Contacts of the helix formed by residues 108 - 126 (chain A) in PDB entry 5NDD
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 ALA 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LYS* 3.3 10.0 - - + +
107A LYS* 1.3 79.6 - - - +
109A PRO* 1.3 77.2 - - + +
110A ALA* 4.2 8.3 - - + +
111A VAL* 3.0 25.6 + - + +
112A ILE* 3.4 11.4 + - - +
176A GLU* 5.6 2.2 - - - +
184A SER* 4.6 3.1 - - - +
2049A ASP* 3.7 22.0 - - - +
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Residues in contact with PRO 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS 4.4 0.4 - - - +
108A ALA* 1.3 87.8 - - + +
110A ALA* 1.3 60.4 + - - +
112A ILE* 3.5 6.4 + - + +
113A TYR* 3.2 33.9 + - + -
172A GLN* 3.3 36.3 - - + +
176A GLU* 4.9 2.5 - - - +
184A SER* 4.7 5.6 - - - +
187A LYS* 3.4 34.3 - - + +
188A ALA 4.4 6.5 - - - +
191A ALA* 3.9 20.4 - - + -
2049A ASP* 5.0 6.7 - - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.1 7.0 - - + +
109A PRO* 1.3 76.6 - - - +
111A VAL* 1.3 67.6 + - + +
113A TYR* 3.5 3.2 + - - -
114A MET* 3.1 31.2 + - + +
169A LEU* 3.7 24.5 - - + +
172A GLN* 4.6 3.6 - - + +
173A ARG* 4.5 14.1 - - + +
176A GLU* 5.0 6.4 + - - +
347A VAL* 4.2 14.8 - - + -
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.7 43.6 - - + +
104A THR* 3.7 26.2 - - + +
106A LYS* 5.2 3.6 - - + -
107A LYS* 4.7 6.7 - - + -
108A ALA* 3.0 26.4 + - + +
110A ALA* 1.3 78.6 - - + +
112A ILE* 1.3 57.7 + - + +
114A MET* 3.3 16.6 + - + +
115A ALA* 2.9 27.8 + - + +
348A SER* 5.5 4.0 - - - +
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Residues in contact with ILE 112 (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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107A LYS* 4.7 9.9 - - + +
108A ALA 3.4 13.4 + - - +
109A PRO* 3.8 5.8 - - + +
110A ALA 3.2 0.4 - - - -
111A VAL* 1.3 75.9 - - + +
113A TYR* 1.3 64.2 + - - +
115A ALA* 3.2 16.2 + - + +
116A ASN* 2.9 30.1 + - - +
188A ALA* 3.2 45.8 - - + +
191A ALA* 4.0 9.9 - - + +
192A ILE* 3.7 29.2 - - + -
195A SER* 4.0 10.8 - - - +
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 3.2 20.4 + - + +
110A ALA* 3.8 4.5 - - - +
111A VAL 3.4 0.2 - - - -
112A ILE* 1.3 75.6 - - - +
114A MET* 1.3 58.2 + - - +
116A ASN* 3.3 6.0 + - - +
117A LEU* 3.0 27.7 + - - +
165A PHE* 4.2 27.4 - + + +
168A CYS* 3.6 44.1 - - + +
169A LEU* 3.7 18.6 - - + -
172A GLN* 4.0 18.9 + - + -
191A ALA* 3.6 33.6 - - + +
194A ILE* 3.5 29.4 - - + +
195A SER* 3.9 11.9 - - - -
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Residues in contact with MET 114 (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 PHE* 3.6 21.0 - - + -
110A ALA* 3.1 21.5 + - + +
111A VAL* 3.7 18.2 - - + +
113A TYR* 1.3 76.6 - - - +
115A ALA* 1.3 57.4 + - - +
117A LEU* 3.4 9.4 - - - +
118A ALA* 2.9 29.3 + - - +
169A LEU* 3.7 22.0 - - + -
343A VAL 4.6 0.2 - - - +
344A TYR* 3.9 29.4 - - + -
347A VAL* 3.6 34.5 - - + -
348A SER* 3.7 24.9 - - - -
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Residues in contact with ALA 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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97A LEU* 3.3 19.8 - - + +
100A PHE* 3.7 23.5 - - + -
101A LEU* 4.3 9.0 - - + -
111A VAL* 2.9 17.7 + - + +
112A ILE* 3.2 10.7 + - + +
114A MET* 1.3 78.1 - - - +
116A ASN* 1.3 58.9 + - - +
118A ALA 3.5 0.5 + - - -
119A LEU* 2.9 25.6 + - - +
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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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112A ILE* 2.9 22.5 + - - +
113A TYR 3.3 5.1 + - - +
115A ALA* 1.3 76.4 - - - +
117A LEU* 1.3 57.3 + - - +
119A LEU* 3.4 15.8 - - - +
120A ALA* 2.6 36.4 + - - +
165A PHE* 3.5 24.4 - - + -
195A SER* 3.0 29.3 + - - -
196A LEU* 6.4 0.2 - - - +
199A TRP* 3.3 25.5 - - - +
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Residues in contact with LEU 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 TYR 3.0 13.9 + - - +
114A MET* 3.4 13.0 - - - +
116A ASN* 1.3 76.7 - - - +
118A ALA* 1.3 57.1 + - - +
120A ALA* 3.4 5.2 + - - +
121A ASP* 3.0 31.9 + - - +
161A CYS 4.9 0.2 - - - -
162A SER* 3.6 33.4 - - - +
165A PHE* 3.6 27.1 - - + +
166A LEU* 4.1 19.1 - - + +
169A LEU* 5.0 4.7 - - + -
340A ASP* 3.4 26.5 - - - +
343A VAL* 4.7 6.3 - - + -
344A TYR* 3.5 22.2 - - + +
2202A NA 4.2 0.2 - - - -
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Residues in contact with ALA 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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93A ASN* 3.6 28.7 - - - +
96A ALA* 4.6 1.1 - - + -
97A LEU* 4.2 15.7 - - + +
100A PHE* 4.8 0.7 - - + -
114A MET 2.9 17.2 + - - +
115A ALA* 3.7 5.4 - - - +
117A LEU* 1.3 76.3 - - - +
119A LEU* 1.3 57.1 + - - +
121A ASP* 3.3 3.1 + - - +
122A LEU* 2.9 34.0 + - - +
344A TYR* 3.1 18.1 + - + +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 4.7 11.0 - - + +
115A ALA 2.9 19.1 + - - +
116A ASN* 3.1 19.7 + - - +
118A ALA* 1.3 75.1 - - - +
120A ALA* 1.3 59.3 + - - +
122A LEU* 3.2 12.0 + - + +
123A LEU* 2.9 58.7 + - + +
199A TRP* 4.1 19.3 - - + -
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Residues in contact with ALA 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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116A ASN 2.6 20.5 + - - +
117A LEU* 3.6 8.1 - - - +
119A LEU* 1.3 72.8 - - - +
121A ASP* 1.3 62.6 + - - +
123A LEU* 3.7 3.4 + - - +
124A SER* 3.6 9.7 + - - -
154A PHE 5.0 0.3 - - - +
158A ASN* 3.4 31.5 - - - +
161A CYS* 3.9 27.6 - - + -
162A SER* 4.8 3.1 - - - +
199A TRP* 4.1 15.8 - - + -
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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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93A ASN* 2.7 34.3 - - - +
117A LEU 3.0 16.8 + - - +
118A ALA 3.3 8.1 - - - +
119A LEU 3.2 0.2 - - - -
120A ALA* 1.3 75.8 - - - +
122A LEU* 1.3 63.1 + - - +
124A SER* 3.2 4.0 + - - -
125A VAL* 3.1 28.6 + - + +
158A ASN* 3.1 5.4 - - - +
337A SER* 3.2 21.9 - - - -
340A ASP* 2.7 19.6 - - - +
344A TYR* 3.2 3.3 + - - -
2202A NA 2.2 27.0 - - - -
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Residues in contact with LEU 122 (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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90A LEU* 3.5 44.2 - - + +
93A ASN* 4.0 21.5 - - + +
94A GLY* 3.8 11.4 - - - +
97A LEU* 4.1 21.3 - - + -
118A ALA 2.9 20.3 + - - +
119A LEU* 3.8 11.7 - - + +
121A ASP* 1.3 71.1 - - - +
123A LEU* 1.3 61.4 + - + +
124A SER 2.9 10.6 + - - -
125A VAL* 3.2 2.9 + - - +
126A ILE* 3.1 38.7 + - + +
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Residues in contact with LEU 123 (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 LEU* 2.9 38.2 + - + +
120A ALA* 4.2 5.6 - - - +
122A LEU* 1.3 78.2 - - + +
124A SER* 1.3 57.6 + - - +
126A ILE* 5.1 10.1 - - + -
127A TRP* 3.2 26.1 + - - +
154A PHE* 3.5 42.3 - - + -
199A TRP* 4.1 22.4 - - + -
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Residues in contact with SER 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 ALA 3.6 8.6 + - - -
121A ASP 3.2 7.5 + - - -
122A LEU 3.0 0.6 - - - -
123A LEU* 1.3 79.5 - - - +
125A VAL* 1.3 66.0 + - - +
126A ILE 3.2 1.8 - - - -
127A TRP* 3.3 15.9 + - - +
128A PHE* 3.2 26.5 - - - -
151A LEU 5.5 0.2 + - - -
154A PHE* 3.7 24.0 + - - -
155A PHE* 4.1 14.4 - - - +
158A ASN* 4.1 12.7 + - - +
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Residues in contact with VAL 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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85A VAL* 4.3 7.6 - - + +
86A PHE* 3.3 40.4 - - + +
89A ALA* 4.1 10.5 - - + -
90A LEU* 3.9 24.7 - - + +
121A ASP 3.1 18.9 + - - +
122A LEU* 3.2 2.4 + - - +
124A SER* 1.3 75.5 - - - +
126A ILE* 1.3 64.6 + - - +
128A PHE* 3.0 31.1 + - + +
337A SER* 3.8 22.0 - - - +
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Residues in contact with ILE 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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86A PHE* 4.7 3.9 - - - -
90A LEU* 3.7 23.3 - - + -
122A LEU* 3.1 28.1 + - + +
123A LEU* 5.1 9.4 - - + -
124A SER 3.2 0.2 - - - -
125A VAL* 1.3 76.8 - - - +
127A TRP* 1.3 72.4 + - + +
128A PHE 3.2 0.4 - - - -
129A PRO* 3.2 17.3 - - - +
130A LEU* 5.1 2.9 - - - +
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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