Contacts of the helix formed by residues 113 - 127 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70F GLU* 5.5 12.0 - - + -
112F ALA* 1.3 78.9 - - - +
114F MET* 1.3 60.3 + - - +
115F MET* 3.2 10.1 - - + +
116F VAL* 3.3 12.5 + - + +
117F GLN* 3.0 24.1 + - - +
67N ALA 5.0 3.8 - - - +
68N LEU* 5.9 2.5 - - - -
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Residues in contact with MET 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ALA 3.8 0.8 + - - -
113F PRO* 1.3 71.7 - - - +
115F MET* 1.3 59.0 + - - +
117F GLN* 3.5 9.1 - - - +
118F GLU* 2.9 30.1 + - - +
159F GLY 5.8 0.7 - - - +
160F THR* 3.4 24.9 - - - +
162F ARG* 5.4 3.4 - - + +
66N ALA 5.0 1.3 - - - +
67N ALA* 3.6 32.6 + - + +
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Residues in contact with MET 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F PRO* 3.2 5.8 - - + -
114F MET* 1.3 79.4 - - - +
116F VAL* 1.3 57.7 + - - +
118F GLU* 3.5 3.0 + - - +
119F LYS* 2.9 32.2 + - - +
67N ALA* 3.7 19.4 + - + +
68N LEU* 4.5 18.2 - - + +
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Residues in contact with VAL 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F GLU* 6.1 5.8 - - + -
74F ASP* 5.6 10.5 - - + -
112F ALA* 4.8 12.8 - - + -
113F PRO* 3.3 15.1 + - + +
115F MET* 1.3 77.2 - - - +
117F GLN* 1.3 54.9 + - - +
119F LYS* 4.5 3.1 - - - -
120F LEU* 2.7 41.9 + - + +
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Residues in contact with GLN 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F LEU 5.2 9.6 - - - +
112F ALA* 5.4 2.0 - - + +
113F PRO 3.0 14.4 + - - +
114F MET* 3.2 14.1 + - + +
116F VAL* 1.3 78.5 - - - +
118F GLU* 1.3 50.4 + - - +
120F LEU* 4.7 1.1 - - - -
121F LEU* 2.7 36.6 + - - +
161F PHE* 5.3 6.5 - - + -
162F ARG* 5.0 13.0 - - - +
165F LEU* 4.1 11.4 - - + +
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Residues in contact with GLU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F MET 2.9 16.3 + - - +
115F MET* 4.1 3.1 - - - +
117F GLN* 1.3 75.0 - - - +
119F LYS* 1.3 60.0 + - - +
121F LEU* 3.5 5.4 - - - +
122F ARG* 2.9 30.8 + - - +
162F ARG* 4.3 18.8 - - + +
164F ASP* 5.5 2.3 - - + +
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Residues in contact with LYS 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F MET 2.9 18.4 + - - +
116F VAL* 4.5 2.9 - - - -
118F GLU* 1.3 75.7 - - - +
120F LEU* 1.3 59.0 + - - +
122F ARG* 4.0 2.7 - - - +
123F VAL* 2.9 31.1 + - - +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F VAL* 2.7 25.1 + - + +
117F GLN* 4.5 1.6 - - - +
119F LYS* 1.3 76.0 - - - +
121F LEU* 1.3 59.6 + - - +
123F VAL* 4.0 7.0 - - - -
124F ILE* 2.9 33.3 + - + +
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F GLN 2.7 23.4 + - - +
118F GLU* 3.1 8.2 + - - +
120F LEU* 1.3 78.9 - - - +
122F ARG* 1.3 50.8 + - - +
124F ILE* 5.3 0.2 - - - -
125F GLU* 2.6 39.9 + - - +
162F ARG* 5.7 0.4 - - + -
164F ASP* 4.0 12.3 - - + +
165F LEU* 3.7 34.5 - - + +
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Residues in contact with ARG 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F GLU 2.9 15.3 + - - +
119F LYS* 4.3 2.9 - - - +
121F LEU* 1.3 74.6 - - - +
123F VAL* 1.3 60.8 + - - +
125F GLU* 3.8 4.4 - - - +
126F TYR* 2.9 32.7 + - - +
164F ASP* 5.1 5.3 - - + +
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Residues in contact with VAL 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F LYS 2.9 21.4 + - - +
120F LEU* 4.0 7.6 - - - -
122F ARG* 1.3 78.0 - - - +
124F ILE* 1.3 59.3 + - - +
126F TYR* 3.8 2.1 - - - +
127F GLY 3.0 23.0 + - - -
128F GLU 3.1 28.6 + - - +
129F LEU* 4.4 3.1 - - - -
130F GLU* 4.4 18.2 - - + +
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Residues in contact with ILE 124 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120F LEU* 2.9 23.0 + - + +
121F LEU 4.8 0.2 - - - +
123F VAL* 1.3 74.9 - - - +
125F GLU* 1.3 61.3 + - - +
127F GLY* 3.5 12.8 + - - +
128F GLU 5.1 1.1 - - - +
129F LEU* 5.4 3.8 - - + +
144F LEU* 5.9 6.5 - - + -
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F LEU 2.6 25.8 + - - +
122F ARG* 3.8 6.5 - - - +
123F VAL 3.1 0.2 - - - -
124F ILE* 1.3 79.8 - - - +
126F TYR* 1.3 60.0 + - - +
164F ASP* 5.8 5.2 - - + +
168F ARG* 5.9 7.4 - - + -
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Residues in contact with TYR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F ARG 2.9 18.3 + - - +
123F VAL* 3.9 3.6 - - - +
125F GLU* 1.3 75.9 - - - +
127F GLY* 1.3 58.7 + - - +
128F GLU* 3.5 6.6 - - + +
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Residues in contact with GLY 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F VAL 3.0 5.3 + - - -
124F ILE* 3.5 10.0 + - - -
125F GLU 3.3 3.6 - - - -
126F TYR* 1.3 78.1 - - - +
128F GLU* 1.3 59.3 + - - +
129F LEU 4.0 1.8 + - - -
139F GLN* 3.5 26.1 - - - +
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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