Contacts of the helix formed by residues 112 - 131 (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 LEU 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A SER* 4.2 1.6 - - - +
100A ILE* 3.7 33.5 - - + +
101A PRO 4.8 0.4 - - - +
102A GLY 3.8 21.3 - - - +
105A PRO* 3.6 31.6 - - + -
109A ARG 3.3 12.1 + - - +
110A SER 3.0 1.0 - - - -
111A GLU* 1.3 79.5 - - + +
113A LEU* 1.3 64.8 + - - +
114A PHE 3.3 2.4 + - - -
115A GLY* 3.5 2.5 + - - -
116A ASN* 3.0 44.6 + - - +
140A ASN* 4.0 7.2 - - + +
141A PRO* 4.2 2.0 - - - -
401A NAD 3.8 23.1 - - - +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A SER* 3.0 18.7 + - - +
111A GLU 3.3 1.2 - - - -
112A LEU* 1.3 77.3 - - - +
114A PHE* 1.3 72.2 + - + +
117A ALA* 3.1 26.3 + - - +
141A PRO* 3.6 30.2 - - + +
144A VAL* 3.7 17.3 - - + -
145A MET* 3.7 15.6 - - + +
325A ILE* 3.6 28.9 - - + +
328A VAL* 3.9 23.3 - - + -
329A LEU* 3.9 19.3 - - + +
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A SER 6.0 0.2 - - - -
111A GLU 5.1 4.6 + - - -
112A LEU 3.4 0.4 - - - -
113A LEU* 1.3 85.2 - - + +
115A GLY* 1.3 67.1 + - - +
117A ALA* 3.6 5.6 + - - +
118A ARG* 3.5 22.9 + - - +
328A VAL* 3.7 32.1 - - + -
329A LEU* 4.5 5.6 - - + -
331A ASN 5.4 0.9 - - - -
332A ALA* 3.4 39.3 - - + -
333A PRO* 3.9 19.1 - - + -
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Residues in contact with GLY 115 (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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100A ILE* 3.9 26.1 - - - +
112A LEU 3.5 3.9 + - - -
113A LEU 3.5 0.2 - - - -
114A PHE* 1.3 80.2 - - - +
116A ASN* 1.3 64.6 + - - +
118A ARG* 3.1 19.0 + - - +
119A ILE* 3.2 13.7 + - - +
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Residues in contact with ASN 116 (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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98A ALA 4.6 0.2 - - - -
99A SER* 3.1 20.1 + - - -
100A ILE* 2.8 31.4 + - - +
112A LEU* 3.0 28.6 + - - +
115A GLY* 1.3 71.7 - - - +
117A ALA* 1.3 66.3 + - - +
119A ILE* 3.2 6.0 + - - +
120A LEU* 3.0 28.1 + - - +
139A THR* 3.2 21.1 - - + +
140A ASN 2.8 27.6 + - - +
145A MET* 3.7 7.0 - - - -
401A NAD 3.7 3.0 + - - -
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Residues in contact with ALA 117 (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 3.1 20.6 + - - +
114A PHE 3.6 5.8 - - - +
115A GLY 3.3 0.2 - - - -
116A ASN* 1.3 76.3 - - - +
118A ARG* 1.3 62.3 + - + +
120A LEU 3.3 1.4 + - - -
121A ASP* 3.2 13.5 + - - +
145A MET* 3.6 15.7 - - + -
148A HIS* 3.1 33.8 + - + +
329A LEU* 3.6 24.2 - - + -
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Residues in contact with ARG 118 (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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114A PHE 3.5 15.0 + - - +
115A GLY* 3.1 9.7 + - - +
117A ALA* 1.3 74.9 - - + +
119A ILE* 1.3 67.5 + - + +
121A ASP* 3.2 32.8 + - - +
122A SER* 3.4 6.1 + - - -
332A ALA* 5.7 4.8 - - - +
333A PRO 4.5 19.8 - - - -
405A GOL 5.4 5.5 + - - -
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Residues in contact with ILE 119 (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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98A ALA* 3.7 26.7 - - + +
99A SER* 3.6 9.4 - - - -
100A ILE* 3.5 39.3 - - + +
115A GLY 3.2 8.3 + - - +
116A ASN* 3.5 16.2 - - - +
118A ARG* 1.3 78.4 - - + +
120A LEU* 1.3 60.5 + - + +
122A SER* 3.0 22.7 + - - -
123A VAL* 3.0 16.5 + - + +
401A NAD 3.6 38.4 - - + +
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Residues in contact with LEU 120 (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* 4.1 16.8 - - + -
116A ASN 3.0 18.8 + - - +
117A ALA 3.7 4.9 - - - +
118A ARG 3.3 0.2 - - - -
119A ILE* 1.3 81.6 - - + +
121A ASP* 1.3 58.6 + - - +
123A VAL* 3.9 5.1 - - + +
124A ALA* 2.8 35.5 + - - +
137A CYS* 4.2 8.1 - - - -
139A THR* 4.0 24.9 - - + +
145A MET* 3.2 52.5 - - + +
148A HIS* 4.1 9.6 - - + -
149A PHE* 4.0 21.6 - - + +
152A VAL* 5.5 0.4 - - - -
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Residues in contact with ASP 121 (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 3.2 15.5 + - - +
118A ARG* 3.3 34.6 + - - +
119A ILE 3.2 0.4 - - - -
120A LEU* 1.3 74.8 - - - +
122A SER* 1.3 63.4 + - - +
124A ALA* 3.5 3.1 + - - +
125A GLU* 3.3 28.4 + - - +
148A HIS* 2.8 24.9 + - - -
152A VAL* 3.4 24.8 - - + +
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 4.3 15.5 + - - -
118A ARG 3.4 6.3 + - - -
119A ILE* 3.0 11.5 + - - -
121A ASP* 1.3 75.9 - - - +
123A VAL* 1.3 66.7 + - - +
125A GLU* 3.0 19.0 + - - +
126A GLY* 3.2 8.8 + - - -
401A NAD 5.1 9.5 + - - -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.8 25.6 - - + -
85A TYR* 3.4 21.4 + - + +
96A ILE* 3.6 39.9 - - + -
98A ALA* 4.7 0.7 - - + -
119A ILE* 3.0 29.2 + - + +
120A LEU* 3.4 10.3 + - - +
122A SER* 1.3 76.0 - - - +
124A ALA* 1.3 63.1 + - - +
126A GLY* 3.2 2.3 + - - -
127A VAL* 3.0 30.5 + - + +
149A PHE* 4.1 2.9 - - + -
401A NAD 4.7 2.2 - - - +
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Residues in contact with ALA 124 (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 2.8 22.3 + - - +
121A ASP 3.6 5.6 - - - +
123A VAL* 1.3 73.4 - - - +
125A GLU* 1.3 59.0 + - - +
127A VAL* 4.0 0.5 - - - +
128A LYS* 2.9 31.8 + - - +
149A PHE* 3.5 23.3 - - + -
152A VAL* 3.8 22.9 - - + -
153A SER* 3.9 18.9 - - - +
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Residues in contact with GLU 125 (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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121A ASP 3.3 15.5 + - - +
122A SER* 3.0 10.7 + - - +
124A ALA* 1.3 75.0 - - - +
126A GLY* 1.3 66.3 + - - +
128A LYS* 4.0 15.1 + - - +
129A LYS* 3.1 25.8 + - - +
152A VAL* 4.2 19.4 - - - +
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Residues in contact with GLY 126 (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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85A TYR* 4.0 33.4 - - - -
88A ILE* 4.4 1.5 - - - +
122A SER 3.2 6.4 + - - -
123A VAL 3.2 5.6 + - - -
125A GLU* 1.3 79.6 - - - +
127A VAL* 1.3 56.9 + - - +
129A LYS* 3.5 0.8 + - - -
130A TYR* 2.8 39.6 + - - +
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Residues in contact with VAL 127 (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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27A ILE* 5.5 0.4 - - + -
85A TYR* 5.5 0.7 - - + -
88A ILE* 4.3 10.3 - - + -
94A VAL* 4.1 25.8 - - + -
123A VAL* 3.0 29.6 + - + +
124A ALA 4.0 2.9 - - - +
126A GLY* 1.3 75.0 - - - +
128A LYS* 1.3 63.0 + - - +
131A CYS* 2.9 57.8 + - - +
133A ALA* 5.1 0.2 - - + -
135A VAL* 4.3 9.9 - - + -
149A PHE* 4.2 11.9 - - + -
155A LEU* 3.9 25.4 - - + -
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Residues in contact with LYS 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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124A ALA 2.9 20.1 + - - +
125A GLU* 4.0 17.0 + - - +
127A VAL* 1.3 77.0 - - - +
129A LYS* 1.3 60.5 + - - +
132A PRO* 3.6 23.7 - - + +
152A VAL 5.1 6.2 + - - +
153A SER* 3.5 28.4 + - - +
154A GLY* 5.8 1.4 - - - -
155A LEU* 4.7 6.7 - - + +
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Residues in contact with LYS 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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125A GLU 3.1 18.4 + - - +
126A GLY* 3.8 3.1 - - - +
128A LYS* 1.3 80.2 - - - +
130A TYR* 1.3 103.4 + - + +
131A CYS 3.7 0.2 - - - -
132A PRO* 4.3 4.3 - - - +
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Residues in contact with TYR 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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84A ASP* 5.3 1.1 + - - -
85A TYR* 3.4 33.4 - - + +
86A ALA* 3.7 39.8 - - + +
88A ILE* 4.2 5.2 - - + -
89A SER* 3.3 31.3 + - - -
90A GLY 3.4 4.0 + - - -
126A GLY* 2.8 28.9 + - - +
129A LYS* 1.3 119.4 + - + +
131A CYS* 1.3 62.0 + - - +
132A PRO* 3.8 2.5 - - - +
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Residues in contact with CYS 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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88A ILE* 3.6 45.5 - - - +
90A GLY* 4.1 2.7 - - - +
91A SER* 3.9 22.0 - - - +
94A VAL* 3.7 21.5 - - - -
127A VAL* 2.9 22.8 + - - +
130A TYR* 1.3 78.9 - - - +
132A PRO* 1.3 71.1 - - - +
133A ALA* 3.2 12.5 + - - +
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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
------------------------------------------------------------
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