Contacts of the helix formed by residues 141 - 154 (chain A) in PDB entry 4ND1
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 PRO 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ARG 3.9 12.6 - - - +
110A SER* 4.1 10.8 - - - +
113A LEU* 3.6 53.4 - - + +
140A ASN* 1.4 80.2 - - + +
142A LEU* 1.3 66.0 + - - +
143A ASP 3.2 2.8 + - - -
144A VAL* 3.2 3.2 + - + -
145A MET* 3.0 28.0 + - + +
325A ILE* 4.4 6.3 - - + -
404A GOL 3.4 28.9 - - - +
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Residues in contact with LEU 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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137A CYS* 3.3 29.8 - - - +
138A ILE* 3.7 14.4 - - - +
139A THR 3.4 8.5 - - - +
140A ASN* 2.9 19.5 + - - +
141A PRO* 1.3 68.7 - - - +
143A ASP* 1.3 64.6 + - - +
145A MET* 3.2 3.6 + - - +
146A VAL* 2.9 34.6 + - + +
162A GLY* 3.9 7.9 - - - -
163A MET 3.4 17.3 - - - +
164A ALA* 3.7 16.6 - - + -
195A HIS* 4.0 13.2 - - + -
272A SER* 3.4 31.0 - - - -
401A NAD 3.8 4.0 - - - +
404A GOL 3.3 3.2 + - - -
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Residues in contact with ASP 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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141A PRO 3.2 0.2 + - - -
142A LEU* 1.3 82.2 - - - +
144A VAL* 1.3 63.6 + - - +
146A VAL* 3.5 3.2 + - - +
147A SER* 3.2 22.0 + - - -
164A ALA* 5.5 0.7 - - - +
193A GLY 4.1 0.5 - - - +
194A GLY* 3.3 8.9 - - - -
195A HIS* 2.6 37.0 + - - +
272A SER* 2.8 28.6 + - - +
286A TYR* 4.0 17.3 - - - +
287A MET* 3.5 12.9 - - - -
288A GLY* 3.6 5.9 + - - -
322A VAL* 4.5 10.8 - - + -
404A GOL 3.4 12.3 + - - +
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Residues in contact with VAL 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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113A LEU* 3.7 26.2 - - + -
141A PRO* 3.2 6.5 + - + +
143A ASP* 1.3 74.3 - - - +
145A MET* 1.3 61.2 + - + +
147A SER* 3.4 6.6 + - - -
148A HIS* 2.9 28.6 + - - +
322A VAL* 3.8 25.4 - - + +
325A ILE* 3.8 24.5 - - + -
326A SER* 3.9 20.0 - - - +
329A LEU* 3.7 16.8 - - + -
404A GOL 3.6 10.9 + - - +
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Residues in contact with MET 145 (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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113A LEU* 3.7 37.9 - - + +
116A ASN* 3.7 16.4 - - - -
117A ALA* 3.6 31.2 - - + -
120A LEU* 3.2 31.3 - - + +
137A CYS* 4.1 3.4 - - - -
139A THR* 3.5 15.9 - - + +
140A ASN 3.5 18.2 - - - +
141A PRO* 3.0 18.1 + - + +
142A LEU 3.5 7.4 - - - +
144A VAL* 1.3 79.5 - - - +
146A VAL* 1.3 55.7 + - - +
148A HIS* 3.7 3.9 - - + +
149A PHE* 2.9 24.1 + - - +
329A LEU* 4.2 6.3 - - + -
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Residues in contact with VAL 146 (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 CYS* 3.7 17.5 - - + -
142A LEU* 2.9 26.4 + - + +
143A ASP 3.7 6.5 - - - +
145A MET* 1.3 77.4 - - - +
147A SER* 1.3 62.9 + - - +
149A PHE* 3.2 5.7 + - - +
150A GLN* 3.0 22.5 + - - +
160A VAL* 4.1 6.8 - - + +
161A CYS* 3.8 16.8 - - - -
162A GLY* 3.4 29.4 - - - +
272A SER* 4.2 2.7 - - - +
286A TYR* 3.4 35.9 - - + -
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Residues in contact with SER 147 (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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143A ASP 3.2 10.9 + - - -
144A VAL* 3.7 10.1 - - - -
146A VAL* 1.3 78.7 - - - +
148A HIS* 1.3 63.2 + - - +
150A GLN* 3.4 3.6 + - - +
151A LYS* 3.0 24.7 + - - +
286A TYR* 3.6 29.5 + - - -
326A SER* 5.6 4.2 + - - -
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Residues in contact with HIS 148 (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 ALA* 3.1 35.1 + - + -
120A LEU* 4.1 14.1 - - + -
121A ASP* 2.8 30.4 + - - -
144A VAL 2.9 17.4 + - - +
145A MET* 3.7 6.5 - - + +
146A VAL 3.3 0.2 - - - -
147A SER* 1.3 75.6 - - - +
149A PHE* 1.3 58.3 + - - +
151A LYS* 3.4 11.2 + - - +
152A VAL* 3.0 43.0 + - + +
329A LEU* 3.9 26.5 - - + +
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Residues in contact with PHE 149 (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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96A ILE* 3.6 28.7 - - + -
120A LEU* 4.0 25.8 - - + -
123A VAL* 4.1 2.9 - - + -
124A ALA* 3.5 28.7 - - + -
127A VAL* 4.2 18.2 - - + -
135A VAL* 3.7 26.7 - - + -
137A CYS* 5.6 3.1 - - + -
145A MET 2.9 17.6 + - - +
146A VAL* 3.6 6.5 - - - +
148A HIS* 1.3 77.9 - - - +
150A GLN* 1.3 55.8 + - - +
152A VAL* 4.9 2.0 - - - -
153A SER* 2.7 61.1 + - - -
155A LEU* 4.5 1.8 - - + -
160A VAL* 3.8 19.5 - - + -
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Residues in contact with GLN 150 (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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146A VAL 3.0 15.8 + - - +
147A SER 3.8 4.6 - - - +
149A PHE* 1.3 80.2 - - - +
151A LYS* 1.3 62.4 + - - +
153A SER* 3.5 6.0 + - - -
154A GLY* 2.9 30.1 + - - -
155A LEU 2.8 26.8 + - - +
156A PRO* 4.3 0.6 - - - +
157A HIS* 3.4 41.2 + - + +
160A VAL* 4.1 10.3 - - + -
286A TYR* 3.4 29.9 - - + +
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Residues in contact with LYS 151 (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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147A SER* 3.0 18.4 + - - +
148A HIS* 3.6 12.3 - - - +
149A PHE 3.2 0.2 - - - -
150A GLN* 1.3 84.9 + - - +
152A VAL* 1.3 65.9 - - + +
154A GLY* 3.7 6.8 + - - -
330A ASP* 4.5 14.6 + - - -
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Residues in contact with VAL 152 (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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120A LEU 5.4 0.2 - - - +
121A ASP* 3.4 33.4 - - + +
124A ALA* 3.8 18.8 - - + -
125A GLU* 4.2 17.2 - - - +
128A LYS* 5.1 6.2 + - - +
148A HIS* 3.0 32.4 + - + +
149A PHE* 4.2 2.0 - - - +
151A LYS* 1.3 81.7 - - + +
153A SER* 1.3 62.5 + - - +
154A GLY 3.6 0.3 + - - -
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Residues in contact with SER 153 (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 ALA* 3.9 23.5 - - - +
128A LYS* 3.5 27.0 - - - +
149A PHE* 2.7 49.9 + - - -
150A GLN* 3.5 4.2 + - - -
152A VAL* 1.3 75.0 - - - +
154A GLY* 1.3 62.7 + - - +
155A LEU* 3.2 29.8 + - - +
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Residues in contact with GLY 154 (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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128A LYS* 5.8 1.3 - - - -
150A GLN* 2.9 16.9 + - - -
151A LYS 3.7 4.9 + - - -
152A VAL 3.4 3.0 + - - -
153A SER* 1.3 77.4 - - - +
155A LEU* 1.3 64.9 + - - +
156A PRO* 3.8 1.6 - - - +
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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