Contacts of the strand formed by residues 164 - 173 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASN* 4.0 7.0 - - - +
73A ALA 3.0 15.8 + - - -
75A ILE* 3.2 34.9 - - - +
113A ILE* 4.2 0.7 - - - -
157A LEU 5.1 1.3 - - - -
158A VAL* 5.6 1.3 - - - -
161A VAL* 3.1 22.3 + - - +
162A SER 3.8 7.3 - - - +
163A GLU* 1.3 81.3 - - - +
165A ASN* 1.3 69.2 + - - +
166A GLY* 3.3 14.3 + - - -
167A LYS 4.3 1.7 + - - -
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Residues in contact with ASN 165 (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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72A ASN* 3.4 45.4 + - - +
73A ALA 3.2 5.3 + - - +
74A PRO* 3.4 18.0 - - - +
164A SER* 1.3 74.8 + - - +
166A GLY* 1.3 58.3 + - - +
167A LYS* 3.1 26.1 + - - +
376A LEU 2.8 27.3 + - - -
377A VAL* 4.5 0.2 - - - +
378A ASP* 3.1 22.7 + - - +
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Residues in contact with GLY 166 (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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158A VAL* 3.4 42.5 - - - +
164A SER* 3.3 11.2 + - - -
165A ASN* 1.3 77.6 - - - +
167A LYS* 1.3 58.4 + - - +
190A ALA* 3.4 14.2 - - - +
192A LYS* 5.1 1.4 - - - -
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Residues in contact with LYS 167 (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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74A PRO* 3.7 1.6 - - - +
75A ILE* 3.1 24.6 + - - +
164A SER* 4.4 1.2 + - - -
165A ASN* 3.1 21.2 + - - +
166A GLY* 1.3 82.3 - - - +
168A VAL* 1.3 63.4 + - - +
190A ALA 3.9 3.4 - - - -
192A LYS* 4.1 19.1 - - + +
375A TYR 3.9 15.6 + - - +
376A LEU* 3.5 32.5 + - + +
377A VAL 4.7 2.4 + - - -
378A ASP* 3.0 32.5 + - - +
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Residues in contact with VAL 168 (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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75A ILE* 3.4 24.0 - - + +
77A LEU* 4.1 19.5 - - + -
154A ILE* 3.9 43.3 - - + +
157A LEU* 5.2 2.9 - - + -
158A VAL* 3.9 16.6 - - + -
167A LYS* 1.3 78.8 - - - +
169A GLY* 1.3 71.7 + - - +
170A MSE 4.6 0.2 - - + -
190A ALA 3.0 12.4 + - - +
191A LEU* 3.4 6.6 - - + -
192A LYS 2.9 26.3 + - - -
376A LEU* 3.4 7.2 - - - +
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Residues in contact with GLY 169 (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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75A ILE 2.9 11.3 + - - -
76A VAL* 3.3 3.7 - - - -
77A LEU 2.8 25.5 + - - -
168A VAL* 1.3 77.3 - - - +
170A MSE 1.3 62.9 + - - -
193A VAL* 3.3 24.7 - - - -
372A PHE* 4.2 6.7 - - - -
376A LEU* 3.7 7.7 - - - +
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Residues in contact with MSE 170 (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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77A LEU* 3.3 25.4 - - + +
79A ARG* 3.9 33.4 - - + +
150A ALA* 4.6 1.6 - - + -
154A ILE* 4.2 12.6 - - - -
168A VAL* 4.6 1.6 - - + -
169A GLY* 1.3 75.7 - - - +
171A ILE* 1.3 64.4 + - - +
179A THR* 3.8 22.9 - - - +
180A VAL* 4.1 23.1 - - + +
183A ALA* 3.5 25.6 - - + -
191A LEU* 3.6 24.0 - - + +
193A VAL 3.0 7.8 + - - +
194A ALA* 3.4 3.1 - - + -
195A VAL 2.9 24.5 + - - -
372A PHE* 3.8 3.3 - - - -
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Residues in contact with ILE 171 (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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76A VAL* 3.5 28.7 - - + -
77A LEU 3.2 4.2 + - - +
78A THR* 2.6 32.3 + - - +
107A PHE* 4.1 13.0 - - + -
114A ARG* 3.8 15.3 - - - +
170A MSE 1.3 75.7 - - - +
172A GLY* 1.3 63.9 + - - +
176A GLU 4.0 0.3 - - - +
180A VAL* 3.7 10.4 - - - +
195A VAL* 3.5 28.3 - - + +
197A GLU* 3.7 24.7 - - - +
344A ASN* 5.7 2.2 - - - +
368A LEU* 3.8 29.4 - - + -
372A PHE* 4.2 4.7 - - + -
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Residues in contact with GLY 172 (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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78A THR* 4.4 1.6 - - - -
114A ARG* 6.0 0.2 - - - -
171A ILE* 1.3 84.7 - - - +
173A SER* 1.3 58.7 + - - -
176A GLU* 3.4 22.4 + - - -
177A GLY* 3.0 14.5 - - - -
180A VAL* 4.0 0.4 - - - +
195A VAL 3.6 1.6 + - - -
197A GLU* 2.9 30.5 + - - -
344A ASN* 6.0 0.4 - - - -
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Residues in contact with SER 173 (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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82A TYR* 5.3 1.7 - - - -
172A GLY* 1.3 74.5 - - - -
174A SER* 1.3 67.5 + - - +
175A TYR 3.3 0.2 + - - -
176A GLU* 3.1 26.2 + - - +
177A GLY 3.5 0.4 - - - -
197A GLU* 3.1 23.7 + - - +
198A SER* 4.0 8.8 + - - -
341A SER* 2.6 34.9 + - - -
343A VAL* 5.0 0.9 - - - +
344A ASN* 3.9 14.7 - - - +
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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