Contacts of the helix formed by residues 140 - 155 (chain C) in PDB entry 2F4N
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 GLY 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C VAL* 5.9 0.9 - - - -
141C ARG* 1.3 68.1 + - - +
142C ASP* 3.1 9.7 + - - -
143C VAL* 3.3 25.9 + - - +
144C TYR* 3.0 35.8 + - - -
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Residues in contact with ARG 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 4.8 11.0 - - + -
27C TYR* 6.1 4.3 - - + +
31C MSE 3.5 34.0 - - + +
82C VAL* 5.4 2.2 - - - -
140C GLY* 1.3 78.9 - - - +
142C ASP* 1.3 59.2 + - - +
144C TYR* 4.5 3.3 - - - +
145C ALA* 3.5 14.7 + - - +
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Residues in contact with ASP 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B TYR* 6.4 1.6 - - + -
34C ARG* 4.0 35.8 + - - +
131C ARG* 4.4 10.4 - - - +
140C GLY 4.4 7.3 + - - -
141C ARG* 1.3 78.7 - - - +
143C VAL* 1.3 81.9 + - - +
145C ALA* 3.1 6.1 + - - +
146C VAL* 2.6 41.8 + - - +
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Residues in contact with VAL 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C SER* 5.7 1.8 - - - +
127C ILE* 4.3 19.5 - - + -
129C GLU* 4.4 20.0 - - - +
131C ARG* 4.1 26.5 - - + -
140C GLY* 3.3 19.4 + - - +
142C ASP* 1.3 95.7 + - - +
144C TYR* 1.3 62.0 + - + +
146C VAL* 3.1 3.9 + - - +
147C VAL* 2.7 54.7 + - + +
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Residues in contact with TYR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C MSE 5.9 0.2 - - + -
80C VAL* 3.7 29.2 - - + +
82C VAL* 3.9 27.8 - - + -
91C ARG* 5.6 4.0 - - - +
92C LYS 4.4 0.5 + - - -
93C SER* 3.1 31.2 + - - -
105C VAL* 4.0 10.9 - - + +
106C GLY* 3.3 37.5 - - - -
107C PRO* 3.5 27.9 - - + +
127C ILE* 4.9 4.7 - - + -
140C GLY* 3.0 33.9 + - - +
141C ARG 4.5 1.8 - - - +
143C VAL* 1.3 80.7 - - + +
145C ALA* 1.3 62.6 + - - +
147C VAL* 3.8 1.5 - - - +
148C GLY* 2.9 21.0 + - - -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C MSE 3.9 23.0 - - + +
34C ARG* 4.1 16.2 - - + -
35C ILE* 3.6 27.8 - - + +
80C VAL* 4.7 3.3 - - - +
141C ARG 3.5 14.5 + - - +
142C ASP* 3.1 10.0 + - - +
144C TYR* 1.3 78.1 - - - +
146C VAL* 1.3 63.6 + - - +
148C GLY* 3.0 11.0 + - - -
149C ALA* 3.1 11.8 + - - +
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Residues in contact with VAL 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 3.5 35.2 - - + +
38C ILE* 3.7 26.1 - - + +
131C ARG* 4.8 15.9 - - + +
142C ASP* 2.6 29.5 + - - +
143C VAL* 3.7 4.0 - - - +
145C ALA* 1.3 72.1 - - - +
147C VAL* 1.3 59.3 + - + +
148C GLY 3.2 0.2 + - - -
149C ALA* 3.3 1.7 + - - +
150C GLU* 2.9 41.2 + - + +
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C VAL* 3.9 28.0 - - + -
105C VAL* 4.0 13.7 - - + -
127C ILE* 4.1 11.0 - - + -
131C ARG* 3.7 28.7 - - - +
143C VAL* 2.7 39.1 + - + +
144C TYR 3.9 3.8 - - - +
146C VAL* 1.3 71.7 - - - +
148C GLY* 1.3 58.8 + - - +
150C GLU* 3.6 9.0 - - - +
151C ILE* 2.9 33.2 + - + +
157C TYR* 3.9 14.4 - - + -
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Residues in contact with GLY 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 3.9 18.6 - - - +
78C VAL* 4.3 10.2 - - - +
80C VAL* 4.2 8.1 - - - -
105C VAL* 4.8 1.3 - - - -
144C TYR 2.9 14.8 + - - -
145C ALA 3.0 3.1 + - - -
147C VAL* 1.3 77.0 - - - +
149C ALA* 1.3 65.6 + - - +
151C ILE* 3.1 15.5 + - - +
152C LEU* 3.2 14.6 + - - +
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Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 4.1 2.2 - - - +
35C ILE* 3.9 20.2 - - + +
38C ILE* 3.9 20.2 - - + -
39C LEU* 3.8 23.7 - - + +
145C ALA 3.1 11.0 + - - +
146C VAL 3.9 5.6 - - - +
148C GLY* 1.3 75.0 - - - +
150C GLU* 1.3 58.0 + - - +
152C LEU* 2.9 13.1 + - - +
153C ILE* 2.9 31.8 + - - +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 4.9 2.0 - - + +
130C GLU* 5.5 0.5 - - - +
131C ARG* 2.9 29.6 + - - -
146C VAL* 2.9 22.9 + - + +
147C VAL* 3.6 7.3 - - - +
149C ALA* 1.3 77.8 - - - +
151C ILE* 1.3 56.9 + - - +
153C ILE* 3.2 13.0 + - - +
154C ASN* 2.9 44.1 + - - +
156C GLY 4.9 0.2 - - - -
157C TYR* 3.3 23.8 - - + -
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Residues in contact with ILE 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.8 4.5 - - + +
78C VAL* 3.9 14.6 - - + -
95C VAL* 4.1 9.2 - - + -
103C TYR* 3.8 37.9 - - + -
105C VAL* 3.6 28.7 - - + -
147C VAL* 2.9 27.4 - - + +
148C GLY* 3.1 8.6 + - - +
150C GLU* 1.3 75.8 - - - +
152C LEU* 1.3 53.6 + - - +
155C ASN* 2.6 34.5 + - - -
156C GLY 3.6 21.8 - - - +
157C TYR* 3.7 18.2 - - + -
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Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.4 40.8 - - + +
13C ASP* 3.9 13.0 - - - +
14C ILE 4.1 8.3 - - - +
15C ILE* 3.7 33.4 - - + -
35C ILE* 5.2 0.4 - - + -
39C LEU* 4.3 17.0 - - + -
44C LYS* 3.3 24.3 + - - +
46C ALA* 3.7 21.1 - - + -
78C VAL* 4.3 8.3 - - + -
148C GLY 3.2 9.8 + - - +
149C ALA* 2.9 10.8 + - - +
151C ILE* 1.3 78.0 - - - +
153C ILE* 1.3 62.3 + - - +
155C ASN* 3.4 11.3 + - - +
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Residues in contact with ILE 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 3.3 36.8 - - + +
39C LEU* 4.0 13.9 - - + -
42C TYR* 3.7 44.0 - - + -
44C LYS* 4.1 20.3 - - + +
149C ALA 2.9 17.3 + - - +
150C GLU* 3.5 9.9 - - - +
152C LEU* 1.3 77.8 - - - +
154C ASN* 1.3 70.2 + - - +
155C ASN* 5.3 0.3 - - - +
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Residues in contact with ASN 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLU* 2.9 29.4 + - - +
153C ILE* 1.3 95.3 + - - +
155C ASN* 1.3 72.1 + - - +
156C GLY* 3.4 14.3 + - - +
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Residues in contact with ASN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.0 26.7 - - - +
12C LEU* 2.5 53.9 + - - +
103C TYR* 4.5 2.1 + - - -
151C ILE 2.6 19.3 + - - -
152C LEU 3.4 7.3 + - - +
154C ASN* 1.3 77.6 - - - +
156C GLY* 1.3 55.0 + - - +
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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