Contacts of the strand formed by residues 174 - 180 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D LEU* 3.9 25.8 - - + -
141D SER* 4.1 7.0 - - - -
142D VAL 3.6 26.2 - - - +
143D TRP* 4.1 14.4 - - + -
167D ARG 3.9 0.5 - - - +
168D LEU* 3.5 3.1 - - - -
169D ARG* 2.6 40.1 + - + +
172D SER* 3.2 30.5 - - - +
173D GLY* 1.3 81.9 - - - +
175D TRP* 1.3 62.7 + - - +
176D GLU* 5.2 2.7 - - + +
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Residues in contact with TRP 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D SER* 3.0 4.5 - - - -
142D VAL* 2.9 43.7 + - + +
144D ALA* 2.8 31.1 + - + -
147D ALA 3.0 25.1 + - - -
148D ARG* 4.3 0.9 - - - -
149D ARG* 3.1 25.8 - - - -
150D VAL* 3.3 38.0 - - + +
166D MET* 3.3 47.5 - - + +
167D ARG 3.4 4.9 - - - -
168D LEU* 3.6 41.4 - - + +
174D ILE* 1.3 72.5 - - - +
176D GLU* 1.3 61.5 + - - +
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Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ARG* 2.5 47.9 + - - +
140D PHE 2.9 13.2 - - - +
141D SER* 3.8 11.2 - - - -
166D MET* 3.9 3.4 - - - -
167D ARG* 2.9 30.4 + - - +
169D ARG* 3.1 53.2 + - - +
174D ILE* 4.1 3.4 + - + +
175D TRP* 1.3 75.2 - - - +
177D LEU* 1.3 64.4 + - - +
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ARG* 3.5 5.2 - - - +
140D PHE* 2.7 44.5 + - - -
152D VAL* 4.5 2.7 - - + -
164D HIS* 3.5 34.3 - - + +
165D PRO 3.2 24.9 - - - +
166D MET* 3.9 15.5 - - + +
167D ARG 5.6 0.4 - - - +
169D ARG* 6.0 0.2 - - - +
176D GLU* 1.3 80.6 + - - +
178D PHE* 1.3 79.7 + - - +
179D ILE* 4.0 12.1 - - + -
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Residues in contact with PHE 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ASP* 3.6 27.8 - - + -
131D THR* 3.8 2.5 - - - -
132D MET* 3.4 37.5 - - + -
135D VAL* 3.3 31.0 - - + -
136D THR 4.4 0.7 - - - -
137D GLY* 3.5 18.8 - - - -
138D THR 3.5 31.0 - - - -
139D ARG* 3.7 23.3 - - + +
177D LEU* 1.3 92.1 - - + +
179D ILE* 1.3 59.3 + - - +
180D PRO* 3.8 23.9 - - + +
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Residues in contact with ILE 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLY* 4.4 1.6 - - - -
138D THR 3.2 13.2 + - - -
140D PHE* 3.8 26.2 - - + -
152D VAL* 4.0 21.1 - - + -
156D PHE* 4.4 12.8 - - + -
164D HIS* 3.9 46.9 - - + +
177D LEU* 4.0 11.0 - - + -
178D PHE* 1.3 80.5 - - - +
180D PRO* 1.3 75.8 - - + +
182D ALA* 3.0 31.8 + - + +
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Residues in contact with PRO 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D VAL* 3.3 33.4 - - + -
136D THR 3.2 8.7 - - - +
137D GLY* 3.9 2.5 - - - -
178D PHE* 3.8 18.8 - - + +
179D ILE* 1.3 94.4 - - + +
181D GLY* 1.3 58.8 + - - +
182D ALA 3.3 1.4 + - - -
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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