Contacts of the strand formed by residues 39 - 43 (chain A) in PDB entry 3GZN
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 HIS 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER 4.2 0.4 + - - +
38A ALA* 1.3 76.2 - - - +
40A VAL* 1.3 62.9 + - - +
63A SER* 3.0 36.4 + - - +
64A PHE* 3.5 5.3 + - - -
65A THR* 2.7 32.1 + - - -
110A SER* 5.1 2.5 + - - -
129A ARG* 3.9 22.5 + - - +
130A PHE* 3.2 25.2 - + - -
131A THR* 2.7 40.9 + - - +
35D GLU* 3.0 34.5 + - + +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 4.2 0.2 - - - -
39A HIS* 1.3 73.1 - - - +
41A CYS* 1.3 71.2 + - - +
42A LEU* 4.0 1.2 + - + -
53A LEU* 4.3 15.7 - - + +
56A LEU* 4.5 9.2 - - + -
61A ILE* 3.9 24.2 - - + -
63A SER 3.1 13.2 + - - +
64A PHE* 3.2 12.7 - - + +
65A THR 3.0 23.7 + - - +
130A PHE* 4.0 3.1 - - - -
132A VAL* 3.5 16.2 - - + +
134A VAL* 4.1 17.9 - - + -
512A VAL* 4.4 14.4 - - + -
516A ILE* 5.3 2.5 - - + -
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Residues in contact with CYS 41 (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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40A VAL* 1.3 75.5 - - - +
42A LEU* 1.3 63.0 + - - +
43A ILE* 4.4 4.5 - - - -
65A THR 3.4 8.5 - - - -
67A ILE* 3.6 31.9 - - - -
127A PHE* 4.4 7.4 - - - -
130A PHE* 3.4 42.9 - - + -
132A VAL 3.0 9.0 + - - +
133A VAL* 3.5 7.4 - - + -
134A VAL* 2.8 34.7 + - - +
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Residues in contact with LEU 42 (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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40A VAL* 4.0 0.9 + - + -
41A CYS* 1.3 74.0 - - - +
43A ILE* 1.3 74.0 + - - +
44A ASN 3.6 15.0 - - - +
45A ALA* 4.4 5.4 - - - -
49A GLY* 3.4 34.1 - - - +
50A THR* 4.4 1.3 - - - +
52A ILE* 5.7 0.9 - - + -
53A LEU* 3.3 39.5 - - + -
64A PHE* 6.4 0.2 - - + -
65A THR 2.8 10.3 + - - +
66A ILE* 3.4 15.3 - - + -
67A ILE* 2.9 27.7 + - - +
134A VAL* 3.3 24.9 - - + +
136A THR* 3.8 7.6 - - + -
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Residues in contact with ILE 43 (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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41A CYS* 4.4 4.9 - - - -
42A LEU* 1.3 77.8 - - - +
44A ASN* 1.3 76.5 + - - +
67A ILE* 3.4 18.4 - - + +
116A PRO* 3.9 36.6 - - + -
127A PHE* 4.4 9.0 - - + -
133A VAL* 3.9 16.8 - - + -
134A VAL 2.9 5.5 + - - -
135A ALA* 3.9 14.4 - - + -
136A THR* 2.9 20.8 + - - -
138A LEU* 4.1 13.9 - - + -
146A LEU* 3.6 37.9 - - + -
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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