Contacts of the strand formed by residues 51 - 58 (chain A) in PDB entry 1MJV
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 ALA 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.4 19.5 - - + +
33A VAL 3.3 25.6 - - - +
34A ASP* 4.0 5.8 - - + +
35A ILE* 4.1 1.3 - - - -
49A PRO* 3.3 6.6 - - - +
50A SER* 1.3 86.4 + - - +
52A VAL* 1.3 62.7 + - - +
24B SER* 3.4 21.7 + - - +
59B GLY* 6.4 0.4 - - - -
60B ALA* 5.7 1.5 + - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR 3.3 0.5 - - - +
32A LEU* 3.4 3.3 - - - -
33A VAL* 2.8 29.1 + - - +
35A ILE* 3.3 24.9 - - + -
49A PRO* 3.8 19.1 - - + -
51A ALA* 1.3 78.7 - - - +
53A PRO* 1.3 69.2 - - + +
54A LEU* 3.5 19.3 + - + -
78A MET* 3.9 28.5 - - + -
80A ILE* 4.0 7.2 - - + -
96A PHE* 4.3 10.3 - - + -
20B VAL* 3.9 7.6 - - + -
24B SER* 3.8 4.3 - - - +
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Residues in contact with PRO 53 (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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30A GLU* 3.7 34.6 - - + +
31A THR 3.4 6.3 - - - +
32A LEU* 4.0 17.5 - - + -
52A VAL* 1.3 85.8 - - + +
54A LEU* 1.3 67.9 + - - +
78A MET* 3.8 12.1 - - + +
98A GLN* 4.5 2.9 + - - -
20B VAL* 5.1 0.9 - - + +
23B ARG* 3.8 31.4 - - + +
24B SER* 3.2 18.6 - - - +
27B HIS* 6.1 0.7 - - + -
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Residues in contact with LEU 54 (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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30A GLU* 4.2 2.5 - - - -
31A THR* 2.7 43.4 + - - +
33A VAL* 3.8 20.4 - - + -
52A VAL* 4.0 10.8 - - + +
53A PRO* 1.3 82.6 - - - +
55A MET* 1.3 63.1 + - - +
56A ARG* 3.3 36.9 + - - +
76A ILE* 3.8 10.1 - - + -
78A MET* 3.7 21.8 - - + -
96A PHE* 3.7 33.7 - - + -
97A LEU 3.8 4.0 - - - +
98A GLN* 3.4 11.9 - - + +
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Residues in contact with MET 55 (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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28A PRO* 3.7 33.0 - - + +
29A ILE 3.5 1.8 - - - -
30A GLU* 3.6 36.3 - - + +
54A LEU* 1.3 70.2 - - - +
56A ARG* 1.3 66.2 + - - +
98A GLN* 2.8 30.1 - - + +
99A HIS 2.9 41.4 + - - +
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Residues in contact with ARG 56 (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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28A PRO* 4.2 2.2 - - - -
29A ILE* 2.8 33.1 + - - +
31A THR* 4.1 15.6 + - + +
33A VAL* 4.1 21.2 - - + +
37A GLN* 5.2 2.8 - - - +
38A GLU* 2.9 33.7 + - - -
54A LEU* 3.6 27.8 - - - +
55A MET* 1.3 87.1 + - - +
57A CYS* 1.3 67.2 + - - +
58A GLY 3.5 1.0 + - - -
97A LEU* 2.9 39.3 + - - +
99A HIS* 3.4 30.9 + - + +
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Residues in contact with CYS 57 (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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27A HIS 3.4 1.1 - - - -
56A ARG* 1.3 76.1 - - - +
58A GLY* 1.3 59.0 - - - +
68A CYS* 3.8 24.4 - - - +
69A VAL* 3.7 0.7 - - - -
70A PRO* 3.4 32.3 - - + -
99A HIS* 2.9 24.6 + - + +
102A CYS* 2.0 49.1 - - - -
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Residues in contact with GLY 58 (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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27A HIS* 2.9 32.1 + - - +
29A ILE* 3.6 14.0 - - - +
56A ARG 3.5 1.0 + - - -
57A CYS* 1.3 76.5 - - - +
59A GLY* 1.3 59.0 + - - -
68A CYS* 3.6 9.8 - - - -
32B LEU* 3.6 9.6 - - - -
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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