
113D GLN* 1.3 63.4 + - + +
114D GLY 3.3 4.3 + - - -
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Residues in contact with GLN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C SER 4.8 11.3 + - - -
87C VAL 5.0 4.2 + - - -
88C ARG* 4.8 7.5 - - - +
89C PRO* 4.0 24.2 - - - +
113C GLN* 3.1 62.5 + - + +
89D PRO* 4.0 7.8 - - - +
109D LEU* 2.5 31.0 + - + +
110D ALA* 3.2 8.3 + - - -
112D ARG* 1.3 79.8 + - + +
114D GLY* 1.3 56.5 + - - +
115D VAL* 3.5 6.8 + - + +
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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