Contacts of the helix formed by residues 98 - 110 (chain D) in PDB entry 1A4Y
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 GLY 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D THR* 1.3 78.5 + - - +
99D ALA* 1.3 61.0 + - - +
101D CYS* 3.1 19.6 + - - +
102D GLY 4.3 1.4 + - - -
123D LEU 3.6 7.1 + - - -
124D LEU 3.4 21.3 + - - -
127D ALA* 5.7 2.0 - - - -
128D GLY* 4.0 14.5 - - - -
131D LEU* 4.9 5.9 - - - +
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Residues in contact with ALA 99 (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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69D ASP* 3.9 7.2 - - + +
97D THR* 2.9 12.0 + - - +
98D GLY* 1.3 75.7 - - - +
100D GLY* 1.3 58.7 + - - +
101D CYS 3.6 0.3 + - - -
102D GLY* 3.8 9.4 + - - -
103D VAL* 5.0 2.8 + - - +
131D LEU* 5.7 1.0 - - - +
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Residues in contact with GLY 100 (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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69D ASP* 3.5 30.5 + - - -
72D VAL* 5.7 1.0 - - - +
76D LEU* 5.7 0.7 - - - +
96D LEU* 4.1 13.6 - - - +
97D THR 3.2 6.0 + - - -
98D GLY 3.1 1.0 - - - -
99D ALA* 1.3 77.5 - - - +
101D CYS* 1.3 58.9 + - - +
102D GLY 3.0 6.3 + - - -
103D VAL* 3.5 19.8 + - - +
104D LEU* 3.6 11.1 + - - +
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Residues in contact with CYS 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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96D LEU* 4.6 3.6 - - - -
97D THR 3.7 14.8 - - - -
98D GLY* 3.1 10.5 + - - +
100D GLY* 1.3 76.6 - - - +
102D GLY* 1.3 59.1 + - - +
103D VAL 3.5 0.2 - - - -
104D LEU* 3.7 10.1 - - - +
105D SER* 2.9 29.3 + - - -
124D LEU* 3.8 26.2 - - - -
128D GLY* 3.6 38.4 - - - +
129D LEU* 5.3 0.2 - - - -
131D LEU* 4.3 5.6 - - + +
132D LEU* 3.8 15.4 - - + +
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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
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99D ALA 3.8 8.8 + - - -
100D GLY 3.0 1.6 - - - -
101D CYS* 1.3 76.2 - - - +
103D VAL* 1.3 60.6 + - - +
105D SER* 3.2 4.3 + - - -
106D SER* 3.0 30.7 + - - -
131D LEU* 3.8 26.4 - - - +
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Residues in contact with VAL 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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69D ASP 5.2 2.5 - - - +
72D VAL* 6.2 0.4 - - + -
73D HIS* 3.1 46.7 - - + +
76D LEU* 4.1 20.6 - - + -
80D GLN* 6.0 1.8 - - - +
99D ALA 5.2 1.6 - - - +
100D GLY* 4.0 16.2 - - - +
101D CYS 3.5 0.2 - - - -
102D GLY* 1.3 72.3 - - - +
104D LEU* 1.3 53.9 + - - +
106D SER* 3.0 10.1 + - - -
107D THR* 2.8 43.4 + - - +
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Residues in contact with LEU 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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72D VAL* 5.2 0.9 - - + -
76D LEU* 4.3 26.2 - - + +
89D LEU* 5.1 2.0 - - + -
91D LEU* 4.8 9.0 - - + -
96D LEU* 3.5 33.7 - - + -
100D GLY 3.6 7.6 + - - +
101D CYS* 3.7 4.3 - - - +
103D VAL* 1.3 77.6 - - - +
105D SER* 1.3 64.5 + - - +
107D THR* 3.9 2.6 - - - +
108D LEU* 3.0 39.1 + - + +
117D LEU* 4.4 25.8 - - + -
119D LEU* 3.6 20.2 - - + -
132D LEU* 3.6 22.4 - - + -
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Residues in contact with SER 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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101D CYS 2.9 19.8 + - - -
102D GLY 3.2 6.0 + - - -
104D LEU* 1.3 76.6 - - - +
106D SER* 1.3 59.1 + - - +
108D LEU* 3.7 9.2 + - - +
109D ARG* 3.1 31.2 + - - +
131D LEU* 2.9 40.8 + - - +
132D LEU* 4.1 3.8 - - - +
134D GLU* 4.1 1.2 - - - +
135D GLY* 3.3 21.1 + - - -
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Residues in contact with SER 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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102D GLY 3.0 14.5 + - - -
103D VAL* 3.0 14.5 + - - -
105D SER* 1.3 76.3 - - - +
107D THR* 1.3 65.6 + - - +
109D ARG* 3.3 24.1 + - - +
110D THR* 3.3 13.6 - - - +
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Residues in contact with THR 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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76D LEU* 4.1 36.2 - - + +
79D LEU* 5.2 0.7 - - + -
80D GLN* 3.7 27.1 + - - +
103D VAL* 2.8 26.6 + - - +
104D LEU* 4.1 5.4 - - - -
106D SER* 1.3 71.5 - - - +
108D LEU* 1.3 61.1 + - + +
110D THR* 2.8 31.0 + - - -
111D LEU* 3.4 33.3 + - + +
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Residues in contact with LEU 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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89D LEU* 6.5 0.2 - - + -
104D LEU* 3.0 33.6 + - + +
105D SER* 3.7 6.1 - - - +
106D SER 3.4 0.2 - - - -
107D THR* 1.3 76.3 - - - +
109D ARG* 1.3 59.0 + - - +
110D THR 3.5 0.3 + - - -
111D LEU* 3.7 15.7 + - + +
114D LEU* 3.6 30.2 - - + +
117D LEU* 4.2 19.1 - - + -
132D LEU* 4.3 23.8 - - + +
135D GLY 4.7 4.7 - - - -
136D LEU* 3.7 32.1 - - + +
141D CYS* 3.8 28.9 - - - +
143D LEU* 4.8 4.9 - - + -
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Residues in contact with ARG 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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105D SER* 3.1 37.1 + - - +
106D SER* 3.3 17.1 + - - +
107D THR 3.0 0.2 + - - -
108D LEU* 1.3 74.6 - - - +
110D THR* 1.3 61.7 + - + +
111D LEU 3.5 0.8 + - - -
134D GLU* 3.6 23.2 + - - +
135D GLY* 4.0 11.5 + - - +
138D ASP* 2.7 47.6 + - + +
140D GLN* 3.3 29.8 - - - +
141D CYS 4.8 0.7 - - - +
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Residues in contact with THR 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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79D LEU 5.4 0.2 + - - -
80D GLN* 3.7 19.5 + - - +
106D SER 3.3 20.6 - - - +
107D THR* 2.8 9.2 + - - -
109D ARG* 1.3 82.2 - - + +
111D LEU* 1.3 66.7 + - - +
112D PRO* 3.4 12.0 - - - +
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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