Contacts of the strand formed by residues 45 - 49 (chain A) in PDB entry 3ZG6
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 VAL 45 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.2 17.0 - - + +
42A SER* 3.9 26.9 - - - +
43A SER 4.4 0.9 + - - -
44A SER* 1.3 77.1 + - - +
46A VAL* 1.3 63.6 + - - +
47A PHE* 3.7 27.9 + - + -
104A LEU* 3.5 21.7 - - - +
105A LEU* 3.6 2.8 - - - -
106A ARG* 2.7 34.3 + - - +
107A PHE 3.6 1.2 + - - +
207A LEU* 3.3 16.8 - - + +
209A ILE* 3.9 18.2 - - + -
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 4.7 0.9 - - - +
45A VAL* 1.3 78.4 - - - +
47A PHE* 1.3 68.3 + - - +
48A HIS* 3.5 25.8 - - + +
106A ARG* 4.4 7.4 - - + -
107A PHE* 3.4 18.6 - - + +
109A VAL* 4.1 12.3 - - + -
201A ALA* 3.5 37.5 - - + +
202A SER* 4.4 6.1 - - - +
205A ALA* 3.8 8.1 - - + -
207A LEU 2.9 7.1 + - - +
208A SER* 3.3 13.2 - - - +
209A ILE* 2.9 25.8 + - - +
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Residues in contact with PHE 47 (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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39A VAL* 5.2 2.7 - - + -
45A VAL* 3.7 20.0 - - + -
46A VAL* 1.3 79.4 - - - +
48A HIS* 1.3 62.6 + - - +
49A THR* 4.9 1.8 - - + -
96A LEU* 3.5 18.6 - - + -
99A LEU* 3.7 25.1 - - + -
104A LEU 4.5 1.8 - - - -
105A LEU* 3.5 30.3 - - + -
107A PHE 3.1 8.1 + - - +
108A LEU* 3.4 19.7 - - + +
109A VAL 2.9 26.0 + - - -
209A ILE* 3.3 39.7 - - + -
211A LEU* 3.7 16.2 - - + -
260A MET* 3.9 15.3 - - + -
263A LEU* 5.0 4.7 - - + -
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Residues in contact with HIS 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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46A VAL* 3.5 17.7 - - + +
47A PHE* 1.3 77.8 - - - +
49A THR* 1.3 62.8 + - - +
109A VAL* 3.2 22.6 - - + +
111A GLN* 5.7 2.5 - - - +
202A SER* 3.4 26.0 - - - -
208A SER* 2.9 28.9 + - - -
209A ILE 2.9 16.8 + - - +
210A THR* 3.3 11.5 - - + -
211A LEU 2.8 27.0 + - - +
213A THR* 4.2 5.8 - - + +
215A LEU* 5.6 0.9 - - + -
220A SER 4.9 2.7 + - - +
223A LEU* 4.0 4.8 - - + +
224A PRO* 3.5 36.3 - - + +
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Residues in contact with THR 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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47A PHE* 4.9 0.4 - - + -
48A HIS* 1.3 80.1 - - - +
50A GLY* 1.3 59.7 + - - +
53A ILE* 3.5 28.7 - - + +
96A LEU* 4.0 11.4 - - + -
108A LEU* 3.8 19.4 - - + +
109A VAL 3.0 6.3 + - - +
110A SER* 2.9 23.0 + - - -
111A GLN* 3.0 30.9 + - - +
112A ASN* 4.7 0.2 - - - -
117A HIS* 2.9 11.4 - - - -
211A LEU* 3.4 20.2 - - + -
213A THR* 4.6 0.9 - - - -
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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