Contacts of the strand formed by residues 45 - 51 (chain Y) in PDB entry 4MXV
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 LEU 45 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36X TYR* 5.6 0.2 - - + -
44X PRO* 3.9 33.9 - - + -
87X TYR* 4.0 23.5 - - + -
98X PHE* 3.3 66.9 + - + +
99X GLY 5.2 0.2 + - - -
37Y VAL* 4.1 14.6 - - + -
38Y ARG 3.4 1.6 - - - -
39Y GLN* 3.7 35.7 - - + +
44Y GLY* 1.3 76.4 - - - -
46Y GLU* 1.3 62.7 + - - +
91Y TYR* 4.9 2.5 - - + -
103Y TRP* 4.7 2.2 - - + -
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Residues in contact with GLU 46 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X PHE* 4.7 1.3 - - - -
37Y VAL* 3.3 5.4 - - - -
38Y ARG* 2.7 66.3 + - + +
44Y GLY 5.4 0.7 - - - +
45Y LEU* 1.3 75.1 - - - +
47Y TRP* 1.3 71.6 + - - +
48Y VAL* 3.8 1.8 + - - +
60Y ASN* 4.2 5.9 + - - +
62Y LYS* 2.6 44.0 + - - +
63Y PHE* 3.8 10.6 - - + -
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Residues in contact with TRP 47 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X THR* 3.2 32.1 - - + -
95X PRO* 3.5 22.8 - - + +
96X TRP* 3.5 39.6 + + + +
97X THR* 6.4 0.2 - - - +
98X PHE* 4.7 4.7 - - + -
35Y HIS* 3.0 23.1 + + - -
36Y TRP 3.9 10.1 - - - -
37Y VAL* 4.0 9.6 - - + +
46Y GLU* 1.3 74.0 - - - +
48Y VAL* 1.3 61.1 + - - +
49Y GLY* 3.5 20.1 - - - -
50Y TYR* 3.7 10.3 - + - -
58Y ASN* 3.5 23.3 - - - -
59Y TYR 3.9 5.2 - - - -
60Y ASN* 2.8 50.7 + - + +
63Y PHE* 4.1 1.6 - - - -
100Y PHE* 3.7 27.1 - + + -
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Residues in contact with VAL 48 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Y TRP* 2.8 34.4 + - + +
37Y VAL 4.5 0.2 - - - -
38Y ARG* 4.1 20.2 - - + +
46Y GLU 4.0 8.1 - - - +
47Y TRP* 1.3 77.2 - - - +
49Y GLY* 1.3 62.5 + - - +
59Y TYR* 3.5 7.1 - - + +
60Y ASN* 2.7 25.6 + - - +
63Y PHE* 3.8 27.6 - - + +
67Y PHE* 4.2 20.6 - - + -
69Y ILE* 4.1 12.1 - - + -
80Y LEU* 4.4 6.1 - - + -
90Y TYR* 5.0 7.0 - - + -
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Residues in contact with GLY 49 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Y HIS* 3.5 1.6 - - - -
36Y TRP 2.8 27.0 + - - +
47Y TRP* 3.5 15.5 + - - -
48Y VAL* 1.3 83.6 - - - +
50Y TYR* 1.3 60.5 + - - -
58Y ASN 3.1 14.8 - - - -
59Y TYR* 4.0 1.1 - - - -
69Y ILE* 3.5 17.3 - - - +
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Residues in contact with TYR 50 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LEU* 3.6 12.9 - - + +
144D GLY* 3.5 27.7 + - - -
146D GLN* 4.4 2.2 + - - -
96X TRP* 4.0 9.4 - + - -
33Y VAL* 3.1 32.8 - - + -
34Y ILE 3.4 8.3 - - - +
35Y HIS* 3.3 33.0 - + - +
47Y TRP* 3.7 13.7 - + - -
49Y GLY* 1.3 71.4 - - - -
51Y ASN* 1.3 62.8 + - - +
52Y ASN* 4.7 2.2 - - + -
56Y GLY 5.2 2.0 - - - -
57Y THR* 3.3 7.1 - - - -
58Y ASN* 3.0 72.9 + - + +
69Y ILE* 4.0 5.1 - - - +
98Y LEU* 3.9 20.5 - - + +
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Residues in contact with ASN 51 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y VAL* 3.9 3.6 - - - -
34Y ILE* 3.2 28.0 + - - +
50Y TYR* 1.3 78.1 - - - +
52Y ASN* 1.3 69.0 + - - +
55Y ALA* 3.5 13.3 + - - +
56Y GLY 3.3 9.3 + - - -
57Y THR* 3.3 21.7 - - + +
69Y ILE* 3.5 28.1 + - + -
70Y SER* 3.5 15.5 - - - +
71Y SER* 2.4 33.4 + - - +
78Y ALA* 5.1 2.4 - - + +
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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