Contacts of the helix formed by residues 99 - 109 (chain A) in PDB entry 4GL5
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 LYS 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A GLU* 3.4 33.8 + - + +
84A PHE* 4.8 12.6 - - + +
97A ILE* 3.4 2.8 - - + +
98A SER* 1.3 75.9 - - - +
100A SER* 1.3 65.3 + - - +
101A SER* 4.0 7.0 - - - +
102A SER* 3.2 16.0 + - - +
103A MET* 3.0 22.0 + - - +
384A ASP* 3.9 19.1 - - + +
386A TYR* 5.3 10.5 + - + -
401A MET* 4.4 0.7 - - - -
405A GLU* 4.2 5.8 - - - +
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Residues in contact with SER 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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98A SER 3.4 3.8 + - - -
99A LYS* 1.3 71.0 - - - +
101A SER* 1.3 52.6 + - - +
103A MET* 3.4 3.3 - - - +
104A PHE* 2.8 34.5 + - - +
401A MET* 3.7 23.1 - - - -
405A GLU* 2.9 37.1 + - - -
425A ARG* 2.8 34.3 + - - -
426A TYR* 3.6 8.4 - - - -
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 4.0 10.6 - - - +
100A SER* 1.3 74.0 - - - +
102A SER* 1.3 61.0 + - - +
104A PHE* 3.5 2.3 + - - +
105A HIS* 3.1 23.6 + - - +
384A ASP* 2.6 35.1 + - - +
405A GLU* 4.4 1.8 + - - -
425A ARG* 3.1 20.9 - - - +
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.4 15.1 - - - -
97A ILE* 3.2 27.9 - - - +
99A LYS* 3.2 5.7 + - - +
101A SER* 1.3 74.6 + - - +
103A MET* 1.3 67.3 + - - +
105A HIS* 3.1 3.6 + - - +
106A ILE* 2.9 29.9 + - - +
383A ILE* 3.3 32.1 - - - +
384A ASP* 3.4 14.2 + - - -
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Residues in contact with MET 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 ILE* 5.3 1.1 - - + +
98A SER* 5.8 0.7 - - - -
99A LYS 3.0 10.9 + - - +
100A SER 3.4 16.6 - - - +
102A SER* 1.3 80.8 - - - +
104A PHE* 1.3 70.8 + - + +
106A ILE* 3.2 1.4 + - - +
107A MET* 3.2 52.4 + - - +
396A LEU* 3.7 28.3 - - + +
398A ILE* 4.2 15.3 - - + -
401A MET* 3.6 39.3 - - + -
425A ARG 4.0 15.0 - - - +
428A GLN* 3.7 21.8 - - + -
432A PHE* 4.8 0.2 - - - -
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Residues in contact with PHE 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 SER 2.8 21.6 + - - +
101A SER 3.9 4.5 - - - +
102A SER 3.2 0.2 - - - -
103A MET* 1.3 83.1 - - + +
105A HIS* 1.3 65.0 + - - +
108A LYS* 3.1 50.7 + - + +
424A TYR* 4.0 21.3 - + - -
425A ARG* 3.9 43.3 - - + +
432A PHE* 3.3 37.4 - + - -
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Residues in contact with HIS 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 SER 3.1 14.3 + - - +
102A SER 3.4 8.1 - - - +
104A PHE* 1.3 81.5 - - - +
106A ILE* 1.3 68.3 + - - +
108A LYS* 3.6 7.3 - - - +
109A HIS* 3.2 56.8 + + - +
112A TYR* 3.9 16.6 - + - -
381A ASP* 3.4 25.0 + - - -
382A VAL 4.2 6.8 + - - -
383A ILE* 3.7 27.3 - - + +
384A ASP* 6.0 0.7 - - - +
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Residues in contact with ILE 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 ILE* 3.7 20.6 - - + -
102A SER 2.9 14.3 + - - +
103A MET 3.6 6.5 - - - +
105A HIS* 1.3 81.6 - - - +
107A MET* 1.3 65.5 + - - +
108A LYS 3.1 1.7 + - - -
109A HIS 3.3 11.4 + - - +
112A TYR* 3.4 47.2 - - + +
375A ARG* 4.1 18.1 + - + +
383A ILE* 4.9 8.3 - - + -
394A ILE* 3.5 38.6 - - + -
396A LEU* 3.7 24.0 - - + -
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Residues in contact with MET 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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103A MET* 3.2 29.0 + - - +
106A ILE* 1.3 73.5 - - - +
108A LYS* 1.3 60.6 + - - +
109A HIS 4.3 0.4 - - - +
373A VAL* 5.2 6.3 - - - -
375A ARG* 3.8 21.2 + - - +
396A LEU* 3.8 21.8 - - + -
398A ILE* 5.3 3.6 - - - -
428A GLN* 3.5 17.9 - - + +
431A GLY* 3.3 28.0 - - - -
432A PHE* 3.3 39.3 - - + +
433A GLY* 3.6 0.5 - - - -
434A PRO* 3.2 22.3 - - - +
600A HEM 3.8 18.4 - - - +
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Residues in contact with LYS 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 PHE* 3.1 42.8 + - + +
105A HIS* 3.6 6.3 - - - +
106A ILE 3.1 0.6 + - - -
107A MET* 1.3 80.5 - - - +
109A HIS* 1.3 91.2 + - + +
110A ASN* 3.8 1.0 + - - -
432A PHE* 4.0 20.1 - - + -
433A GLY* 4.6 2.1 - - - -
434A PRO* 3.6 11.6 - - - +
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Residues in contact with HIS 109 (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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105A HIS* 3.2 53.2 + + - +
106A ILE 3.3 9.9 + - - +
107A MET 4.3 0.7 - - - +
108A LYS* 1.3 111.0 + - + +
110A ASN* 1.3 63.4 + - - +
111A HIS* 3.4 28.7 + + + +
112A TYR* 3.6 13.6 + - + +
113A SER* 4.2 1.2 + - - -
375A ARG* 5.4 0.7 + - - -
381A ASP* 4.6 2.0 - - - -
434A PRO* 4.1 6.7 - - - +
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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