Contacts of the helix formed by residues 127 - 148 (chain F) in PDB entry 4NFI
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 ASP 127 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F ARG* 3.9 18.9 + - - +
123F GLY 4.5 7.1 - - - +
124F VAL 3.4 15.6 - - - +
125F GLY 3.2 0.6 + - - -
126F LEU* 1.3 76.5 - - - +
128F ALA* 1.3 62.3 + - - +
129F ILE 3.1 0.2 - - - -
130F ASN* 3.0 20.3 + - + +
131F ASP* 3.2 13.5 + - - +
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Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F VAL* 3.6 8.3 - - + +
105F ILE* 4.0 9.2 - - + -
118F TRP* 3.8 22.0 - - + -
119F TYR* 3.9 17.3 - - + -
124F VAL* 4.0 2.5 - - + +
125F GLY 3.1 16.7 + - - +
126F LEU 3.0 0.4 - - - -
127F ASP* 1.3 77.7 - - - +
129F ILE* 1.3 57.3 + - - +
131F ASP* 3.6 13.3 + - - +
132F ALA* 2.9 31.4 + - - +
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Residues in contact with ILE 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ALA* 6.3 1.3 - - - +
105F ILE* 4.1 20.2 - - + -
126F LEU* 3.1 36.1 + - + +
127F ASP 3.1 0.6 - - - -
128F ALA* 1.3 77.2 - - - +
130F ASN* 1.3 63.6 + - - +
132F ALA* 3.4 5.0 + - - +
133F ASN* 3.3 30.4 + - - +
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Residues in contact with ASN 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F ASP* 3.0 12.8 + - - +
129F ILE* 1.3 78.4 - - - +
131F ASP* 1.3 62.8 + - - +
133F ASN* 3.2 8.9 + - - +
134F LEU* 2.9 43.2 + - - +
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Residues in contact with ASP 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ARG* 2.7 45.1 + - - +
48F VAL* 3.5 31.8 - - + +
101F VAL* 5.3 0.7 - - + -
118F TRP* 2.7 23.3 + - + +
127F ASP 3.2 11.8 + - - +
128F ALA* 3.6 8.7 - - - +
130F ASN* 1.3 80.3 + - - +
132F ALA* 1.3 63.6 + - - +
134F LEU* 3.2 12.8 + - - +
135F LEU* 3.2 24.0 + - - +
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Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F PHE* 3.2 40.8 - - + +
101F VAL* 3.8 13.9 - - + +
102F ALA* 4.4 9.2 - - + +
128F ALA 2.9 16.8 + - - +
129F ILE* 3.5 7.4 - - - +
130F ASN 3.2 0.2 - - - -
131F ASP* 1.3 78.1 - - - +
133F ASN* 1.3 62.6 + - - +
135F LEU* 3.1 25.3 + - - +
136F GLU 3.2 5.0 + - - -
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Residues in contact with ASN 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F PHE* 3.8 16.5 - - - -
129F ILE* 3.3 24.4 + - - +
130F ASN* 3.2 13.7 + - - +
132F ALA* 1.3 80.2 - - - +
134F LEU* 1.3 61.8 + - - +
136F GLU* 3.1 31.4 + - - +
137F ALA* 3.0 20.8 + - - +
401F JD5 5.9 0.7 - - - -
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Residues in contact with LEU 134 (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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41F ALA* 5.1 7.2 - - + +
44F ARG* 5.9 2.9 - - + -
45F LEU* 4.2 39.5 - - + +
48F VAL* 6.1 1.1 - - + -
130F ASN* 2.9 29.1 + - - +
131F ASP* 3.5 16.6 - - - +
132F ALA 3.2 0.2 - - - -
133F ASN* 1.3 77.1 - - - +
135F LEU* 1.3 62.2 + - - +
137F ALA* 3.1 15.7 + - + +
138F CYS* 3.0 28.2 + - - -
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 4.9 2.7 - - + -
48F VAL* 3.8 29.6 - - + +
49F LEU* 3.6 35.9 - - + -
52F ASN* 4.4 3.6 - - + -
53F ALA* 5.2 0.9 - - + -
94F LEU* 3.9 31.2 - - + +
97F ALA* 3.8 34.1 - - + +
98F PHE 3.9 1.8 - - - +
101F VAL* 4.4 8.1 - - + -
131F ASP 3.2 10.7 + - - +
132F ALA* 3.1 13.8 + - - +
134F LEU* 1.3 79.4 - - - +
136F GLU* 1.3 62.9 + - - +
138F CYS* 3.2 20.0 + - - +
139F ILE* 3.6 3.8 + - - +
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Residues in contact with GLU 136 (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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95F LEU* 4.9 1.8 - - + -
98F PHE* 3.6 42.2 - - + +
132F ALA 3.2 2.4 + - - -
133F ASN* 3.1 32.5 + - - +
135F LEU* 1.3 78.7 - - - +
137F ALA* 1.3 61.4 + - - +
139F ILE* 3.2 32.8 + - + +
140F TYR* 3.4 22.2 + - + -
161F LEU* 5.7 2.8 - - - +
164F SER* 4.5 11.3 + - - +
168F GLU* 4.6 4.0 - - - +
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Residues in contact with ALA 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ASN 3.0 12.4 + - - +
134F LEU* 3.1 21.9 + - + +
136F GLU* 1.3 77.9 - - - +
138F CYS* 1.3 61.2 + - - +
140F TYR* 3.1 21.0 + - - +
141F ARG* 3.2 18.6 + - + +
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Residues in contact with CYS 138 (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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28F LEU* 3.8 27.8 - - + -
45F LEU* 3.8 37.5 - - - -
49F LEU* 5.0 2.5 - - - -
94F LEU* 4.0 11.7 - - + -
134F LEU* 3.0 20.7 + - - -
135F LEU* 3.2 11.8 + - - +
137F ALA* 1.3 73.9 - - - +
139F ILE* 1.3 64.6 + - - +
141F ARG* 3.5 11.1 + - - +
142F LEU* 3.0 27.7 + - - +
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Residues in contact with ILE 139 (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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91F CYS* 3.6 31.0 - - + +
94F LEU* 3.9 12.8 - - + +
95F LEU* 3.5 47.8 - - + +
135F LEU 3.9 0.9 - - - +
136F GLU* 3.2 23.3 - - + +
138F CYS* 1.3 78.1 - - - +
140F TYR* 1.3 71.8 + - + +
142F LEU* 3.2 3.1 + - - +
143F LEU* 3.0 35.2 + - + +
160F PHE* 3.7 28.7 - - + -
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Residues in contact with TYR 140 (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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95F LEU* 5.6 0.3 - - - +
136F GLU* 3.4 36.2 + - + -
137F ALA* 3.1 9.6 + - - +
139F ILE* 1.3 82.4 - - + +
141F ARG* 1.3 60.0 + - + +
143F LEU* 3.8 16.6 - - + +
144F LYS* 3.0 29.1 + - - +
153F TYR* 4.9 1.2 + - - -
157F ILE* 4.0 18.8 - - + -
160F PHE* 3.3 35.5 + - + +
161F LEU* 3.3 43.9 + - + +
164F SER* 4.3 5.0 + - - -
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Residues in contact with ARG 141 (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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27F VAL 4.5 4.0 + - - -
28F LEU* 3.9 43.8 + - + +
42F ILE* 5.7 4.0 - - - +
45F LEU* 5.9 2.2 - - - +
137F ALA* 3.2 20.3 + - + +
138F CYS* 3.7 11.0 - - - +
140F TYR* 1.3 77.6 - - + +
142F LEU* 1.3 59.4 + - - +
144F LYS* 3.4 5.3 + - - +
145F LEU* 2.9 48.5 + - + +
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Residues in contact with LEU 142 (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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24F ILE* 4.1 27.4 - - + -
27F VAL* 3.7 29.4 - - + -
28F LEU* 3.9 17.3 - - + -
87F THR* 3.9 9.2 - - + +
90F TRP* 5.2 0.2 - - + -
91F CYS* 3.7 18.2 - - - +
94F LEU* 3.7 29.4 - - + -
138F CYS 3.0 13.3 + - - +
139F ILE 3.6 3.8 - - - +
141F ARG* 1.3 77.7 - - - +
143F LEU* 1.3 65.0 + - - +
145F LEU* 3.2 4.9 + - + +
146F TYR* 2.9 43.3 + - + +
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Residues in contact with LEU 143 (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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87F THR* 5.7 0.7 - - + -
88F VAL* 4.1 15.5 - - + -
91F CYS* 4.1 13.0 - - - -
139F ILE* 3.0 33.0 + - + +
140F TYR* 3.8 20.9 - - + +
142F LEU* 1.3 74.9 - - - +
144F LYS* 1.3 58.4 + - - +
147F CYS* 2.8 39.7 + - + +
148F ARG 3.4 2.1 + - - -
153F TYR* 3.5 14.2 - - + -
156F LEU* 3.9 27.6 - - + -
157F ILE* 4.2 20.9 - - + +
160F PHE* 4.2 19.5 - - + -
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Residues in contact with LYS 144 (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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140F TYR 3.0 17.7 + - - +
141F ARG* 3.8 6.1 - - - +
143F LEU* 1.3 78.4 - - - +
145F LEU* 1.3 64.5 + - + +
146F TYR 3.4 0.2 + - - -
148F ARG* 3.3 51.2 + - - +
153F TYR* 3.5 25.2 - - - +
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Residues in contact with LEU 145 (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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27F VAL* 4.7 19.5 - - + +
28F LEU* 5.0 1.8 - - + -
141F ARG* 2.9 48.3 + - + +
142F LEU* 3.2 13.7 + - + +
144F LYS* 1.3 78.6 - - + +
146F TYR* 1.3 71.9 + - + +
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Residues in contact with TYR 146 (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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20F HIS* 4.3 2.6 + - - -
23F GLN* 3.8 18.7 + - - +
24F ILE* 4.9 1.5 - - + +
27F VAL* 3.5 29.6 - - + +
83F GLN* 3.9 30.7 - - + -
84F ARG* 3.4 27.3 + - + +
87F THR* 3.5 34.5 - - + -
142F LEU* 2.9 37.6 + - + +
145F LEU* 1.3 89.3 - - + +
147F CYS* 1.3 69.3 + - - +
148F ARG 3.8 1.3 - - - -
150F GLN* 4.7 2.1 + - - +
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Residues in contact with CYS 147 (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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84F ARG* 4.3 7.0 - - - -
87F THR* 5.6 0.9 - - - -
88F VAL* 4.0 22.7 - - - -
143F LEU* 2.8 28.2 + - + +
146F TYR* 1.3 85.5 - - - +
148F ARG* 1.3 63.9 + - - +
149F GLU 3.2 3.1 - - - -
150F GLN* 3.0 22.7 + - - +
152F TYR* 3.9 33.9 - - + -
153F TYR* 3.4 17.5 - - + +
156F LEU* 4.5 5.2 - - + -
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Residues in contact with ARG 148 (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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143F LEU 3.4 2.8 + - - -
144F LYS* 3.3 54.2 + - - +
146F TYR 3.8 1.0 - - - -
147F CYS* 1.3 78.0 - - - +
149F GLU* 1.3 64.1 + - + +
150F GLN 3.6 1.4 + - - +
153F TYR* 3.6 43.7 + - + +
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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