Contacts of the helix formed by residues 138 - 154 (chain C) in PDB entry 4R7P
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 PHE 138 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C MET* 4.6 11.4 - - + -
127C LYS* 3.0 50.7 - - + -
128C SER* 3.2 12.1 + - - +
130C ILE* 3.6 21.8 - - + -
132C VAL* 3.4 18.7 - - + +
137C THR* 1.3 74.0 - - - +
139C LEU* 1.3 63.2 + - - +
141C LEU* 3.2 9.1 + - - +
142C THR* 3.0 25.7 + - - -
252C ILE* 3.3 31.8 - - + +
253C ASP* 3.7 11.4 - - + -
255C LEU* 3.4 28.0 - - + -
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C LYS* 6.5 0.2 - - + -
114C ASN* 5.6 0.4 - - - +
128C SER* 3.4 14.4 + - - +
129C LEU* 4.6 9.4 - - + -
137C THR* 3.3 8.9 + - - +
138C PHE* 1.3 76.8 - - - +
140C ASP* 1.3 57.4 + - - +
142C THR* 3.0 8.8 + - + -
143C VAL* 2.8 46.6 + - + +
159C LEU* 4.6 5.6 - - + -
161C LEU* 4.0 29.8 - - + -
171C THR* 4.7 2.2 - - + -
174C ILE* 3.9 18.2 - - + -
175C LEU* 4.1 12.6 - - + -
178C TYR* 3.7 31.9 - - + +
185C ILE* 5.9 0.9 - - + -
252C ILE* 4.6 14.3 - - + +
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Residues in contact with ASP 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU 4.3 3.8 - - - +
136C ASN* 4.0 10.6 - - - +
137C THR* 2.7 38.5 + - - +
139C LEU* 1.3 73.6 - - - +
141C LEU* 1.3 57.4 + - - +
143C VAL* 3.9 0.9 - - - +
144C GLN* 2.8 50.1 + - - +
177C LYS* 2.8 26.2 + - - -
178C TYR* 2.4 41.1 + - - -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 3.8 31.9 - - + -
133C ARG* 5.2 7.9 - - + +
136C ASN* 3.9 23.8 - - + +
137C THR 3.0 16.0 + - - +
138C PHE* 3.3 9.4 - - - +
139C LEU 3.1 0.2 - - - -
140C ASP* 1.3 77.2 - - - +
142C THR* 1.3 57.1 + - - +
144C GLN* 3.2 15.6 + - - +
145C GLN* 2.8 43.1 + - - +
255C LEU* 4.3 19.3 - - + -
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C VAL* 5.1 0.9 - - + -
112C LYS* 3.5 31.5 + - + +
138C PHE 3.0 13.7 + - - -
139C LEU* 3.0 11.7 + - + -
141C LEU* 1.3 76.0 - - - +
143C VAL* 1.3 65.3 + - - +
145C GLN* 2.9 26.5 + - - +
146C ILE* 3.0 19.9 + - + +
159C LEU* 3.3 27.1 - - + -
252C ILE* 3.8 18.6 + - - +
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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
----------------------------------------------------------
139C LEU* 2.8 37.2 + - + +
140C ASP 3.9 3.6 - - - +
142C THR* 1.3 71.8 - - - +
144C GLN* 1.3 64.8 + - + +
146C ILE* 3.4 9.1 - - - +
147C GLU* 2.9 39.2 + - - +
159C LEU* 5.0 5.2 - - + -
178C TYR* 3.7 34.5 - - + -
181C CYS* 4.3 2.7 - - + -
183C VAL* 3.9 20.6 - - + -
185C ILE* 4.0 22.4 - - + -
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Residues in contact with GLN 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ASN* 3.2 39.6 + - - +
140C ASP* 2.8 35.8 + - - +
141C LEU* 3.3 13.4 - - - +
143C VAL* 1.3 74.6 - - + +
145C GLN* 1.3 64.0 + - - +
147C GLU* 3.6 11.9 - - - +
148C HIS* 2.9 26.8 + - - +
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Residues in contact with GLN 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C LYS* 5.5 2.3 + - - -
141C LEU* 2.8 30.0 + - - +
142C THR* 2.9 16.9 + - - +
144C GLN* 1.3 77.0 - - + +
146C ILE* 1.3 63.3 + - + +
148C HIS* 3.1 5.0 + - - +
149C LEU* 2.9 32.5 + - + +
255C LEU 4.4 9.3 + - - -
257C ALA 4.6 3.0 + - - +
258C THR* 3.5 40.1 - - - +
259C VAL* 4.8 2.4 + - - +
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Residues in contact with ILE 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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110C VAL* 4.2 25.8 - - + -
142C THR* 3.0 9.8 + - + +
143C VAL* 3.4 12.8 - - - +
145C GLN* 1.3 81.1 - - + +
147C GLU* 1.3 63.8 + - - +
149C LEU* 3.2 21.6 + - + +
150C ASN* 2.8 34.7 + - - +
157C VAL* 4.7 9.1 - - + +
158C PRO 5.0 0.9 - - - +
159C LEU* 3.1 39.0 - - + +
183C VAL* 3.2 30.7 - - + -
259C VAL* 4.8 4.3 - - + -
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Residues in contact with GLU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C VAL* 2.9 23.6 + - - +
144C GLN* 3.6 11.7 - - - +
146C ILE* 1.3 78.9 - - - +
148C HIS* 1.3 59.4 + - + +
150C ASN* 3.1 3.5 + - - +
151C LYS* 2.8 64.3 + - + +
181C CYS* 3.3 41.1 - - - +
182C ARG 3.6 29.6 - - - +
183C VAL* 4.7 2.9 - - + -
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Residues in contact with HIS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C GLN 2.9 18.4 + - - +
145C GLN* 3.6 4.9 - - - +
147C GLU* 1.3 73.3 - - + +
149C LEU* 1.3 67.6 + - - +
151C LYS* 4.3 14.6 - - + -
152C THR* 2.9 49.0 + - + +
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Residues in contact with LEU 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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105C LEU* 4.6 16.2 - - + -
145C GLN* 2.9 15.3 + - + +
146C ILE* 3.2 24.5 - - + +
147C GLU 3.2 0.2 - - - -
148C HIS* 1.3 76.5 - - - +
150C ASN* 1.3 60.3 + - - +
152C THR* 3.1 5.0 + - - +
153C TYR* 2.8 59.8 + - + +
155C THR* 4.4 2.7 - - - -
157C VAL* 5.2 7.4 - - + -
259C VAL* 4.1 35.7 - - + +
261C LEU* 5.2 7.2 - - + -
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Residues in contact with ASN 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ILE 2.8 22.0 + - - -
147C GLU 3.5 5.4 - - - +
149C LEU* 1.3 73.3 - - - +
151C LYS* 1.3 57.9 + - - +
154C ASN* 2.8 28.4 + - - -
155C THR* 3.0 29.7 + - - +
156C ASP* 4.0 2.7 + - - +
157C VAL* 2.8 51.1 + - - +
182C ARG* 3.1 37.3 + - - +
183C VAL* 4.1 6.3 - - - +
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Residues in contact with LYS 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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147C GLU* 2.8 55.1 + - + +
148C HIS* 3.8 16.2 - - + +
149C LEU 3.2 0.2 - - - -
150C ASN* 1.3 75.6 - - - +
152C THR* 1.3 62.7 + - + +
154C ASN* 4.1 4.0 + - - +
180C HIS 5.8 1.4 + - - -
181C CYS* 5.8 0.4 - - - +
182C ARG* 3.9 35.8 + - + +
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Residues in contact with THR 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 HIS* 2.9 45.1 + - + +
149C LEU* 3.1 8.0 + - - +
151C LYS* 1.3 80.7 - - + +
153C TYR* 1.3 80.6 + - - +
154C ASN* 3.3 2.6 + - - +
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Residues in contact with TYR 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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101C ILE* 3.6 37.0 - - + +
102C SER* 3.3 21.3 + - - +
105C LEU* 3.3 24.5 - - + -
149C LEU* 2.8 41.8 + - + +
152C THR* 1.3 86.9 + - - +
154C ASN* 1.3 71.1 + - - +
155C THR* 3.1 12.6 + - + -
261C LEU* 3.8 26.2 - - + +
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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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102C SER* 5.5 1.6 - - - -
106C ASN* 5.5 0.9 + - - -
150C ASN 2.8 12.3 + - - -
151C LYS 4.1 2.9 + - - +
152C THR 3.3 4.7 - - - +
153C TYR* 1.3 79.8 - - - +
155C THR* 1.3 56.4 + - - +
182C ARG* 3.5 20.8 + - - +
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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