Contacts of the helix formed by residues 112 - 131 (chain B) 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 LEU 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B SER* 4.3 3.6 - - - +
100B ILE* 3.9 27.7 - - + +
101B PRO 5.1 0.7 - - - +
102B GLY 4.2 17.0 - - - +
105B PRO* 4.1 25.1 - - + -
109B ARG 3.9 8.3 - - - +
110B SER 3.0 1.2 + - - -
111B GLU* 1.3 82.2 - - + +
113B LEU* 1.3 63.5 + - - +
114B PHE 3.3 1.9 + - - -
115B GLY* 3.5 3.7 + - - -
116B ASN* 3.2 46.4 + - - +
140B ASN* 4.0 12.3 - - + +
141B PRO* 4.4 1.8 - - - -
401B NAD 3.9 25.4 - - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B SER* 3.0 16.7 + - - +
111B GLU 3.3 2.6 + - - -
112B LEU* 1.3 76.7 - - - +
114B PHE* 1.3 75.1 + - + +
117B ALA* 3.1 29.3 + - - +
141B PRO* 3.9 12.7 - - + +
144B VAL* 4.0 21.1 - - + -
145B MET* 3.8 11.8 - - + +
325B ILE* 3.9 39.0 - - + +
328B VAL* 4.0 23.3 - - + -
329B LEU* 4.1 17.9 - - + +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLU 5.3 0.6 + - - -
112B LEU 3.5 0.2 - - - -
113B LEU* 1.3 91.0 - - + +
115B GLY* 1.3 69.1 + - - +
117B ALA* 3.4 5.8 + - + +
118B ARG* 3.2 20.3 + - - +
328B VAL* 3.8 36.3 - - + -
329B LEU* 4.3 22.7 - - + -
331B ASN 5.0 0.7 - - - -
332B ALA* 5.2 3.8 - - + -
333B PRO* 4.8 20.2 - - + -
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE* 4.1 23.8 - - - +
112B LEU 3.5 5.2 + - - -
114B PHE* 1.3 80.4 - - - +
116B ASN* 1.3 63.0 + - - +
118B ARG* 3.2 6.5 + - - +
119B ILE* 3.2 22.9 + - - +
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Residues in contact with ASN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B SER* 3.3 20.1 + - - -
100B ILE* 2.8 32.1 + - - +
112B LEU* 3.2 32.0 + - - +
115B GLY* 1.3 71.8 - - - +
117B ALA* 1.3 60.5 + - - +
119B ILE* 3.3 5.7 + - - +
120B LEU* 2.9 34.7 + - - +
139B THR* 3.3 23.3 - - + +
140B ASN 2.7 25.4 + - - +
145B MET* 3.8 7.0 - - - -
401B NAD 3.8 0.4 + - - -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU 3.1 21.2 + - - +
114B PHE* 3.6 5.8 - - + +
115B GLY 3.3 0.2 - - - -
116B ASN* 1.3 77.2 - - - +
118B ARG* 1.3 59.9 + - - +
120B LEU 3.5 0.9 + - - -
121B ASP* 3.2 28.4 + - - +
145B MET* 3.7 15.4 - - + -
148B HIS* 3.3 16.7 + - + +
329B LEU* 3.6 27.4 - - + -
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE 3.2 9.9 + - - +
115B GLY* 3.2 10.1 + - - +
117B ALA* 1.3 76.5 - - - +
119B ILE* 1.3 65.5 + - - +
121B ASP* 3.2 27.0 + - + +
122B SER* 3.7 4.9 + - - -
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA* 3.6 33.2 - - + +
99B SER* 3.5 8.3 - - - -
100B ILE* 3.5 40.2 - - + +
115B GLY 3.2 8.8 + - - +
116B ASN* 3.5 16.6 - - - +
118B ARG* 1.3 76.6 - - + +
120B LEU* 1.3 63.5 + - + +
122B SER* 2.7 26.3 + - - -
123B VAL* 3.3 6.8 + - + +
401B NAD 3.6 32.8 - - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 4.2 14.1 - - + -
98B ALA 4.1 5.8 - - - +
116B ASN 2.9 21.6 + - - +
117B ALA* 3.9 4.7 - - - +
118B ARG 3.3 0.2 - - - -
119B ILE* 1.3 78.7 - - + +
121B ASP* 1.3 60.3 + - - +
123B VAL* 3.7 6.6 - - + +
124B ALA* 2.8 31.4 + - - +
137B CYS* 4.1 12.8 - - - -
139B THR* 3.8 28.0 - - + +
145B MET* 3.6 46.7 - - + +
148B HIS* 4.5 9.4 - - + -
149B PHE* 4.1 18.2 - - + -
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA 3.2 12.5 + - - +
118B ARG* 3.3 19.5 - - + +
119B ILE 3.2 0.6 - - - -
120B LEU* 1.3 76.3 - - - +
122B SER* 1.3 58.1 + - - +
124B ALA* 3.3 4.7 + - - +
125B GLU* 3.0 25.5 + - - +
148B HIS* 2.6 30.7 + - - -
152B VAL* 3.5 26.0 - - + +
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 4.0 15.0 + - - -
118B ARG 3.7 4.1 + - - -
119B ILE* 2.7 21.6 + - - -
121B ASP* 1.3 76.6 - - - +
123B VAL* 1.3 60.6 + - - +
125B GLU* 3.3 8.5 + - - +
126B GLY* 2.9 24.4 + - - -
401B NAD 4.0 14.6 + - - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 3.8 31.0 - - + -
85B TYR* 3.3 19.8 - - + +
96B ILE* 3.8 36.6 - - + -
98B ALA* 4.5 1.3 - - + -
119B ILE* 3.3 26.2 + - + +
120B LEU* 3.7 12.3 - - - +
122B SER* 1.3 75.9 + - - +
124B ALA* 1.3 58.7 + - - +
126B GLY* 3.1 2.3 + - - -
127B VAL* 2.9 33.8 + - + +
149B PHE* 4.0 3.1 - - + -
401B NAD 4.7 1.6 - - - +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU 2.8 18.5 + - - +
121B ASP 3.5 4.9 - - - +
123B VAL* 1.3 76.9 - - - +
125B GLU* 1.3 56.2 + - - +
127B VAL* 4.0 0.9 - - - +
128B LYS* 3.0 31.6 + - - +
149B PHE* 3.4 21.2 - - + +
152B VAL* 3.7 25.4 - - + -
153B SER* 3.8 21.8 - - - +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASP 3.0 13.8 + - - +
122B SER* 3.5 12.3 - - - +
124B ALA* 1.3 74.1 - - - +
126B GLY* 1.3 64.5 + - - +
128B LYS* 3.4 13.6 + - - +
129B LYS* 3.1 38.1 + - - +
152B VAL* 5.2 1.2 - - + +
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Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TYR* 3.8 34.8 - - - -
88B ILE* 4.3 1.6 - - - +
122B SER 2.9 12.4 + - - -
123B VAL 3.1 3.5 + - - -
125B GLU* 1.3 77.8 - - - +
127B VAL* 1.3 55.7 + - - +
129B LYS* 4.9 0.4 - - - -
130B TYR* 3.1 38.7 + - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 5.5 0.2 - - + -
85B TYR* 5.6 0.2 - - + -
88B ILE* 4.2 10.8 - - + -
94B VAL* 4.0 27.4 - - + -
123B VAL* 2.9 24.9 + - + +
124B ALA 4.0 0.7 - - - +
126B GLY* 1.3 73.0 - - - +
128B LYS* 1.3 67.5 + - - +
131B CYS* 3.0 53.4 + - - +
132B PRO 3.2 0.2 - - - -
135B VAL* 4.3 6.5 - - + -
149B PHE* 4.0 20.2 - - + -
155B LEU* 3.8 27.4 - - + -
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ALA 3.0 19.2 + - - +
125B GLU* 3.8 15.9 + - - +
127B VAL* 1.3 78.9 - - - +
129B LYS* 1.3 63.5 + - - +
132B PRO* 3.5 22.7 - - + +
152B VAL 4.6 9.8 + - - +
153B SER* 3.5 26.8 + - - +
154B GLY* 5.9 0.6 - - - -
155B LEU* 4.7 5.1 - - + +
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLU* 3.1 32.5 + - + +
126B GLY* 4.0 2.9 - - - +
128B LYS* 1.3 80.2 - - - +
130B TYR* 1.3 102.9 + - + +
132B PRO* 4.4 4.0 - - - +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASP* 5.1 2.1 + - - -
85B TYR* 3.4 33.9 - - + +
86B ALA* 3.6 39.3 + - + +
88B ILE* 4.3 2.9 - - + -
89B SER* 3.4 29.7 + - - +
90B GLY 3.5 4.0 + - - -
126B GLY* 3.1 24.7 + - - +
129B LYS* 1.3 122.8 + - + +
131B CYS* 1.3 62.0 + - - +
132B PRO* 3.7 3.7 - - - +
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Residues in contact with CYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ILE* 3.5 39.0 - - - +
90B GLY* 3.9 2.9 - - - +
91B SER* 3.9 20.6 - - - +
94B VAL* 3.6 30.1 - - - -
127B VAL* 3.0 21.8 + - - +
130B TYR* 1.3 80.3 - - - +
132B PRO* 1.3 68.0 - - - +
133B ALA* 3.2 12.6 + - - +
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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
------------------------------------------------------------
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