Contacts of the helix formed by residues 99 - 110 (chain A) in PDB entry 5CO8
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 SER 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLY 3.8 3.4 + - - -
98A VAL* 1.3 79.2 - - - +
100A THR* 1.3 62.1 + - - +
101A ALA* 3.1 20.1 + - - +
102A MSE 3.4 35.5 + - - +
103A ALA* 3.1 23.6 + - - +
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Residues in contact with THR 100 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A PHE* 4.0 18.0 - - + -
98A VAL 3.5 4.2 + - - -
99A SER* 1.3 72.3 + - - +
101A ALA* 1.3 59.7 + - - +
103A ALA* 3.3 6.0 + - - +
104A LYS* 2.9 56.8 + - + +
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Residues in contact with ALA 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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99A SER* 3.1 9.0 + - - +
100A THR* 1.3 81.1 - - - +
102A MSE 1.3 58.5 + - + +
104A LYS* 3.4 7.1 + - - +
105A ARG* 2.9 28.8 + - - +
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Residues in contact with MSE 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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54A ASN* 4.1 20.6 - - - +
57A ILE* 4.4 20.8 - - + +
97A GLY 5.8 1.1 - - - +
98A VAL* 5.1 2.9 - - + -
99A SER* 3.4 34.3 + - - +
100A THR 3.3 0.2 - - - -
101A ALA* 1.3 75.7 - - + +
103A ALA* 1.3 65.2 + - - +
105A ARG* 3.6 14.4 - - - +
106A LEU* 3.0 25.8 + - - +
309A PHE* 4.2 13.8 - - + -
313A THR* 4.6 19.1 - - - -
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Residues in contact with ALA 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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39A MET* 4.2 24.5 - - + -
57A ILE* 4.2 10.7 - - + +
60A LEU* 4.2 12.6 - - + -
64A PHE* 4.6 0.9 - - - -
78A PHE* 4.3 5.2 - - + -
98A VAL* 4.8 3.8 - - + -
99A SER 3.1 17.4 + - - +
100A THR* 3.5 8.5 - - - +
102A MSE 1.3 78.6 - - - +
104A LYS* 1.3 56.4 + - - +
106A LEU* 3.4 2.9 + - - +
107A ILE* 3.0 35.4 + - + +
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Residues in contact with LYS 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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78A PHE* 3.7 30.7 - - + -
100A THR* 2.9 38.0 + - + +
101A ALA* 3.8 6.5 - - - +
103A ALA* 1.3 74.8 - - - +
105A ARG* 1.3 66.1 + - - +
107A ILE* 3.4 9.3 + - - +
108A ARG* 3.1 52.3 + - - +
114A ALA* 4.3 8.5 - - + +
116A ASP* 2.5 39.6 + - - -
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Residues in contact with ARG 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 ALA 2.9 18.8 + - - +
102A MSE 3.6 13.9 - - - +
103A ALA 3.3 0.2 - - - -
104A LYS* 1.3 76.1 - - - +
106A LEU* 1.3 62.8 + - - +
108A ARG* 3.3 11.0 + - - +
109A LEU* 3.1 37.2 + - + +
305A GLY 5.0 2.0 + - - -
308A GLU* 4.7 11.5 + - - +
309A PHE* 3.4 50.2 - - - +
312A GLU* 5.4 9.1 - - - +
313A THR* 4.7 5.5 + - - -
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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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57A ILE* 4.2 17.5 - - + +
60A LEU* 4.6 2.0 - - + -
61A PHE* 4.0 29.2 - - + +
64A PHE* 3.9 25.6 - - + -
102A MSE 3.0 17.0 + - - +
103A ALA* 3.8 4.0 - - - +
105A ARG* 1.3 74.3 - - - +
107A ILE* 1.3 65.5 + - - +
109A LEU* 3.2 6.4 + - + +
110A PHE* 3.1 47.9 + - + -
306A LEU* 3.7 18.2 - - + -
309A PHE* 3.8 31.9 - - + -
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Residues in contact with ILE 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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39A MET* 4.7 2.5 - - - -
64A PHE* 3.8 25.4 - - + -
76A PHE* 3.7 31.4 - - + -
78A PHE* 3.9 23.8 - - + -
103A ALA* 3.0 24.2 + - + +
104A LYS* 3.5 10.1 - - - +
106A LEU* 1.3 76.7 - - - +
108A ARG* 1.3 61.2 + - + +
110A PHE* 3.2 6.3 + - - +
112A PHE* 2.9 55.9 + - + +
113A THR 3.7 15.3 - - - +
114A ALA* 3.8 7.9 - - + +
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Residues in contact with ARG 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 LYS* 3.1 36.0 + - - +
105A ARG* 3.3 10.3 + - - +
107A ILE* 1.3 75.9 - - + +
109A LEU* 1.3 66.3 + - + +
110A PHE 3.1 2.0 - - - -
111A GLY* 3.0 13.7 + - - -
112A PHE 4.2 8.5 - - - +
114A ALA* 4.5 22.2 + - + +
116A ASP* 5.9 0.6 + - - -
300A THR 4.8 2.1 - - - +
302A ASP* 5.2 1.6 - - - +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ARG* 3.1 30.6 + - + +
106A LEU* 3.2 9.6 + - - +
108A ARG* 1.3 77.8 - - + +
110A PHE* 1.3 59.0 + - - +
301A VAL* 3.6 4.5 - - - +
302A ASP* 2.8 47.4 + - + +
305A GLY* 3.8 29.6 - - - +
306A LEU* 3.9 15.7 - - + +
309A PHE* 3.7 42.6 - - + -
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Residues in contact with PHE 110 (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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61A PHE* 3.6 40.6 - + - -
64A PHE* 3.7 41.5 - + + -
65A VAL* 3.8 22.7 - - + -
68A LEU* 4.0 25.1 - - + +
106A LEU* 3.1 33.1 + - + +
107A ILE 3.6 8.7 - - - +
108A ARG 3.1 0.4 - - - -
109A LEU* 1.3 76.7 - - - +
111A GLY* 1.3 60.6 + - - +
112A PHE* 3.2 26.6 + + + -
301A VAL* 3.5 24.4 + - + +
306A LEU* 3.8 14.1 - - + -
329A LEU* 4.3 5.2 - - + -
336A GLN* 4.7 2.3 + - - -
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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