Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 2DMZ
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL 3.3 1.2 - - - +
36A TYR* 3.2 30.2 + - - +
46A SER* 1.3 75.1 - - - +
48A ILE* 1.3 66.9 + - - -
49A TYR* 3.1 18.5 - - - -
70A LYS* 5.3 3.4 - - - -
80A GLN 5.8 3.6 - - - -
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Residues in contact with ILE 48 (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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33A ILE* 3.8 34.1 - - + -
34A VAL 3.3 12.3 - - - +
35A GLY* 4.1 5.2 - - - -
47A GLY* 1.3 73.4 - - - -
49A TYR* 1.3 63.2 + - - +
70A LYS* 3.5 9.0 - - - +
71A ILE* 3.1 47.9 + - + +
79A ILE* 4.3 14.1 - - + +
80A GLN 5.8 2.2 + - - +
82A PHE 4.6 11.4 - - - +
84A ASN* 4.0 29.8 - - - +
87A VAL* 4.1 17.9 - - + -
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Residues in contact with TYR 49 (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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33A ILE* 3.4 2.7 - - - -
34A VAL* 2.8 40.5 + - + +
36A TYR* 4.0 16.4 - + + -
45A ALA* 3.7 25.5 - - + +
46A SER 3.8 10.6 + - - -
47A GLY* 3.1 42.6 - - - -
48A ILE* 1.3 73.9 - - - +
50A VAL* 1.3 62.8 + - - +
51A LYS 2.9 4.0 + - - -
68A ASN* 5.3 3.6 - - - +
69A ASP 3.1 26.0 - - - +
70A LYS* 3.4 32.8 - - + +
71A ILE* 4.0 5.4 - - - -
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Residues in contact with VAL 50 (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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31A ILE* 4.3 11.0 - - + -
32A ARG 3.3 7.4 - - - +
49A TYR* 1.3 68.6 - - - +
51A LYS* 1.3 63.1 + - - +
52A SER 3.3 23.3 - - - +
53A VAL* 3.8 6.5 - - + -
65A ILE* 4.0 17.9 - - + -
66A GLN* 3.6 20.0 - - - +
67A VAL* 3.2 34.8 - - - +
68A ASN 3.7 3.3 + - - -
69A ASP* 3.1 13.1 + - + +
71A ILE* 3.4 24.0 - - + -
102A LEU* 4.7 0.2 - - + -
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Residues in contact with LYS 51 (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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32A ARG* 2.9 17.2 + - + +
33A ILE 4.1 15.7 - - - +
34A VAL* 4.1 25.5 - - + +
49A TYR 2.9 6.4 + - - -
50A VAL* 1.3 71.8 - - - +
52A SER* 1.3 72.8 + - - +
67A VAL* 3.3 10.2 - - - +
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Residues in contact with SER 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE 4.0 0.2 - - - -
32A ARG* 3.0 39.0 + - - +
50A VAL* 3.3 12.1 - - - +
51A LYS* 1.3 89.2 + - - +
53A VAL* 1.3 67.2 + - - +
67A VAL* 3.4 11.3 - - - +
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Residues in contact with VAL 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 GLY 3.7 12.8 - - - +
31A ILE* 5.5 1.3 - - + -
50A VAL* 3.8 8.5 - - + -
52A SER* 1.3 85.5 - - - +
54A ILE* 1.3 66.8 + - - +
55A PRO* 3.3 7.5 - - - +
59A ALA* 3.9 7.4 - - + -
60A TYR* 3.8 36.8 - - + +
65A ILE* 3.8 6.5 - - + +
66A GLN* 3.8 31.4 - - + -
67A VAL* 4.0 6.6 - - + +
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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