Contacts of the helix formed by residues 130 - 144 (chain A) in PDB entry 1LD7
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 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR* 3.5 29.4 + - - +
103A PHE* 5.5 1.2 - - - -
124A ILE* 5.7 0.2 - - - +
127A ASN* 3.2 29.9 + - - +
128A ALA 3.3 0.6 - - - -
129A ALA* 1.3 75.4 - - - +
131A TYR* 1.3 58.7 + - - +
132A THR* 3.0 14.1 + - - -
133A VAL* 3.0 37.2 + - + +
134A TRP* 3.2 17.1 + - - -
597B ASP* 4.7 3.8 + - - -
598B ALA* 3.9 11.3 - - - +
646B GLN* 4.3 21.6 + - - +
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Residues in contact with TYR 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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129A ALA 3.0 14.1 + - - -
130A ASN* 1.3 68.1 - - - +
132A THR* 1.3 89.6 + - - +
133A VAL 3.3 0.2 - - - -
134A TRP* 3.7 5.6 - - - +
135A HIS* 3.0 23.7 + - - +
167A GLN* 3.9 25.8 - - + +
598B ALA* 3.9 24.9 - - + -
641B GLY* 3.4 2.1 - - - -
642B GLY 2.9 23.1 + - - -
646B GLN* 3.9 3.0 + - - -
647B TYR* 2.7 36.5 + + + -
648B PRO 4.0 2.2 - - - -
649B HIS* 3.5 42.1 - + + +
652B PRO* 4.9 1.6 - - + -
694B HIS* 3.9 30.9 - - + +
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Residues in contact with THR 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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103A PHE* 4.0 8.5 - - + -
107A LEU* 3.8 24.7 - - + -
130A ASN* 3.0 11.5 + - - -
131A TYR* 1.3 90.2 - - - +
133A VAL* 1.3 63.0 + - - +
135A HIS* 3.4 3.6 + - - +
136A PHE* 3.1 22.0 + - - +
646B GLN* 3.7 12.7 + - + +
647B TYR* 2.9 54.4 + - + +
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 3.9 18.4 - - + +
103A PHE* 3.6 31.4 - - + -
120A THR* 3.7 23.6 - - - +
123A ALA* 3.9 8.5 - - + -
124A ILE* 3.7 26.7 - - + +
130A ASN* 3.0 34.6 + - + +
132A THR* 1.3 78.1 - - - +
134A TRP* 1.3 56.7 + - - +
136A PHE* 3.2 3.1 + - - +
137A ARG* 2.8 27.0 + - - +
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Residues in contact with TRP 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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124A ILE* 3.4 46.4 - - + +
128A ALA* 2.8 24.9 + - + +
130A ASN 3.2 22.3 + - - -
131A TYR* 3.7 7.6 - - - +
132A THR 3.3 0.6 - - - -
133A VAL* 1.3 80.3 - - - +
135A HIS* 1.3 61.7 + - - +
137A ARG* 3.3 8.0 + - - +
138A ARG* 3.0 42.6 + - - +
154A TYR* 4.1 12.8 - + - -
155A ILE* 3.7 18.4 - - + -
158A ILE* 4.4 3.4 - - + -
167A GLN* 3.5 28.6 - - + +
168A VAL* 3.7 19.5 - - + -
171A HIS* 3.5 47.5 + + + -
694B HIS* 6.5 0.2 - - + -
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Residues in contact with HIS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR 3.0 16.7 + - - +
132A THR 3.6 4.3 - - - +
134A TRP* 1.3 76.6 - - - +
136A PHE* 1.3 58.9 + - - +
138A ARG* 3.1 23.8 + - + +
139A VAL* 2.9 48.1 + - + +
647B TYR* 3.2 38.0 + + + -
694B HIS* 5.1 4.3 - - + +
695B VAL* 4.1 34.7 + - + +
696B GLY* 4.8 6.0 - - - -
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Residues in contact with PHE 136 (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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103A PHE* 3.9 23.3 - + + -
106A VAL* 3.6 32.8 - - + -
107A LEU* 3.6 26.2 - - + -
110A ASP* 3.9 22.7 - - - -
111A GLU 3.5 21.5 - - - -
112A ARG* 4.7 7.4 - - - -
116A ALA* 4.4 1.3 - - + -
120A THR* 4.2 5.4 - - + -
132A THR 3.1 11.1 + - - +
133A VAL 3.7 6.1 - - - +
135A HIS* 1.3 79.4 - - - +
137A ARG* 1.3 66.4 + - - +
139A VAL* 3.0 15.7 + - + +
140A LEU* 2.9 51.0 + - + +
647B TYR* 4.6 4.7 - - - +
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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
----------------------------------------------------------
117A PHE* 3.4 37.6 + - + -
120A THR* 2.8 43.9 + - - +
121A ARG* 3.8 22.4 - - - +
124A ILE* 3.7 20.2 - - + -
133A VAL 2.8 17.3 + - - +
134A TRP* 3.6 16.2 - - + +
136A PHE* 1.3 75.9 - - - +
138A ARG* 1.3 57.2 + - - +
140A LEU* 3.2 7.2 + - - +
141A LEU* 2.8 28.8 + - + +
151A GLU* 2.7 42.1 + - - +
154A TYR* 3.5 27.1 - - - -
171A HIS* 4.6 1.6 - - + -
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Residues in contact with ARG 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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134A TRP* 3.0 34.9 + - - +
135A HIS* 3.2 30.3 + - + +
137A ARG* 1.3 79.1 - - - +
139A VAL* 1.3 61.9 + - + +
141A LEU* 3.2 19.3 + - - +
142A LYS* 3.3 10.0 + - - +
167A GLN* 4.4 3.2 + - - +
170A HIS* 3.9 11.9 + - - -
171A HIS* 3.2 48.9 + - + +
174A VAL* 4.0 23.1 - - + +
178A TRP* 3.5 31.9 - - + -
694B HIS* 5.0 6.1 - - - -
696B GLY* 3.3 25.3 + - - -
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASP* 5.3 0.4 - - - +
112A ARG* 3.6 41.7 - - - +
135A HIS* 2.9 43.8 + - + +
136A PHE* 3.0 17.9 + - + +
138A ARG* 1.3 75.7 - - + +
140A LEU* 1.3 58.3 + - - +
142A LYS* 3.4 6.5 + - - +
143A SER* 3.0 31.4 + - - -
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Residues in contact with LEU 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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111A GLU 3.8 7.0 - - - +
112A ARG* 3.3 43.3 - - + -
113A SER 3.8 7.2 - - - +
116A ALA 3.8 4.3 - - - +
117A PHE* 3.5 42.2 - - + +
120A THR* 4.1 6.1 - - + -
136A PHE* 2.9 41.3 + - + +
137A ARG* 3.5 6.5 - - - +
139A VAL* 1.3 73.6 - - - +
141A LEU* 1.3 65.9 + - - +
142A LYS 3.1 1.8 - - - -
143A SER* 4.3 2.5 - - - -
144A LEU* 2.8 36.6 + - + +
146A LYS* 4.7 0.4 - - - -
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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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117A PHE* 3.8 18.8 - - + -
137A ARG 2.8 17.5 + - - +
138A ARG* 3.2 9.6 + - - +
140A LEU* 1.3 74.5 - - - +
142A LYS* 1.3 59.2 + - - +
145A GLN* 3.2 5.0 + - - -
146A LYS* 2.9 56.0 + - + +
148A LEU* 4.4 9.4 - - + +
151A GLU* 3.6 43.3 - - + +
171A HIS* 3.7 20.0 - - + -
175A LEU* 4.1 3.4 - - + -
178A TRP* 4.0 24.5 - - + -
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Residues in contact with LYS 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 ARG 3.3 8.0 + - - +
139A VAL* 3.8 7.9 - - - +
140A LEU 3.1 0.6 - - - -
141A LEU* 1.3 78.6 - - - +
143A SER* 1.3 66.8 + - - +
145A GLN* 3.0 19.7 + - - +
178A TRP* 4.9 15.2 - - + -
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 2.7 53.9 + - - -
139A VAL 3.0 16.2 + - - -
140A LEU* 3.3 4.5 + - - -
142A LYS* 1.3 78.6 - - - +
144A LEU* 1.3 62.2 + - - +
145A GLN* 3.4 6.9 + - - +
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Residues in contact with LEU 144 (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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112A ARG 3.6 25.1 - - - +
113A SER* 3.5 29.2 - - - +
114A GLU* 3.8 11.4 - - + +
117A PHE* 3.8 19.7 - - + -
140A LEU* 2.8 26.4 + - + +
143A SER* 1.3 77.8 - - - +
145A GLN* 1.3 71.6 + - - +
146A LYS* 3.2 22.5 + - + +
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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