Contacts of the strand formed by residues 164 - 173 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ASN* 3.9 8.7 + - - -
73C ALA 2.8 19.0 + - - -
74C PRO* 4.2 1.0 - - - +
75C ILE* 3.4 34.0 + - - +
113C ILE* 4.1 0.9 - - - -
157C LEU 5.2 1.1 - - - -
158C VAL* 5.8 0.4 - - - -
161C VAL* 3.2 20.7 + - - +
162C SER 3.7 8.1 - - - +
163C GLU* 1.3 82.1 - - - +
165C ASN* 1.3 65.3 + - - +
166C GLY* 3.3 15.6 + - - -
167C LYS 4.3 1.2 + - - -
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Residues in contact with ASN 165 (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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72C ASN* 3.4 41.9 + - - +
73C ALA 3.1 1.4 + - - -
74C PRO* 3.3 19.4 - - - +
164C SER* 1.3 75.0 + - - +
166C GLY* 1.3 57.9 + - - +
167C LYS* 3.1 30.1 + - - +
376C LEU 2.8 26.3 + - - -
378C ASP* 3.0 26.4 + - - +
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Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C VAL* 3.3 44.1 - - - +
164C SER* 3.3 11.7 + - - -
165C ASN* 1.3 77.5 - - - +
167C LYS* 1.3 59.2 + - - +
168C VAL* 4.8 0.2 - - - -
190C ALA* 3.4 13.3 - - - +
192C LYS* 5.1 1.4 - - - -
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Residues in contact with LYS 167 (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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74C PRO* 3.7 2.8 - - + +
75C ILE* 3.0 24.6 + - - +
164C SER* 4.3 1.2 + - - -
165C ASN* 3.1 21.9 + - - +
166C GLY* 1.3 81.4 - - - +
168C VAL* 1.3 64.0 + - - +
190C ALA 3.9 3.8 - - - -
192C LYS* 4.1 18.8 - - + +
375C TYR 3.8 17.9 - - - +
376C LEU* 3.8 26.1 + - + +
377C VAL 5.4 0.6 - - - -
378C ASP* 2.8 30.1 + - - +
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Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 3.3 23.3 - - + +
77C LEU* 4.2 13.9 - - + -
154C ILE* 4.0 36.3 - - + +
157C LEU* 5.2 3.8 - - + -
158C VAL* 4.0 24.2 - - + -
167C LYS* 1.3 79.8 - - - +
169C GLY* 1.3 72.4 + - - +
170C MSE 4.6 0.4 - - + -
190C ALA 3.0 15.1 + - - +
191C LEU* 3.4 7.3 - - + +
192C LYS 2.9 26.3 + - - -
376C LEU* 3.5 6.7 - - - +
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Residues in contact with GLY 169 (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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75C ILE 2.8 9.2 + - - -
76C VAL* 3.3 4.0 - - - -
77C LEU 2.8 24.9 + - - -
168C VAL* 1.3 77.2 - - - +
170C MSE 1.3 61.8 - - - -
193C VAL* 3.3 24.5 - - - -
372C PHE* 4.2 7.0 - - - -
376C LEU* 3.7 9.8 - - - +
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Residues in contact with MSE 170 (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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77C LEU* 3.3 26.5 - - + +
79C ARG* 3.6 39.9 - - + +
150C ALA* 4.5 1.1 - - + -
154C ILE* 4.2 13.5 - - - -
168C VAL* 4.6 1.8 - - + -
169C GLY* 1.3 73.8 - - - +
171C ILE* 1.3 64.0 + - - +
179C THR* 3.8 18.8 - - - +
180C VAL* 4.1 24.0 - - + -
183C ALA* 3.5 24.9 - - + -
191C LEU* 3.7 24.0 - - + +
193C VAL 3.0 8.8 + - - +
194C ALA* 3.4 2.3 - - + -
195C VAL 2.9 24.6 + - - -
372C PHE* 3.8 3.9 - - - -
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Residues in contact with ILE 171 (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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76C VAL* 3.5 18.8 - - + -
77C LEU 3.2 4.6 + - - +
78C THR* 2.5 31.9 + - - +
107C PHE* 3.9 15.0 - - + -
114C ARG* 3.5 25.4 - - - +
170C MSE 1.3 74.9 - - - +
172C GLY* 1.3 63.0 + - - +
176C GLU 4.0 0.2 - - - +
180C VAL* 3.8 10.6 - - - +
195C VAL* 3.5 21.1 - - + +
197C GLU* 3.6 24.9 - - - +
344C ASN* 5.7 2.0 - - - +
368C LEU* 3.8 35.0 - - + -
372C PHE* 4.3 5.2 - - + -
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Residues in contact with GLY 172 (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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78C THR* 4.3 3.6 - - - -
114C ARG* 5.9 0.2 - - - -
171C ILE* 1.3 85.7 - - - +
173C SER* 1.3 57.8 + - - -
176C GLU* 3.5 19.7 - - - -
177C GLY* 3.0 13.7 - - - -
180C VAL* 4.1 0.4 - - - +
195C VAL 3.6 2.0 + - - +
197C GLU* 2.9 30.0 + - - +
344C ASN* 5.9 0.2 - - - -
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Residues in contact with SER 173 (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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82C TYR* 5.3 1.4 - - - -
172C GLY* 1.3 74.5 - - - -
174C SER* 1.3 67.8 + - - +
176C GLU* 3.1 27.2 + - - +
177C GLY 3.6 0.4 - - - -
197C GLU* 3.1 25.7 + - - +
198C SER* 3.9 9.0 + - - -
341C SER* 2.8 34.2 + - - -
343C VAL* 5.0 0.9 - - - +
344C ASN* 4.0 13.6 - - - +
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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