Contacts of the helix formed by residues 113 - 127 (chain J) in PDB entry 5NSS
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 113 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70J GLU* 3.8 26.1 - - + -
111J THR 4.0 0.6 - - - -
112J ALA* 1.3 78.2 - - - +
114J MET* 1.3 61.2 + - - +
115J MET* 3.1 6.6 + - + +
116J VAL* 3.5 1.5 + - - -
117J GLN* 3.1 25.8 + - - +
160J THR* 3.4 12.6 - - - +
161J PHE* 4.2 1.6 - - - -
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Residues in contact with MET 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J PRO* 1.3 75.3 - - - +
115J MET* 1.3 58.1 + - - +
118J GLU* 2.9 34.5 + - + +
159J GLY 4.6 4.9 - - - +
160J THR 2.7 19.1 + - - +
161J PHE 4.0 1.3 - - - +
162J ARG* 3.5 25.4 - - + +
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Residues in contact with MET 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ALA* 3.3 28.5 - - - +
67G ALA* 3.4 20.2 - - - +
68G LEU 5.3 0.2 - - - +
70J GLU* 4.9 14.4 - - + -
71J ASN* 5.7 0.7 - - + +
74J ASP* 5.2 0.9 - - + -
113J PRO* 3.1 3.6 - - + +
114J MET* 1.3 78.8 - - - +
116J VAL* 1.3 58.1 + - - +
118J GLU* 4.3 1.0 - - - +
119J LYS* 2.9 32.8 + - - +
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Residues in contact with VAL 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J CYS* 5.7 2.5 - - + -
70J GLU* 4.0 24.1 - - - +
73J LEU* 5.8 2.2 - - + -
74J ASP* 4.0 16.8 - - + +
112J ALA* 3.9 24.0 - - + -
113J PRO 3.5 2.8 + - - +
115J MET* 1.3 77.1 - - - +
117J GLN* 1.3 60.2 + - - +
119J LYS* 4.3 1.6 - - - -
120J LEU* 2.9 35.3 + - + +
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Residues in contact with GLN 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J LEU 5.9 1.3 - - - +
112J ALA* 4.8 5.3 - - + +
113J PRO 3.1 19.5 + - - +
116J VAL* 1.3 78.3 - - - +
118J GLU* 1.3 51.0 + - - +
120J LEU* 5.2 0.7 - - - -
121J LEU* 2.7 42.0 + - - +
161J PHE* 4.7 4.3 - - + -
162J ARG* 3.6 25.8 - - + +
165J LEU* 3.7 19.5 - - + -
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Residues in contact with GLU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ALA* 6.2 3.6 - - + -
114J MET* 2.9 20.9 + - + +
115J MET* 4.3 1.8 - - - +
117J GLN* 1.3 76.0 - - - +
119J LYS* 1.3 59.7 + - - +
121J LEU* 4.5 2.5 - - - -
122J ARG* 2.8 36.1 + - + +
162J ARG* 3.5 14.3 - - + +
164J ASP* 4.6 6.7 - - + -
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Residues in contact with LYS 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G ALA* 3.7 23.6 - - + -
74J ASP* 5.1 7.4 - - + -
115J MET 2.9 21.6 + - - +
116J VAL* 4.1 4.5 - - - +
118J GLU* 1.3 78.1 - - - +
120J LEU* 1.3 58.7 + - - +
122J ARG* 5.0 0.4 - - - -
123J VAL* 2.8 35.6 + - - +
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Residues in contact with LEU 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J VAL* 2.9 19.1 + - + +
117J GLN* 4.7 1.1 - - - +
119J LYS* 1.3 75.6 - - - +
121J LEU* 1.3 56.3 + - - +
123J VAL* 4.8 0.9 - - - -
124J ILE* 2.6 40.8 + - + +
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Residues in contact with LEU 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J GLN 2.7 23.2 + - - +
120J LEU* 1.3 78.7 - - - +
122J ARG* 1.3 51.5 + - - +
124J ILE* 4.5 1.1 - - - +
125J GLU* 2.7 40.0 + - - +
164J ASP* 3.4 38.1 - - + +
165J LEU* 3.6 7.6 - - + +
168J ARG* 4.4 6.0 - - + +
169J LEU* 5.5 4.9 - - + +
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Residues in contact with ARG 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ARG* 4.4 22.7 - - + -
118J GLU* 2.8 22.7 + - + +
119J LYS* 4.6 0.4 - - - +
121J LEU* 1.3 75.3 - - - +
123J VAL* 1.3 60.9 + - - +
125J GLU* 4.0 2.6 - - - +
126J TYR* 2.9 32.4 + - - +
164J ASP* 4.7 4.7 - - + +
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Residues in contact with VAL 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J LYS* 2.8 21.6 + - + +
120J LEU* 4.8 1.6 - - - -
122J ARG* 1.3 77.2 - - - +
124J ILE* 1.3 60.6 + - - +
126J TYR* 4.7 0.9 - - - -
127J GLY 3.5 11.4 + - - -
128J GLU* 3.3 25.0 + - - +
129J LEU* 4.0 27.4 - - + -
130J GLU 5.4 0.4 - - - +
140J VAL* 5.9 1.6 - - - +
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Residues in contact with ILE 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J LEU* 2.6 25.4 + - + +
121J LEU* 4.5 0.9 - - - +
123J VAL* 1.3 77.8 - - - +
125J GLU* 1.3 60.7 + - - +
127J GLY* 3.6 10.7 + - - -
140J VAL* 5.6 9.6 - - - +
141J ASN* 5.3 5.0 - - - -
142J VAL 5.4 5.1 + - - +
144J LEU* 5.2 14.8 - - + -
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Residues in contact with GLU 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G ARG* 5.6 11.0 - - + -
121J LEU 2.7 23.8 + - - +
122J ARG* 4.0 3.4 - - - +
124J ILE* 1.3 78.1 - - - +
126J TYR* 1.3 61.8 + - - +
127J GLY* 3.4 0.7 + - - -
168J ARG* 4.4 16.2 - - + -
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Residues in contact with TYR 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J ARG 2.9 19.1 + - - +
123J VAL* 4.1 4.7 - - - +
124J ILE 3.4 0.2 - - - -
125J GLU* 1.3 74.8 - - - +
127J GLY* 1.3 56.6 + - - +
128J GLU* 3.3 14.6 + - - +
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Residues in contact with GLY 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J VAL 3.5 5.8 + - - -
124J ILE 3.6 7.1 + - - -
125J GLU 3.2 5.4 + - - -
126J TYR* 1.3 75.7 - - - +
128J GLU* 1.3 59.7 + - - +
139J GLN* 5.1 2.9 - - - +
140J VAL* 4.3 3.3 + - - -
141J ASN* 3.3 42.0 + - - +
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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