Contacts of the strand formed by residues 34 - 39 (chain X) in PDB entry 1MHP
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 MET 34 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4X LEU* 4.5 11.0 - - + -
22X CYS* 6.0 2.2 - - - -
24X ALA* 4.8 0.4 - - + -
27X PHE* 3.8 13.9 - - + -
29X PHE* 3.3 41.1 - - + -
32X TYR* 4.1 10.1 - - - +
33X THR* 1.3 75.0 - - - +
35X SER* 1.3 66.3 + - - +
50X THR* 3.4 1.6 - - - +
51X ILE* 3.0 39.3 + - + +
71X ARG* 3.5 12.5 - - - +
78X LEU* 3.7 20.9 - - + -
95X CYS* 6.2 0.2 - - + -
96X THR 3.3 16.2 - - - +
97X ARG* 3.8 33.2 - - + -
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Residues in contact with SER 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X THR* 4.5 3.3 + - - -
34X MET* 1.3 75.2 + - - +
36X TRP* 1.3 65.9 + - - +
47X TRP* 4.4 3.8 - - - -
49X ALA 3.2 7.0 - - - -
50X THR* 2.5 31.6 + - - +
69X ILE* 4.4 1.6 - - - -
78X LEU* 3.7 3.3 - - - +
95X CYS* 3.4 4.3 - - - -
96X THR* 2.7 49.6 + - - -
98X GLY 5.7 0.8 + - - -
102X GLY 4.6 2.4 + - - -
105X PHE* 4.3 12.7 - - - -
95Y TRP* 3.9 8.7 - - - -
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Residues in contact with TRP 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X GLU* 3.0 24.5 - - - -
20X LEU* 3.7 30.3 - - + -
21X SER 3.8 8.5 - - - -
22X CYS* 3.7 20.0 - - + -
35X SER* 1.3 74.4 - - - +
37X VAL* 1.3 58.8 + - - +
47X TRP* 4.0 1.6 - - - -
48X VAL* 2.7 46.7 + - + +
49X ALA* 3.0 9.7 + - + +
69X ILE* 3.8 18.4 - - + -
78X LEU* 2.9 52.8 - - + +
79X TYR 3.6 4.9 + - - -
80X LEU* 3.4 38.5 - - + +
93X TYR* 4.4 5.2 - - + -
94X TYR 3.2 23.8 - - - -
95X CYS* 3.7 6.3 - - + -
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Residues in contact with VAL 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X TRP* 1.3 78.6 - - - +
38X ARG* 1.3 63.6 + - - +
45X LEU* 4.0 11.2 - - + -
46X GLU 3.1 17.0 - - - +
47X TRP* 4.5 5.6 - - + -
48X VAL* 4.4 0.7 - - - -
93X TYR* 4.7 1.3 - - - -
94X TYR* 2.8 47.7 + - + +
96X THR* 4.1 13.5 - - + +
105X PHE* 3.9 34.5 - - + -
108X TRP* 3.8 28.5 - - + -
97Y PHE* 4.0 9.4 - - + -
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Residues in contact with ARG 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X VAL* 1.3 75.8 - - - +
39X GLN* 1.3 63.8 + - - +
40X ALA* 5.2 3.6 - - - +
45X LEU* 3.6 2.5 - - - -
46X GLU* 2.7 92.8 + - + +
48X VAL* 3.4 16.3 - - + +
60X LEU* 4.3 3.0 - - - +
62X SER* 4.6 5.9 + - - -
63X VAL* 3.6 25.3 - - - +
67X PHE* 3.7 6.3 - - - -
88X GLU* 4.5 8.4 + - - +
89X ASP* 3.0 36.0 + - - +
91X ALA* 4.7 7.2 - - + -
92X VAL 3.5 6.7 - - - +
93X TYR* 2.9 49.6 + - + -
94X TYR* 4.9 0.4 - - - -
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Residues in contact with GLN 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X ARG* 1.3 80.1 - - - +
40X ALA* 1.3 63.6 + - - +
41X PRO* 3.5 1.6 - - - +
42X GLY 6.0 0.2 - - - +
43X LYS 3.0 23.1 + - - +
44X GLY 3.1 22.5 - - - +
45X LEU* 3.7 16.2 - - + +
46X GLU* 5.7 0.2 - - - -
91X ALA* 2.9 13.6 - - - +
92X VAL* 3.0 31.7 + - + +
94X TYR* 3.6 11.5 + - + -
37Y GLN* 3.2 31.0 + - - +
86Y TYR* 3.0 22.8 + - - -
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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