Contacts of the helix formed by residues 102 - 107 (chain A) in PDB entry 2POD
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 PRO 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLY 4.2 3.8 - - - +
101A GLN* 1.3 98.9 - - + +
103A ILE* 1.3 67.0 + - - +
104A TYR* 3.6 45.1 - - + +
105A GLN* 3.0 21.2 + - + +
106A LEU* 3.4 5.1 + - - +
333A HIS* 3.9 4.7 - - + -
372A VAL* 5.7 0.4 - - + -
375A GLY 3.6 17.9 - - - +
376A PRO* 4.0 0.9 - - + -
377A GLY 3.7 8.7 - - - +
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE 4.6 0.4 - - - +
92A TRP* 3.6 44.9 - - + +
93A ASP 3.9 1.8 - - - +
102A PRO* 1.3 71.9 - - - +
104A TYR* 1.3 58.8 + - - +
106A LEU* 2.9 27.5 + - + +
107A LEU* 3.0 27.7 + - + +
300A LEU* 4.0 20.2 - - + -
330A ALA* 5.9 0.2 - - - -
333A HIS* 3.5 24.5 + - + +
377A GLY* 3.0 31.0 + - - +
378A LEU* 3.7 24.2 - - + +
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 3.6 27.8 - - + +
103A ILE* 1.3 76.1 - - - +
105A GLN* 1.3 67.5 + - + +
107A LEU* 3.6 9.7 + - - +
108A GLY 3.5 4.7 + - - -
109A GLY* 2.9 24.4 + - - +
110A LYS* 3.7 50.0 + - + +
333A HIS* 3.1 54.5 + + - +
336A LEU* 4.0 16.6 - - + -
337A ASN* 3.9 4.6 - - + +
372A VAL* 3.7 24.9 - - + -
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Residues in contact with GLN 105 (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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101A GLN* 3.4 32.1 - - + +
102A PRO* 3.0 21.5 + - + +
104A TYR* 1.3 85.9 - - + +
106A LEU* 1.3 60.4 + - + +
107A LEU 3.2 0.4 - - - -
108A GLY* 3.0 18.3 + - - -
109A GLY* 3.7 21.0 - - - +
110A LYS 4.9 0.5 + - - -
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Residues in contact with LEU 106 (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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92A TRP* 3.8 32.3 - - + +
95A PHE* 3.7 38.8 - - + -
96A GLY* 3.4 34.1 - - - +
99A THR* 3.7 20.6 - - + +
101A GLN* 3.9 12.8 - - + +
102A PRO 3.8 11.7 - - - +
103A ILE* 2.9 11.3 + - - +
105A GLN* 1.3 76.9 - - + +
107A LEU* 1.3 60.1 + - - +
108A GLY 3.6 0.2 + - - -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TRP* 4.1 18.4 - - + -
103A ILE* 3.0 34.9 + - + +
104A TYR* 3.8 3.8 - - - +
105A GLN 3.2 0.4 - - - -
106A LEU* 1.3 78.1 - - - +
108A GLY* 1.3 55.0 + - - +
300A LEU* 4.7 11.0 - - + -
304A ARG* 3.7 36.4 - - + +
333A HIS 3.9 8.5 - - - +
334A LEU* 3.8 34.3 - - + +
337A ASN* 3.3 32.4 + - + +
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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
------------------------------------------------------------
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