Contacts of the strand formed by residues 135 - 143 (chain C) in PDB entry 1M7X
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 VAL 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C THR* 3.4 0.8 - - - -
132C MET 3.0 33.1 + - - +
133C ASP* 3.3 10.5 - - + +
134C GLY* 1.3 82.0 - - - +
136C THR* 1.3 64.9 + - - +
178C PHE* 3.4 7.6 - - + -
180C PRO* 3.4 31.9 - - + -
181C GLY 5.3 0.2 - - - +
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Residues in contact with THR 136 (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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130C ASP 3.4 9.4 - - - -
131C THR* 3.1 21.8 - - + +
134C GLY 4.1 4.9 + - - +
135C VAL* 1.3 80.7 - - - +
137C GLY* 1.3 59.2 + - - +
178C PHE* 3.8 2.5 - - - -
180C PRO* 3.6 3.7 - - - +
181C GLY* 3.0 18.0 + - - -
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Residues in contact with GLY 137 (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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129C ALA* 3.4 4.7 - - - +
130C ASP 3.0 22.1 + - - +
136C THR* 1.3 75.9 - - - +
138C THR* 1.3 69.5 + - - +
178C PHE* 3.3 11.1 - - - -
179C ILE 3.6 1.3 - - - -
180C PRO* 3.7 0.4 - - - -
181C GLY* 3.5 16.6 - - - -
182C ALA 3.5 8.2 - - - +
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Residues in contact with THR 138 (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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127C ALA* 5.0 1.3 - - - -
128C HIS 3.4 15.5 - - - -
129C ALA* 4.2 9.0 - - + +
137C GLY* 1.3 77.0 - - - +
139C ARG* 1.3 62.3 + - - +
140C PHE* 2.9 29.3 - - - -
178C PHE* 3.1 7.7 - - - -
179C ILE 2.9 27.7 + - - -
182C ALA* 2.9 32.5 - - + +
183C HIS* 4.1 3.6 - - - +
184C ASN* 5.9 0.4 - - - +
220C ILE* 4.1 19.8 - - + +
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Residues in contact with ARG 139 (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 THR* 4.1 24.5 + - - +
126C GLY 3.2 12.0 - - - +
127C ALA* 3.3 3.5 - - - -
128C HIS* 2.9 32.6 + - + +
130C ASP* 4.2 19.2 - - + +
138C THR* 1.3 72.7 - - - +
140C PHE* 1.3 63.0 + - - +
141C SER* 2.5 30.7 + - - +
169C ARG* 4.8 12.5 - - - +
174C ILE* 4.9 7.5 - - - +
176C GLU* 3.2 48.8 + - + +
177C LEU 3.7 4.3 - - - +
178C PHE* 3.5 15.3 - - + -
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Residues in contact with PHE 140 (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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126C GLY 3.4 2.9 - - - -
127C ALA* 3.8 13.2 - - + -
138C THR* 2.9 34.8 - - - -
139C ARG* 1.3 73.2 - - - +
141C SER* 1.3 62.9 + - - +
152C VAL* 3.7 23.3 - - + -
156C PHE* 5.5 2.9 - + - -
166C MET* 3.3 16.2 - - + -
176C GLU* 2.8 8.0 - - - +
177C LEU 2.6 54.8 + - - +
179C ILE* 3.8 27.1 - - + -
182C ALA* 4.4 2.0 - - + -
188C TYR* 3.6 32.1 - + + -
190C TYR* 3.5 17.0 - + - +
220C ILE* 3.8 14.6 - - + -
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Residues in contact with SER 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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124C THR 3.8 5.6 + - - -
125C LEU* 4.1 4.7 - - - -
126C GLY* 3.0 31.0 + - - -
139C ARG* 2.5 48.9 + - - +
140C PHE* 1.3 73.0 + - - +
142C VAL* 1.3 68.7 + - - +
174C ILE* 4.0 8.7 - - - -
175C TRP 2.8 10.1 - - - -
176C GLU* 4.1 0.5 - - - +
190C TYR* 3.3 13.3 + - - -
204C ASP* 4.3 1.0 - - - +
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Residues in contact with VAL 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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125C LEU* 3.8 6.3 - - - +
141C SER* 1.3 80.7 - - - +
143C TRP* 1.3 65.4 + - - +
144C ALA* 3.4 3.6 + - + -
150C VAL* 4.5 11.0 - - + -
166C MET* 4.4 10.5 - - - -
174C ILE* 3.2 8.2 - - - +
175C TRP* 2.8 56.0 + - + +
190C TYR* 4.2 23.3 - - + -
204C ASP* 4.6 6.3 - - - +
205C PRO* 4.7 6.7 - - + -
351C PHE* 4.0 28.9 - - + -
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Residues in contact with TRP 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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125C LEU* 3.9 19.2 - - + +
142C VAL* 1.3 70.0 - - - +
144C ALA* 1.3 62.4 + - - +
145C PRO* 3.7 15.7 - - + +
172C SER 3.4 26.3 + - - -
173C GLY 3.5 8.3 - - - -
174C ILE* 4.2 7.4 - - + +
206C TYR* 6.3 0.9 - - + -
351C PHE* 3.3 12.6 - - - -
356C LEU* 3.3 72.4 - - + +
357C TYR* 3.9 26.6 + + - +
379C ARG* 3.8 15.5 - - + -
381C GLU* 3.1 59.4 + - + +
382C VAL* 4.9 0.9 - - + -
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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