Contacts of the helix formed by residues 127 - 143 (chain A) in PDB entry 1DIZ
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 1.3 78.7 - - - +
128A VAL* 1.3 64.6 + - - +
129A ALA* 3.5 9.7 + - - +
130A MET* 3.0 18.9 + - - +
131A ALA* 3.0 21.4 + - - +
7E A 3.3 33.3 + - - -
8E NRI 3.4 4.3 - - - -
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Residues in contact with VAL 128 (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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21A ALA* 4.0 16.6 - - + +
22A ARG* 3.8 49.3 - - + +
126A VAL 4.0 0.2 + - - -
127A SER* 1.3 73.5 - - - +
129A ALA* 1.3 61.3 + - - +
131A ALA* 4.2 6.2 - - + +
132A ALA* 3.4 21.5 + - - +
8E NRI 3.3 20.8 + - - +
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Residues in contact with ALA 129 (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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21A ALA 5.4 1.8 - - - -
127A SER* 3.0 9.6 + - - +
128A VAL* 1.3 80.4 - - - +
130A MET* 1.3 56.8 + - - +
132A ALA* 3.4 7.0 - - - +
133A LYS* 3.1 23.6 + - - +
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Residues in contact with MET 130 (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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126A VAL* 3.3 40.8 - - + -
127A SER* 3.0 11.0 + - - +
129A ALA* 1.3 74.5 - - - +
131A ALA* 1.3 60.7 + - - +
132A ALA 3.1 2.0 - - - -
133A LYS* 3.2 7.4 + - + +
134A LEU* 2.8 51.6 + - + +
173A GLY 4.2 15.5 - - - +
7E A 5.7 0.9 - - - -
19F T 3.5 12.3 - - - +
20F C 3.4 46.9 - - - +
21F A 5.1 5.6 - - - +
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Residues in contact with ALA 131 (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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119A ARG 5.6 0.2 - - - +
122A LEU* 3.2 27.9 - - + +
123A GLY* 3.9 12.3 - - - -
126A VAL* 3.5 6.7 - - + +
127A SER 3.0 15.1 + - - +
128A VAL* 4.2 7.0 - - - +
130A MET* 1.3 76.9 - - - +
132A ALA* 1.3 57.2 + - - +
134A LEU* 3.6 3.7 - - - +
135A THR* 2.9 37.1 + - - +
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Residues in contact with ALA 132 (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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21A ALA 4.3 13.2 - - - +
22A ARG* 4.8 9.9 - - - +
23A ALA 4.6 14.7 - - - +
24A VAL* 5.0 3.3 - - - +
128A VAL 3.4 17.7 + - - +
129A ALA* 3.4 7.9 - - - +
131A ALA* 1.3 77.0 - - - +
133A LYS* 1.3 65.1 + - - +
135A THR* 4.0 5.5 - - - -
136A ALA* 3.0 23.2 + - - +
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Residues in contact with LYS 133 (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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129A ALA 3.1 14.4 + - - +
130A MET* 3.2 11.6 + - + +
132A ALA* 1.3 75.7 - - - +
134A LEU* 1.3 67.6 + - + +
136A ALA* 3.2 7.4 + - - +
137A ARG* 2.9 40.3 + - - +
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Residues in contact with LEU 134 (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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122A LEU* 4.0 35.4 - - + +
126A VAL* 4.7 9.9 - - + -
130A MET* 2.8 54.7 + - + +
131A ALA* 3.6 5.2 - - - +
133A LYS* 1.3 78.1 - - + +
135A THR* 1.3 58.4 + - - +
137A ARG* 3.0 25.5 + - - +
138A VAL* 2.9 30.5 + - - +
172A LEU* 5.1 3.5 - - + +
173A GLY 4.5 13.2 - - - +
174A MET* 4.5 25.5 - - + +
175A PRO* 6.1 0.7 - - + -
178A ARG* 6.2 2.0 - - + +
20F C 6.2 0.7 - - - -
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Residues in contact with THR 135 (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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24A VAL* 3.3 28.7 - - + -
118A VAL* 5.3 0.7 - - + -
119A ARG* 4.5 17.8 - - + +
122A LEU* 3.4 25.2 - - + +
131A ALA* 2.9 20.5 + - - +
132A ALA* 4.0 2.9 - - - -
134A LEU* 1.3 74.3 - - - +
136A ALA* 1.3 62.9 + - - +
138A VAL* 3.4 3.1 + - + +
139A ALA* 2.9 22.0 + - - +
155A PHE* 3.5 28.0 - - + -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.6 19.5 - - + +
25A SER* 4.5 15.7 - - - +
132A ALA 3.0 18.8 + - - +
133A LYS* 3.4 7.6 - - - +
135A THR* 1.3 76.4 - - - +
137A ARG* 1.3 58.7 + - + +
139A ALA* 3.1 1.4 + - - +
140A GLN* 2.8 42.2 + - - +
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Residues in contact with ARG 137 (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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133A LYS* 2.9 30.4 + - - +
134A LEU* 3.4 20.6 - - - +
136A ALA* 1.3 78.0 - - + +
138A VAL* 1.3 62.2 + - - +
140A GLN* 3.5 5.2 + - - +
141A LEU* 3.1 25.3 + - - +
172A LEU* 2.7 57.4 + - + +
173A GLY* 4.3 5.7 - - - -
20F C 5.3 9.3 + - - -
21F A 5.7 3.2 + - - -
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Residues in contact with VAL 138 (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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118A VAL* 5.1 9.9 - - + -
122A LEU* 4.0 11.4 - - + -
134A LEU 2.9 19.0 + - - +
135A THR* 3.8 6.7 - - + +
137A ARG* 1.3 74.2 - - - +
139A ALA* 1.3 58.7 + - - +
141A LEU 3.4 0.2 + - - -
142A TYR* 2.9 42.6 + - + +
155A PHE* 5.7 1.3 - - + -
156A PRO* 4.0 14.4 - - + -
161A LEU* 4.1 16.2 - - + -
169A LEU* 4.0 9.9 - - + -
172A LEU* 4.1 7.9 - - + -
174A MET* 3.7 29.6 - - + -
182A LEU* 4.6 4.0 - - + -
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Residues in contact with ALA 139 (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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24A VAL* 4.1 17.0 - - + -
27A VAL* 4.3 12.1 - - + -
135A THR 2.9 17.8 + - - +
136A ALA 3.5 4.3 - - - +
138A VAL* 1.3 75.3 - - - +
140A GLN* 1.3 63.6 + - - +
143A GLY 2.7 27.7 + - - -
153A ILE* 3.0 15.2 - - + +
155A PHE* 4.8 3.1 - - + -
156A PRO* 3.7 22.2 - - + -
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Residues in contact with GLN 140 (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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25A SER* 3.7 23.6 + - - -
26A SER* 3.5 20.1 + - - -
136A ALA* 2.8 33.6 + - - +
137A ARG* 4.0 6.1 - - - +
139A ALA* 1.3 75.5 - - - +
141A LEU* 1.3 59.3 + - - +
143A GLY 4.8 2.3 + - - +
145A ARG* 5.5 9.9 + - - +
153A ILE* 3.9 11.1 - - + +
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Residues in contact with LEU 141 (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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137A ARG 3.1 16.5 + - - +
138A VAL 3.8 2.5 - - - +
139A ALA 3.1 0.8 - - - -
140A GLN* 1.3 80.2 - - - +
142A TYR* 1.3 95.0 + - + +
143A GLY 5.1 0.8 - - - +
160A ARG* 4.0 10.4 + - - -
168A ALA* 4.2 8.7 - - + +
172A LEU* 3.7 29.8 - - + -
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Residues in contact with TYR 142 (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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138A VAL* 2.9 28.2 + - + +
141A LEU* 1.3 105.3 - - + +
143A GLY* 1.3 63.3 + - - +
144A GLU* 5.0 1.4 - - - +
156A PRO* 3.9 20.8 - - + +
157A THR 5.0 0.3 + - - -
160A ARG* 3.1 55.5 + - + +
161A LEU* 4.1 6.5 - - + -
164A ALA* 3.5 32.7 - - + +
165A ASP 4.2 0.5 + - - -
168A ALA* 3.5 27.9 - - - +
169A LEU* 3.2 31.8 - - + +
172A LEU* 4.7 0.2 - - + -
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Residues in contact with GLY 143 (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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139A ALA 2.7 23.1 + - - -
140A GLN 4.6 1.8 - - - +
141A LEU 5.1 1.4 - - - -
142A TYR* 1.3 78.1 + - - +
144A GLU* 1.3 63.3 + - - +
153A ILE* 3.8 6.6 - - - +
154A CYS 3.3 17.3 - - - -
155A PHE 4.6 0.2 - - - -
156A PRO* 3.9 10.2 - - - +
160A ARG* 4.0 6.6 + - - -
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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