Contacts of the strand formed by residues 47 - 53 (chain D) in PDB entry 3MX4
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 GLY 47 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA* 1.3 75.7 - - - +
48D VAL* 1.3 63.5 + - - -
79D LYS* 3.4 1.7 - - - -
80D ALA 2.8 39.4 + - - +
101D LEU* 3.7 10.1 - - - +
128D VAL 3.1 10.3 - - - -
130D PHE* 3.8 12.6 - - - -
138D ILE* 3.6 8.3 - - - +
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Residues in contact with VAL 48 (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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29D PHE* 4.4 7.6 - - + -
47D GLY* 1.3 75.6 - - - -
49D TYR* 1.3 65.2 + - - +
77D VAL* 3.9 11.9 - - + -
78D GLY 3.3 13.2 - - - +
79D LYS* 4.5 1.1 - - + -
101D LEU* 3.7 5.1 - - - +
127D PHE* 3.4 4.3 - - - +
128D VAL* 2.9 30.5 + - + +
130D PHE* 4.1 16.5 - - + -
138D ILE* 3.4 31.6 - - + +
141D VAL* 4.2 6.1 - - + -
142D GLN* 3.9 13.0 - - + +
145D LEU* 3.7 26.9 - - + -
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PHE* 4.2 4.9 - - - -
48D VAL* 1.3 74.4 - - - +
50D ALA* 1.3 61.2 + - - +
51D LEU* 3.6 30.3 - - + -
76D TYR* 3.7 16.6 + + - -
77D VAL* 3.3 8.3 - - - +
78D GLY* 2.8 61.2 + - - +
79D LYS* 3.7 12.1 + - - -
101D LEU* 3.5 17.3 - - + -
104D ARG* 4.3 14.9 - - + +
105D ILE* 3.6 29.2 - - + -
108D HIS* 3.0 41.7 + + + -
125D CYS* 5.4 0.7 - - + -
126D ARG 3.2 13.2 - - - +
127D PHE* 3.9 1.1 - - + +
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Residues in contact with ALA 50 (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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29D PHE* 3.6 25.4 - - + -
49D TYR* 1.3 76.8 - - - +
51D LEU* 1.3 64.2 + - - +
52D TYR* 3.7 10.5 - - + +
74D PRO* 3.9 17.9 - - + -
76D TYR 3.2 9.6 - - - +
77D VAL* 4.1 7.2 - - + -
125D CYS* 3.0 27.5 - - - +
126D ARG 3.0 11.2 + - - -
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Residues in contact with LEU 51 (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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37D LEU* 4.0 30.1 - - + -
49D TYR* 3.6 24.9 - - + -
50D ALA* 1.3 82.2 - - - +
52D TYR* 1.3 58.0 + - - +
74D PRO* 3.1 5.9 - - - +
75D ILE* 2.7 44.4 + - + -
76D TYR* 2.9 24.5 + - + +
105D ILE* 5.5 0.2 - - + -
108D HIS* 4.6 4.3 - - + -
112D ILE* 4.9 2.7 - - + -
123D PHE* 4.7 5.8 - - + -
124D SER 3.1 3.4 - - - +
125D CYS* 3.8 15.7 - - + -
153D TRP* 5.0 2.2 - - + -
160D PHE* 3.8 31.9 - - + -
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Residues in contact with TYR 52 (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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29D PHE* 4.2 5.7 - - - -
30D SER* 5.9 0.5 - - - -
34D VAL* 5.3 0.9 - - + -
50D ALA* 3.7 28.8 - - + +
51D LEU* 1.3 75.8 - - - +
53D TYR* 1.3 60.4 + - - +
54D THR* 5.2 0.6 - - - +
67D ASN* 4.3 4.5 - - - +
71D TYR* 3.5 52.7 + + + -
72D ASN 4.1 1.2 + - - -
73D LEU 3.5 18.2 - - - -
74D PRO* 3.7 25.9 - - + +
75D ILE* 4.5 3.4 - - - +
122D ASP 3.8 0.2 - - - +
123D PHE* 3.1 10.7 - - - -
124D SER* 2.7 45.4 + - - +
125D CYS* 4.2 1.6 - - - -
126D ARG* 3.0 42.9 + - + -
149D TYR* 5.9 2.3 - - - -
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Residues in contact with TYR 53 (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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52D TYR* 1.3 73.2 - - - +
54D THR* 1.3 65.1 + - - +
55D GLY* 3.2 31.3 - - - -
56D HIS 3.2 4.1 + - - -
57D TYR* 3.0 31.0 + - + +
60D TYR* 3.6 38.6 - + + -
63D TYR* 3.3 25.1 - + + +
67D ASN* 3.2 21.5 + - - +
73D LEU 5.1 0.6 + - - -
75D ILE* 4.3 11.8 - - + +
117D ASN 5.1 0.2 + - - -
118D LEU* 3.9 12.8 - - + +
119D ASP 4.8 3.6 + - - -
122D ASP* 3.4 27.8 + - + -
123D PHE* 3.3 39.3 - + + -
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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