Contacts of the strand formed by residues 174 - 180 (chain A) 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 ILE 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A LEU* 4.2 19.5 - - + -
141A SER* 4.3 15.9 - - - +
142A VAL 3.3 8.1 - - - +
143A TRP* 3.8 17.9 - - + -
167A ARG 4.3 0.5 - - - +
168A LEU* 3.8 1.0 - - - -
169A ARG* 3.3 28.1 + - + +
172A SER* 2.7 36.1 + - - +
173A GLY* 1.3 75.5 - - - +
175A TRP* 1.3 76.5 + - - +
176A GLU* 4.5 11.0 - - - +
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Residues in contact with TRP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A SER* 3.3 0.7 - - - -
142A VAL* 2.7 33.4 + - + +
144A ALA* 2.8 30.9 + - + +
146A ASN 4.3 2.7 - - - -
147A ALA* 3.3 23.9 - - + +
148A ARG* 3.8 4.0 - - - -
149A ARG* 3.1 26.7 - - - -
150A VAL* 3.4 31.0 - - + -
166A MET* 3.7 37.9 - - + -
167A ARG 4.0 5.4 - - - -
168A LEU* 3.7 42.3 - - + +
173A GLY 3.6 12.3 - - - -
174A ILE* 1.3 84.8 - - - +
176A GLU* 1.3 67.5 + - - +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ARG* 3.6 24.7 + - - +
140A PHE 3.2 17.5 - - - +
141A SER* 4.0 5.8 + - - +
166A MET* 4.0 7.9 - - - +
167A ARG* 2.9 45.9 + - - +
169A ARG* 3.3 36.5 + - - +
174A ILE* 4.5 10.2 - - + +
175A TRP* 1.3 80.6 - - - +
177A LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ARG* 4.5 3.3 - - - +
140A PHE* 3.3 32.7 + - - +
152A VAL* 3.6 11.7 - - + -
164A HIS* 3.3 49.1 - - + +
165A PRO* 3.3 20.9 - - + +
166A MET* 3.8 12.7 - - + +
167A ARG* 5.4 1.8 - - + +
176A GLU* 1.3 78.8 - - - +
178A PHE* 1.3 74.7 + - - +
179A ILE* 4.2 2.4 - - + +
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP* 3.6 27.8 - - + -
132A MET* 3.4 31.6 - - + -
135A VAL* 3.5 17.0 - - + -
136A THR 3.7 0.2 - - - -
137A GLY* 3.2 44.2 - - - -
138A THR 4.1 2.5 - - - -
139A ARG* 3.9 33.9 - - + +
164A HIS* 5.3 0.3 + - - -
177A LEU* 1.3 83.8 - - - +
179A ILE* 1.3 64.5 + - - +
180A PRO* 3.3 36.9 - - + +
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY* 3.0 2.1 - - - -
138A THR 3.0 32.0 + - - +
140A PHE* 3.9 9.4 - - + -
152A VAL* 3.8 22.7 - - + -
156A PHE* 3.8 33.0 - - + -
164A HIS* 3.0 45.5 - - + +
177A LEU* 4.2 7.2 - - + +
178A PHE* 1.3 85.4 - - - +
180A PRO* 1.3 76.1 - - + +
182A ALA* 3.2 18.9 - - + +
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Residues in contact with PRO 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL* 3.5 27.4 - - + -
136A THR 3.5 9.0 - - - +
164A HIS* 5.5 2.9 - - + -
178A PHE* 3.3 24.9 - - + +
179A ILE* 1.3 93.4 - - + +
181A GLY* 1.3 66.3 + - - +
182A ALA 3.1 2.6 + - - -
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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