Contacts of the helix formed by residues 140 - 154 (chain C) in PDB entry 4U7D
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 LEU 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C CYS* 4.3 0.8 - - - -
139C PRO* 1.3 91.0 - - + +
141C ILE* 1.3 65.0 + - - +
142C SER* 3.8 17.9 - - - +
143C LEU* 3.3 29.9 + - + +
144C MET* 3.1 26.8 + - - +
190C THR* 5.8 0.4 - - - -
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Residues in contact with ILE 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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139C PRO 4.3 0.8 + - - +
140C LEU* 1.3 71.6 - - - +
142C SER* 1.3 51.9 + - - +
144C MET* 3.3 13.7 + - + +
145C GLU* 2.7 64.6 + - + +
160C MET* 4.4 3.6 - - + -
162C ASN* 3.4 42.0 - - - +
190C THR* 4.8 7.9 - - + -
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Residues in contact with SER 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU* 3.8 17.0 - - - +
141C ILE* 1.3 76.7 - - - +
143C LEU* 1.3 58.7 + - - +
145C GLU* 3.4 15.5 + - - +
146C ASP* 2.5 44.4 + - - +
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Residues in contact with LEU 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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138C CYS* 3.6 20.9 - - - -
139C PRO* 4.4 7.4 - - + -
140C LEU* 3.3 37.6 + - + +
142C SER* 1.3 82.0 + - - +
144C MET* 1.3 63.0 - - - +
146C ASP* 3.2 28.8 - - + +
147C GLN* 3.2 16.1 + - - +
219C ASP* 5.9 0.2 - - - +
220C GLU* 3.8 24.2 - - - +
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Residues in contact with MET 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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138C CYS* 3.6 24.5 - - + +
140C LEU 3.1 9.9 + - - +
141C ILE* 3.5 26.9 - - + +
143C LEU* 1.3 75.0 - - - +
145C GLU* 1.3 65.6 + - - +
147C GLN* 3.0 13.7 + - - +
148C LEU* 3.1 19.3 + - + +
160C MET* 3.4 33.7 - - + -
161C LEU 4.3 10.3 - - - +
162C ASN* 4.6 1.1 - - - +
188C TYR* 3.7 35.8 - - + -
189C VAL 3.9 24.0 - - - +
190C THR* 4.4 6.5 - - + -
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Residues in contact with GLU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ILE* 2.7 46.2 + - + +
142C SER* 3.4 15.4 + - - +
144C MET* 1.3 74.9 - - - +
146C ASP* 1.3 63.5 + - - +
147C GLN 3.4 0.3 + - - -
148C LEU* 4.4 6.4 - - - +
149C MET* 3.5 21.0 + - - +
160C MET* 3.9 19.3 - - + +
162C ASN* 5.3 0.2 + - - -
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Residues in contact with ASP 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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142C SER* 2.5 22.1 + - - +
143C LEU* 3.2 27.4 - - + +
145C GLU* 1.3 75.2 - - - +
147C GLN* 1.3 65.3 + - + +
149C MET* 3.8 8.6 + - - +
150C VAL* 3.8 16.5 - - - +
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Residues in contact with GLN 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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120C SER* 2.9 26.6 + - - -
123C TYR* 2.6 26.9 + - - -
124C GLN* 3.1 16.8 + - - +
138C CYS* 6.3 0.7 - - - -
143C LEU 3.3 15.0 - - - +
144C MET 3.0 7.6 + - - +
146C ASP* 1.3 78.5 - - + +
148C LEU* 1.3 65.3 + - - +
150C VAL* 3.2 22.1 + - - +
151C LEU* 3.2 18.5 + - - +
188C TYR* 3.8 27.1 - - + +
219C ASP* 4.6 4.6 - - - +
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Residues in contact with LEU 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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144C MET* 3.1 16.9 + - + +
145C GLU* 3.6 4.9 + - - +
146C ASP 3.5 0.2 - - - -
147C GLN* 1.3 72.7 - - - +
149C MET* 1.3 65.3 + - - +
151C LEU* 3.8 4.1 - - + +
152C LYS* 3.0 27.1 + - - +
158C ALA* 3.5 35.2 - - + +
159C THR* 3.7 13.0 - - - +
160C MET* 3.7 45.5 - - + +
188C TYR* 3.9 19.1 - - + -
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Residues in contact with MET 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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145C GLU 3.5 14.0 + - - +
146C ASP* 3.8 6.1 - - - +
147C GLN 3.2 0.2 - - - -
148C LEU* 1.3 80.7 - - - +
150C VAL* 1.3 64.8 + - + +
152C LYS* 3.6 5.1 + - - +
153C GLN* 3.3 20.8 + - - +
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Residues in contact with VAL 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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124C GLN* 5.8 4.3 - - - +
146C ASP 3.8 13.2 - - - +
147C GLN* 3.2 16.7 + - - +
149C MET* 1.3 78.8 - - + +
151C LEU* 1.3 66.2 + - + +
153C GLN* 3.6 6.6 + - - +
154C LEU* 3.3 37.1 + - + +
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Residues in contact with LEU 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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87C PHE* 5.0 2.9 - - + -
124C GLN* 4.1 29.6 - - + +
147C GLN 3.2 25.2 + - - +
148C LEU* 3.8 10.1 - - - +
149C MET 3.3 0.2 - - - -
150C VAL* 1.3 79.2 - - + +
152C LYS* 1.3 65.7 + - - +
154C LEU* 3.1 12.2 + - + +
155C GLY 3.2 0.2 + - - -
156C ILE* 2.9 61.7 + - + +
158C ALA* 3.9 21.3 - - + -
186C LEU* 4.6 5.8 - - + -
188C TYR* 3.8 21.5 - - + +
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Residues in contact with LYS 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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148C LEU 3.0 17.0 + - - +
149C MET* 3.9 5.6 - - - +
151C LEU* 1.3 74.6 - - - +
153C GLN* 1.3 59.1 + - - +
155C GLY* 2.8 21.1 + - - -
156C ILE 4.0 10.2 + - - -
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Residues in contact with GLN 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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149C MET 3.3 11.1 + - - +
150C VAL* 3.7 12.1 - - - +
151C LEU 3.2 0.4 - - - -
152C LYS* 1.3 79.9 - - - +
154C LEU* 1.3 62.6 + - + +
155C GLY 3.2 0.7 + - - -
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Residues in contact with LEU 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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86C VAL* 3.4 35.3 - - - +
87C PHE* 3.9 42.4 - - + +
88C LYS* 4.4 12.5 + - + +
150C VAL* 3.3 29.6 + - + +
151C LEU* 3.1 11.5 + - + +
153C GLN* 1.3 78.0 - - + +
155C GLY* 1.3 61.4 + - - +
156C ILE* 3.3 15.7 + - + -
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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
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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