Contacts of the helix formed by residues 99 - 108 (chain A) in PDB entry 3PM0
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 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASP* 3.8 25.8 + - - +
98A ASN* 1.3 78.0 - - - +
100A GLU* 1.3 61.9 + - - -
101A ARG 3.5 1.8 - - - -
102A ALA* 4.0 4.5 - - - +
103A ILE* 3.0 31.0 + - - +
426A SER 5.2 2.5 - - - -
427A VAL* 3.6 5.4 - - - -
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Residues in contact with GLU 100 (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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99A GLY* 1.3 70.9 - - - -
101A ARG* 1.3 64.4 + - + +
103A ILE* 3.7 2.6 - - - +
104A HIS* 2.6 48.6 + - + +
427A VAL* 3.5 33.4 - - + +
433A LYS* 3.7 22.8 - - - +
459A ARG* 3.7 22.6 + - - +
461A MET* 4.5 16.5 - - + +
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Residues in contact with ARG 101 (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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83A ASP* 6.1 0.7 - - - +
99A GLY* 3.5 0.6 - - - -
100A GLU* 1.3 84.5 - - + +
102A ALA* 1.3 57.3 + - - +
104A HIS* 4.5 13.2 + - - -
105A GLN* 3.0 42.0 + - - +
109A GLN* 3.2 28.9 + - - +
410A LEU* 4.8 16.2 - - + +
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Residues in contact with ALA 102 (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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83A ASP* 4.3 12.5 + - + -
84A VAL* 4.1 9.2 - - + -
97A LEU* 4.5 4.4 - - + +
98A ASN 4.7 4.9 - - - +
99A GLY* 3.7 9.0 + - - +
100A GLU 3.2 0.6 - - - -
101A ARG* 1.3 75.7 - - - +
103A ILE* 1.3 61.8 + - - +
106A ALA* 3.0 32.1 + - - +
409A VAL* 3.8 20.7 - - + +
410A LEU* 3.6 27.4 - - + +
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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
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97A LEU* 3.9 21.3 - - + +
98A ASN 3.9 4.3 - - - +
99A GLY 3.0 26.1 + - - +
100A GLU* 3.7 2.0 - - - +
102A ALA* 1.3 76.4 - - - +
104A HIS* 1.3 60.4 + - - +
107A LEU* 3.0 33.5 + - + +
422A VAL* 3.6 28.5 - - + -
423A ASN 3.3 29.6 - - - +
427A VAL* 3.5 13.5 - - + -
461A MET* 3.5 33.0 - - + -
465A VAL* 4.2 9.4 - - + -
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Residues in contact with HIS 104 (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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100A GLU* 2.6 32.5 + - + +
101A ARG* 4.2 14.6 + - - +
103A ILE* 1.3 77.5 - - + +
105A GLN* 1.3 54.7 + - - +
106A ALA 3.4 0.2 - - - -
108A VAL* 2.8 51.5 + - + +
109A GLN* 3.0 42.8 + - + -
461A MET* 5.8 2.2 - - + -
465A VAL* 5.0 0.4 - - + -
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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 ARG* 3.0 32.4 + - - +
102A ALA* 3.3 4.2 + - - +
104A HIS* 1.3 74.7 + - - +
106A ALA* 1.3 61.6 + - - +
109A GLN* 3.5 22.6 + - + +
110A GLN* 3.1 36.4 + - + +
408A SER 4.3 2.4 - - - +
409A VAL* 3.3 10.8 - - + +
410A LEU* 2.6 43.2 + - - +
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Residues in contact with ALA 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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97A LEU* 3.7 23.1 - - + -
102A ALA 3.0 17.3 + - - +
103A ILE 4.1 0.2 - - - +
105A GLN* 1.3 76.9 - - - +
107A LEU* 1.3 62.2 + - - +
108A VAL 3.3 0.2 + - - -
110A GLN 3.0 32.2 - - - +
111A GLY* 3.0 1.7 + - - -
114A PHE* 3.7 23.1 - - + -
409A VAL* 3.7 21.3 - - + +
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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
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97A LEU* 4.9 0.7 - - + -
103A ILE* 3.0 16.9 + - + +
106A ALA* 1.3 83.6 - - + +
108A VAL* 1.3 56.9 + - - +
111A GLY* 3.1 17.6 - - - -
114A PHE* 3.6 22.4 - - + +
401A HIS* 3.5 34.1 - - + +
420A VAL* 6.2 0.2 - - + -
422A VAL* 3.5 35.2 - - + -
464A SER* 3.8 10.1 - - - +
465A VAL* 3.3 34.8 - - + +
466A GLY* 3.3 18.3 - - - -
467A LYS* 4.3 1.4 + - - -
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Residues in contact with VAL 108 (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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104A HIS* 2.8 52.2 + - + +
107A LEU* 1.3 76.9 - - - +
109A GLN* 1.3 67.3 + - + +
110A GLN 3.2 1.1 - - - -
111A GLY* 3.0 12.1 + - - +
465A VAL* 3.6 33.0 - - + -
466A GLY* 4.8 4.3 - - - +
467A LYS* 4.9 3.9 + - - +
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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