Contacts of the strand formed by residues 32 - 37 (chain A) in PDB entry 2Z9I
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 GLU 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A MSE 2.8 33.0 - - + +
22A LEU 3.4 4.5 - - - +
23A GLU* 3.8 12.1 - - + +
31A GLU* 1.3 81.8 - - - +
33A GLY* 1.3 63.5 + - - +
50A VAL* 4.5 3.3 - - - +
122A SER* 2.6 41.3 - - - +
124A LEU* 4.3 2.3 + - - -
125A GLY* 3.5 12.4 + - - -
166A PRO 4.7 0.5 - - - -
167A GLY* 3.4 21.9 + - - -
411D VAL 4.3 4.7 - - - +
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MSE 3.6 10.4 - - - +
22A LEU 2.8 31.6 + - - +
32A GLU* 1.3 77.6 - - - +
34A SER* 1.3 60.4 + - - -
50A VAL* 3.7 17.8 - - - +
167A GLY* 3.5 15.5 - - - -
169A SER 3.8 4.5 - - - -
411D VAL 5.0 1.3 - - - -
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 5.0 0.4 - - - -
20A VAL 3.2 12.1 - - - -
22A LEU* 3.6 8.8 - - - +
33A GLY* 1.3 72.5 - - - -
35A GLY* 1.3 59.8 + - - +
46A THR* 2.8 22.9 + - - -
50A VAL* 4.4 0.2 - - - +
121A GLY* 3.5 8.2 - - - -
122A SER* 2.9 18.8 + - - -
167A GLY 2.5 24.9 + - - -
168A ASN 3.7 2.2 + - - -
169A SER 2.8 16.3 + - - +
170A GLY* 3.4 2.7 - - - -
171A GLY* 3.6 19.7 - - - -
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.5 10.0 - - - +
20A VAL* 2.8 36.2 + - - +
22A LEU* 4.3 4.5 - - - -
34A SER* 1.3 76.6 - - - +
36A ILE* 1.3 64.6 + - - -
44A ILE* 4.0 13.2 - - - -
45A LEU 3.2 11.7 - - - -
170A GLY 3.3 3.8 - - - -
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Residues in contact with ILE 36 (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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18A SER 3.5 7.2 - - - +
19A VAL* 5.1 1.1 - - + -
35A GLY* 1.3 75.2 - - - +
37A ILE* 1.3 63.1 + - - +
38A LEU* 3.3 2.8 + - + -
44A ILE* 3.2 7.8 - - - +
45A LEU* 2.7 46.0 + - + +
103A ILE* 3.4 44.0 - - + -
170A GLY 3.5 20.6 - - - +
171A GLY 3.6 23.6 - - - +
172A ALA* 4.0 6.7 - - + +
180A LEU* 3.7 29.4 - - + -
183A VAL* 3.9 13.9 - - + -
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Residues in contact with ILE 37 (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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17A PRO 3.5 24.9 - - - +
18A SER* 2.9 14.3 + - - +
20A VAL* 4.1 25.1 - - + -
36A ILE* 1.3 68.8 - - - +
38A LEU* 1.3 55.6 + - - +
39A SER 3.3 25.4 - - - +
43A LEU 3.6 6.5 - - - +
44A ILE* 4.4 10.1 - - + +
70A PHE* 4.2 7.9 - - + -
100A LEU* 4.1 28.7 - - + -
101A THR 3.7 21.5 - - - +
102A PRO* 3.8 7.2 - - + -
103A ILE* 2.8 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