Contacts of the helix formed by residues 101 - 115 (chain D) in PDB entry 1RZR
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 ASN 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D SER 2.8 22.5 + - - +
99D ASP* 3.2 19.3 + - - +
100D GLN* 1.3 78.9 - - - +
102D GLN* 1.3 74.7 + - - +
103D ASP* 2.7 12.1 - - - +
104D LYS* 3.5 14.6 + - - +
105D GLU* 3.1 21.3 + - - +
754D MG 2.3 30.8 - - - -
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Residues in contact with GLN 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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100D GLN 3.9 1.6 + - - -
101D ASN* 1.3 81.9 - - - +
103D ASP* 1.3 101.6 + - - +
105D GLU* 3.5 3.5 + - - +
106D LEU* 3.2 32.4 + - + +
128D THR* 5.3 7.2 - - + +
130D GLU* 6.0 1.3 - - - +
131D HIS* 4.0 25.3 - - + +
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Residues in contact with ASP 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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101D ASN* 2.7 1.7 - - - +
102D GLN* 1.3 98.7 + - + +
104D LYS* 1.3 92.0 + - - +
106D LEU* 4.3 2.7 - - - +
107D HIS* 3.2 21.0 + - - +
754D MG 1.8 31.7 - - - -
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Residues in contact with LYS 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 ASN 4.7 11.2 - - - +
98D SER* 4.2 8.5 - - - +
99D ASP* 4.1 17.8 + - - +
101D ASN* 3.5 21.2 + - - +
103D ASP* 1.3 97.4 + - - +
105D GLU* 1.3 55.7 + - - +
107D HIS* 3.0 10.1 - - + +
108D LEU* 2.7 43.8 + - + +
754D MG 3.3 19.0 - - - -
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Residues in contact with GLU 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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66D ILE* 3.7 8.6 - - + +
98D SER* 3.4 25.5 - - - -
100D GLN* 2.9 33.4 - - - +
101D ASN 3.1 12.9 - - - +
102D GLN 3.7 6.0 + - - +
103D ASP 3.3 0.2 - - - -
104D LYS* 1.3 72.7 - - - +
106D LEU* 1.3 72.3 + - + +
107D HIS 2.9 1.4 + - - -
108D LEU* 2.9 8.2 + - - +
109D LEU* 2.8 23.0 + - - +
122D PHE* 3.3 27.6 - - + -
124D SER* 3.0 23.5 + - - -
131D HIS* 3.4 15.2 - - - -
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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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102D GLN* 3.2 16.9 + - + +
103D ASP* 4.4 2.5 - - - +
105D GLU* 1.3 78.3 - - + +
107D HIS* 1.3 66.2 + - - +
109D LEU* 3.1 14.2 - - + +
110D ASN* 3.0 29.1 + - - +
130D GLU* 5.4 7.0 - - + +
131D HIS* 3.0 43.3 - - + +
134D GLU* 4.2 31.2 - - + +
135D LEU* 6.2 1.8 - - + -
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Residues in contact with HIS 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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599A SO4 4.1 19.5 + - - -
103D ASP 3.2 16.4 + - - +
104D LYS* 3.0 16.1 + - + +
105D GLU 2.9 1.0 - - - -
106D LEU* 1.3 79.2 - - - +
108D LEU* 1.3 62.6 + - + +
110D ASN* 2.4 38.2 + - + +
111D ASN* 2.9 20.4 + - + +
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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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87A THR* 6.2 0.9 - - + -
92A ASN* 5.8 0.9 - - - +
599A SO4 4.0 24.0 - - - +
66D ILE* 3.9 21.3 - - + -
96D SER* 2.9 41.7 - - - +
97D ASN 3.7 25.6 - - - +
98D SER* 4.3 4.9 - - - +
104D LYS* 2.7 25.5 + - + +
105D GLU 2.9 4.0 + - - +
107D HIS* 1.3 76.1 - - + +
109D LEU* 1.3 56.1 + - - +
110D ASN 2.8 0.3 + - - -
111D ASN* 2.9 9.4 + - + +
112D MSE 2.5 42.5 + - - +
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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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66D ILE* 3.8 14.3 - - + +
105D GLU 2.8 12.3 + - - +
106D LEU* 3.1 18.8 - - + +
108D LEU* 1.3 76.5 - - - +
110D ASN* 1.3 59.5 + - - +
112D MSE 3.4 5.2 - - - +
113D LEU* 3.0 45.5 + - + +
120D ILE* 3.2 34.3 - - + -
122D PHE* 5.5 1.6 - - + -
134D GLU* 3.8 36.3 - - + +
135D LEU* 4.1 27.8 - - + -
138D SER* 5.5 4.0 - - - -
142D VAL* 5.8 0.2 - - + -
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Residues in contact with ASN 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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47A ARG* 4.5 21.0 + - + +
106D LEU* 3.0 26.1 + - - +
107D HIS* 2.4 33.3 + - + +
109D LEU* 1.3 72.1 - - - +
111D ASN* 1.3 64.3 + - - +
112D MSE 3.0 1.3 + - - -
113D LEU* 3.2 6.2 + - - +
114D GLY* 2.8 21.1 + - - -
134D GLU* 4.8 11.6 + - - +
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Residues in contact with ASN 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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92A ASN* 2.4 34.5 + - - +
599A SO4 3.0 30.1 + - - +
107D HIS* 2.9 18.8 + - + +
108D LEU* 2.9 17.2 + - + +
110D ASN* 1.3 71.9 - - - +
112D MSE 1.3 66.6 + - + +
114D GLY* 3.0 4.1 + - - -
115D LYS* 2.9 26.9 + - - +
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Residues in contact with MSE 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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92A ASN* 4.7 1.3 - - - +
64D GLY* 3.7 24.9 - - - +
65D VAL 4.3 4.7 - - - +
66D ILE* 4.7 12.3 - - + -
94D ILE* 3.3 48.7 - - + +
96D SER* 5.1 7.2 - - - -
108D LEU* 2.5 30.0 + - + +
109D LEU* 3.4 9.6 - - - +
111D ASN* 1.3 80.1 + - - +
113D LEU* 1.3 60.8 + - + +
115D LYS* 2.8 27.3 + - + +
116D GLN 3.3 0.3 + - - -
117D VAL* 3.2 27.7 - - + +
120D ILE* 4.7 10.1 - - + -
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Residues in contact with LEU 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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1A MSE 5.2 0.6 - - + +
47A ARG* 3.8 32.5 - - - +
109D LEU* 3.0 31.4 + - + +
110D ASN* 3.2 5.8 + - - +
112D MSE 1.3 70.7 - - - +
114D GLY* 1.3 54.2 + - - +
116D GLN* 2.3 39.8 + - - +
117D VAL* 4.4 7.9 - - + +
120D ILE* 3.7 23.6 - - + -
138D SER* 4.4 9.4 - - - -
139D PRO* 3.8 26.5 - - + -
140D VAL* 4.0 22.4 - - + -
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Residues in contact with GLY 114 (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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47A ARG* 4.1 8.7 - - - +
48A PRO 3.7 17.7 - - - -
49A ASN 3.9 0.2 - - - -
50A ALA* 2.9 25.4 + - - -
110D ASN 2.8 14.1 + - - -
111D ASN* 3.0 4.5 + - - -
113D LEU* 1.3 72.6 - - - +
115D LYS* 1.3 53.8 + - - +
116D GLN* 2.6 25.6 + - - +
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Residues in contact with LYS 115 (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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50A ALA* 3.2 22.0 - - + +
51A VAL* 4.5 9.8 - - - +
53A ARG* 6.1 1.6 - - - +
60A THR* 4.6 10.3 - - - +
61A THR* 5.4 1.8 - - - +
62A THR* 4.0 19.3 - - - +
92A ASN* 4.4 13.2 - - - +
94A ILE* 6.3 0.7 - - - -
60D THR* 4.4 7.4 + - - +
62D THR* 5.7 1.3 - - - +
94D ILE* 4.0 31.1 - - + +
111D ASN* 2.9 27.0 + - - +
112D MSE 2.8 13.6 + - + +
114D GLY* 1.3 71.7 - - - +
116D GLN* 1.3 67.6 + - - +
117D VAL* 3.1 4.2 + - + +
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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