Contacts of the helix formed by residues 107 - 123 (chain D) in PDB entry 4B94
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 GLU 107 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D GLN 3.6 1.2 + - - -
106D ASN* 1.3 70.5 + - - +
108D SER* 1.3 59.5 + - - +
110D ALA* 3.3 4.1 + - - +
111D ARG* 3.0 50.4 + - - +
142D PHE* 3.6 37.8 - - + -
144D PHE* 4.2 17.1 - - + -
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Residues in contact with SER 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D PRO* 3.8 26.0 - - - -
63D GLU* 3.6 21.3 + - - +
66D LEU* 3.9 10.6 - - - +
106D ASN* 2.9 9.9 + - - -
107D GLU* 1.3 73.7 - - - +
109D PHE* 1.3 60.4 + - - +
111D ARG* 2.7 32.6 + - - +
112D ILE* 3.0 31.4 + - - +
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Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.9 7.0 - - - -
62D PRO* 3.6 12.2 - - + +
95D ILE* 5.5 7.6 - - + -
98D LEU* 3.7 40.8 - - + -
100D PRO* 3.8 35.2 - - + -
103D TYR* 3.3 36.8 - + + -
106D ASN* 3.0 14.3 + - - +
108D SER* 1.3 74.3 - - - +
110D ALA* 1.3 63.7 + - - +
112D ILE* 3.2 8.5 + - + +
113D GLN* 3.0 63.6 + - + +
138D ASN* 4.2 6.3 - - + -
139D CYS* 3.4 12.3 - - - -
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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
----------------------------------------------------------
106D ASN 3.1 7.1 + - - +
107D GLU 3.3 9.2 + - - +
109D PHE* 1.3 76.7 - - - +
111D ARG* 1.4 56.0 + - - +
113D GLN* 3.4 4.7 + - - +
114D VAL* 3.0 33.4 + - - +
135D ALA* 5.2 0.4 - - - +
139D CYS* 3.8 21.7 - - + -
142D PHE* 3.7 26.0 - - + -
144D PHE* 3.6 17.3 - - + -
145D VAL* 3.9 4.9 - - + -
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Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LEU* 3.7 26.2 - - + +
107D GLU* 3.0 38.4 + - - +
108D SER* 2.7 41.3 + - - +
110D ALA* 1.4 71.9 - - - +
112D ILE* 1.3 59.9 + - - +
114D VAL* 4.0 1.2 - - - +
115D ARG* 2.9 39.4 + - + +
144D PHE* 3.6 24.2 - - + -
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Residues in contact with ILE 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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62D PRO* 3.5 28.5 - - + +
65D TRP* 3.8 12.1 - - + -
66D LEU* 3.9 17.5 - - + +
69D LEU* 4.1 7.4 - - + -
91D TYR* 3.6 22.7 - - + -
94D ALA* 4.2 11.2 - - + -
95D ILE* 3.9 24.2 - - + +
98D LEU* 3.8 25.4 - - + -
108D SER 3.0 16.9 + - - +
109D PHE* 3.2 10.5 + - + +
111D ARG* 1.3 76.1 - - - +
113D GLN* 1.3 57.6 + - + +
116D PHE* 3.0 28.4 + - - +
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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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130B ASP* 4.0 1.4 - - - +
95D ILE* 4.4 11.4 - - + -
109D PHE* 3.0 56.4 + - + +
110D ALA* 3.9 2.2 - - - +
112D ILE* 1.3 73.0 - - + +
114D VAL* 1.3 65.4 - - - +
116D PHE* 3.4 7.6 + - - +
117D ALA* 3.1 23.7 + - - +
131D TYR* 4.7 1.4 - - - +
134D MET* 3.9 19.3 - - + +
135D ALA* 3.8 24.7 - - + +
138D ASN* 2.8 30.1 + - - +
139D CYS* 3.3 16.6 - - - -
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Residues in contact with VAL 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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110D ALA 3.0 21.3 + - - +
111D ARG* 4.0 3.1 - - - +
113D GLN* 1.3 73.5 - - - +
115D ARG* 1.4 61.9 + - + +
117D ALA* 3.3 7.8 + - - +
118D GLU* 2.9 41.6 + - - +
132D PHE* 5.8 1.3 - - + -
135D ALA* 4.3 6.3 - - + -
144D PHE* 3.8 17.9 - - + -
145D VAL* 3.8 39.3 - - + +
148D SER* 3.4 26.7 - - - +
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Residues in contact with ARG 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PRO* 3.3 25.9 + - - +
79A LEU 2.8 32.9 + - - +
80A SER* 4.8 0.8 - - - +
66D LEU* 5.0 6.7 - - + -
70D LEU* 5.1 3.4 - - + -
73D GLU* 3.1 33.5 + - - -
91D TYR* 3.4 28.5 - - + +
111D ARG* 2.9 27.5 + - + +
112D ILE* 4.9 0.2 - - - -
114D VAL* 1.4 75.6 - - + +
116D PHE* 1.4 57.1 + - - +
118D GLU* 3.0 36.2 + - - +
119D LEU* 2.9 56.9 + - - +
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Residues in contact with PHE 116 (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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134B MET* 3.7 20.4 - - + -
137B ALA* 4.1 7.9 - - + -
138B ASN* 5.7 0.4 - - - -
88D ILE* 3.6 31.6 - - + +
91D TYR* 3.5 27.5 - - + -
92D SER* 4.0 13.5 - - - -
95D ILE* 3.7 20.4 - - + -
112D ILE 3.0 17.6 + - - +
113D GLN 3.7 4.5 - - - +
114D VAL 3.3 0.2 - - - -
115D ARG* 1.4 78.0 - - - +
117D ALA* 1.3 58.0 + - - +
119D LEU* 3.4 4.4 + - - +
120D LYS* 3.0 50.9 + - + +
131D TYR* 3.6 37.5 - + + -
134D MET* 4.6 3.4 - - + -
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Residues in contact with ALA 117 (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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113D GLN 3.1 13.2 + - - +
114D VAL* 3.6 8.7 - - - +
116D PHE* 1.3 76.6 - - - +
118D GLU* 1.4 58.3 + - - +
120D LYS* 3.3 4.4 + - - +
121D ALA* 2.9 27.9 + - - +
128D ALA* 4.2 0.9 - - - +
131D TYR* 3.7 17.9 - - + +
132D PHE* 3.6 49.9 - - + +
135D ALA* 5.4 0.4 - - + -
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Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 5.0 1.8 - - - +
80A SER* 4.4 17.0 - - - -
81A ASP* 4.8 2.4 + - - +
114D VAL* 2.9 30.5 + - - +
115D ARG* 3.0 32.1 + - - +
117D ALA* 1.4 73.0 - - - +
119D LEU* 1.3 63.9 + - - +
121D ALA* 3.5 11.3 + - - +
122D ILE* 3.5 20.8 + - - +
132D PHE* 4.1 10.1 - - + -
148D SER* 2.9 28.9 + - - +
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Residues in contact with LEU 119 (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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79A LEU* 4.0 12.3 - - + +
79D LEU* 6.0 0.7 - - + -
84D LEU* 3.7 22.0 - - + +
87D LEU* 4.0 18.8 - - + -
88D ILE* 3.7 25.6 - - + +
91D TYR* 3.7 37.0 - - + -
115D ARG* 2.9 46.1 + - - +
116D PHE* 3.8 3.8 - - + +
117D ALA 3.4 0.2 - - - -
118D GLU* 1.3 74.0 - - - +
120D LYS* 1.3 58.6 + - - +
122D ILE* 3.3 12.8 + - + +
123D GLN* 3.1 27.2 + - - +
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Residues in contact with LYS 120 (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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137B ALA* 3.7 20.1 + - - +
140B LYS* 5.7 1.0 - - - +
1198B GOL 2.9 28.1 + - - -
1199B MLI 4.3 0.4 + - - -
88D ILE* 3.9 10.5 - - + -
116D PHE* 3.0 44.6 + - + +
117D ALA* 3.3 10.1 + - - +
119D LEU* 1.3 73.0 - - - +
121D ALA* 1.3 58.4 + - - +
123D GLN* 2.9 19.3 + - - +
124D GLU* 2.7 64.7 + - - +
128D ALA* 3.9 5.8 - - + -
131D TYR* 3.9 27.4 - - + -
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Residues in contact with ALA 121 (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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81A ASP* 4.8 14.1 - - + +
117D ALA 2.9 13.6 + - - +
118D GLU* 3.6 13.5 - - - +
119D LEU 3.3 0.2 - - - -
120D LYS* 1.3 78.3 - - - +
122D ILE* 1.4 57.7 + - - +
125D PRO* 3.3 27.2 - - - +
128D ALA* 3.6 10.1 - - + +
132D PHE* 4.2 3.8 - - + -
152D PHE* 3.8 28.7 - - + -
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.0 24.0 - - + +
80A SER* 3.6 29.4 - - - +
81A ASP* 3.6 28.5 - - + +
84A LEU* 3.7 13.9 - - + -
122A ILE* 3.5 41.2 - - + +
123A GLN* 4.5 7.2 - - - +
84D LEU* 3.9 8.1 - - + -
118D GLU 3.5 13.4 + - - +
119D LEU* 3.3 17.4 + - + +
120D LYS 3.2 0.4 - - - -
121D ALA* 1.4 78.1 - - - +
123D GLN* 1.3 62.7 + - - +
124D GLU 3.6 0.2 + - - -
125D PRO* 4.1 5.5 - - - +
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Residues in contact with GLN 123 (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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122A ILE 5.1 5.3 - - - +
125A PRO* 5.9 3.3 - - - +
140B LYS* 5.6 2.0 + - - +
1198B GOL 3.5 18.3 + - - -
81D ASP* 5.9 2.2 - - - +
84D LEU* 4.2 11.4 - - + -
85D ASN* 2.7 29.1 + - - +
88D ILE* 3.5 19.6 - - + +
119D LEU 3.1 13.2 + - - +
120D LYS* 2.9 37.9 + - - +
122D ILE* 1.3 82.1 - - - +
124D GLU* 1.4 64.9 - - + +
125D PRO* 4.2 1.3 - - - +
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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
------------------------------------------------------------
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