Contacts of the strand formed by residues 164 - 173 (chain D) in PDB entry 1MPX
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 SER 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D ASN* 4.0 9.0 + - - -
73D ALA 3.0 16.2 - - - -
75D ILE* 3.7 31.6 - - - +
113D ILE* 4.0 4.3 - - - -
157D LEU 4.3 3.6 + - - -
158D VAL* 4.6 2.1 + - - -
161D VAL* 2.9 21.3 + - - +
162D SER 3.8 7.6 - - - +
163D GLU* 1.3 81.0 - - - +
165D ASN* 1.3 59.8 + - - +
166D GLY* 3.3 13.3 + - - -
167D LYS 5.5 0.4 - - - -
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Residues in contact with ASN 165 (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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72D ASN* 3.5 40.6 + - - +
73D ALA 3.2 3.1 + - - +
74D PRO* 3.4 17.1 - - - +
164D SER* 1.3 71.4 - - - +
166D GLY* 1.3 59.1 + - - +
167D LYS* 3.1 30.7 + - - +
376D LEU 2.8 26.9 + - - -
378D ASP* 3.2 25.4 + - - +
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Residues in contact with GLY 166 (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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75D ILE* 6.1 0.4 - - - -
158D VAL* 3.4 40.7 - - - +
164D SER* 3.3 12.7 + - - -
165D ASN* 1.3 78.4 + - - +
167D LYS* 1.3 60.2 + - - +
168D VAL* 4.9 0.2 - - - -
190D ALA* 3.5 13.0 - - - +
192D LYS* 5.1 1.4 - - - -
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Residues in contact with LYS 167 (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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74D PRO* 3.7 2.9 - - - +
75D ILE* 3.1 25.3 + - - +
164D SER* 5.5 0.4 - - - -
165D ASN* 3.1 21.4 + - - +
166D GLY* 1.3 81.2 - - - +
168D VAL* 1.3 66.3 + - - +
190D ALA 3.9 3.6 - - - -
192D LYS* 4.1 19.1 - - + +
375D TYR 3.8 15.7 + - - +
376D LEU* 3.6 30.6 + - + +
377D VAL 4.6 2.6 + - - -
378D ASP* 2.9 33.9 + - - +
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Residues in contact with VAL 168 (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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75D ILE* 3.3 23.8 - - + +
77D LEU* 4.1 17.7 - - + -
154D ILE* 4.1 35.4 - - + +
157D LEU* 5.2 3.6 - - + -
158D VAL* 4.0 24.0 - - + -
167D LYS* 1.3 80.9 - - - +
169D GLY* 1.3 72.0 + - - +
170D MSE 4.6 0.4 - - + -
190D ALA 3.0 11.6 + - - +
191D LEU* 3.4 5.6 - - + -
192D LYS 2.9 26.2 + - - -
376D LEU* 3.4 8.4 - - - +
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Residues in contact with GLY 169 (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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75D ILE 2.9 10.1 + - - +
76D VAL* 3.3 2.3 - - - -
77D LEU 2.8 24.4 + - - -
168D VAL* 1.3 78.1 - - - +
170D MSE 1.3 63.3 - - - -
191D LEU* 4.1 0.4 - - - -
193D VAL* 3.3 24.0 - - - -
372D PHE* 4.1 7.0 - - - -
376D LEU* 3.7 8.5 - - - +
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Residues in contact with MSE 170 (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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77D LEU* 3.3 26.2 - - + +
79D ARG* 3.7 38.4 - - + +
150D ALA* 4.6 1.1 - - + -
154D ILE* 4.3 12.6 - - - -
168D VAL* 4.6 2.0 - - + -
169D GLY* 1.3 74.5 - - - +
171D ILE* 1.3 63.9 + - - +
179D THR* 3.8 20.9 - - - +
180D VAL* 4.1 24.2 - - + +
183D ALA* 3.5 24.7 - - + -
191D LEU* 3.7 22.9 - - + +
193D VAL 3.1 8.6 + - - +
194D ALA* 3.4 2.7 - - + -
195D VAL 2.9 25.1 + - - -
372D PHE* 3.8 5.1 - - - -
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Residues in contact with ILE 171 (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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76D VAL* 3.5 27.4 - - + -
77D LEU 3.2 4.2 + - - +
78D THR* 2.4 39.3 + - - +
107D PHE* 4.0 13.7 - - + -
114D ARG* 3.7 10.1 - - - +
170D MSE 1.3 76.2 - - - +
172D GLY* 1.3 64.5 + - - +
176D GLU 4.0 0.2 - - - +
180D VAL* 3.7 11.2 - - - +
195D VAL* 3.5 26.7 - - + +
197D GLU* 3.6 25.6 - - - +
344D ASN* 5.7 2.0 - - - +
368D LEU* 3.8 28.3 - - + -
372D PHE* 4.3 3.8 - - + -
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Residues in contact with GLY 172 (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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78D THR* 4.3 2.5 - - - -
114D ARG* 6.0 0.2 - - - -
171D ILE* 1.3 84.8 - - - +
173D SER* 1.3 59.2 + - - -
176D GLU* 3.4 21.5 + - - -
177D GLY* 3.1 13.2 - - - -
180D VAL* 4.0 0.4 - - - +
195D VAL 3.6 2.0 + - - -
197D GLU* 2.9 30.4 + - - +
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Residues in contact with SER 173 (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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82D TYR* 5.3 1.2 - - - -
172D GLY* 1.3 74.4 - - - -
174D SER* 1.3 67.9 + - - +
176D GLU* 3.0 29.2 + - - +
177D GLY 3.5 0.4 - - - -
197D GLU* 3.1 24.6 + - - +
198D SER* 4.0 8.0 + - - -
341D SER* 2.7 35.7 + - - -
343D VAL* 5.1 0.9 - - - +
344D ASN* 4.0 14.0 - - - +
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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