Contacts of the helix formed by residues 99 - 116 (chain C) in PDB entry 5AYR
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C GLY* 3.5 20.8 + - - +
96C GLU* 2.9 44.4 + - - +
98C GLY* 1.3 80.1 - - - +
100C PRO* 1.3 77.9 - - + +
101C TYR* 3.3 20.6 - - + -
102C PHE* 3.2 4.2 + - - +
103C ILE* 3.1 18.4 + - - +
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Residues in contact with PRO 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLY 3.7 2.8 - - - +
99C LYS* 1.3 88.1 - - + +
101C TYR* 1.3 63.9 + - + +
103C ILE* 3.3 11.0 + - + +
104C LYS* 2.9 39.2 + - + +
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Residues in contact with TYR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C GLU* 2.5 36.5 + - - +
99C LYS* 3.7 28.0 - - + -
100C PRO* 1.3 80.8 - - + +
102C PHE* 1.3 79.4 + + + +
104C LYS* 3.4 11.8 + - - +
105C LEU* 2.9 28.7 + - + +
220C ARG 4.6 2.9 - - - +
221C GLY* 3.4 29.6 - - - -
224C GLN* 3.8 43.4 - - + +
225C PHE* 3.5 23.6 - - + +
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Residues in contact with PHE 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C MET* 4.2 10.1 - - - -
96C GLU* 3.0 25.8 - - + +
97C PHE* 3.5 43.3 - + + +
99C LYS 3.2 2.6 + - - +
101C TYR* 1.3 96.9 - + + +
103C ILE* 1.3 65.7 + - - +
105C LEU* 3.4 20.5 - - + +
106C MET* 3.0 54.3 + - + +
126C PHE* 5.1 6.1 - + - -
222C TRP* 4.8 1.1 - + - -
225C PHE* 3.7 40.6 - + - -
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C PHE 3.6 16.8 - - - +
98C GLY* 3.6 22.2 - - - +
99C LYS 3.1 6.1 + - - +
100C PRO* 3.6 10.8 - - + +
102C PHE* 1.3 79.5 - - - +
104C LYS* 1.3 64.6 + - + +
106C MET* 3.4 5.3 + - - +
107C GLY* 3.1 17.5 + - - -
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Residues in contact with LYS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C PRO* 2.9 32.8 + - + +
101C TYR* 3.8 9.6 - - - +
103C ILE* 1.3 74.3 - - + +
105C LEU* 1.3 66.6 + - - +
107C GLY* 3.2 2.6 + - - +
108C PHE* 2.9 26.1 + - - +
220C ARG 5.1 1.1 - - - +
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TYR 2.9 18.3 + - - +
102C PHE* 3.4 22.9 - - + +
104C LYS* 1.3 77.2 - - - +
106C MET* 1.3 68.8 + - + +
108C PHE* 3.0 7.5 + - + +
109C VAL* 2.9 37.5 + - + +
220C ARG* 3.5 32.7 + - + +
221C GLY* 3.9 15.7 - - - +
222C TRP* 3.7 59.7 - - + +
225C PHE* 4.8 0.2 - - + -
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Residues in contact with MET 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C MET* 4.4 20.2 - - + +
102C PHE* 3.0 46.3 + - + +
103C ILE* 3.8 5.8 - - - +
105C LEU* 1.3 96.6 - - + +
107C GLY* 1.3 65.2 + - - +
109C VAL* 3.3 11.6 + - + +
110C ALA* 2.9 26.4 + - - +
126C PHE* 5.4 3.6 - - - -
222C TRP* 3.7 27.8 - - + -
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Residues in contact with GLY 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ILE 3.1 14.0 + - - -
104C LYS* 3.2 4.0 + - - -
106C MET* 1.3 76.4 - - - +
108C PHE* 1.3 57.0 + - - +
110C ALA* 3.8 4.6 - - - +
111C GLU* 2.9 31.2 + - - +
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Residues in contact with PHE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ILE* 4.2 28.5 - - + -
104C LYS 2.9 17.8 + - - +
105C LEU* 3.3 10.1 - - + +
107C GLY* 1.3 76.9 - - - +
109C VAL* 1.3 67.1 + - + +
111C GLU* 3.3 6.2 + - + +
112C GLU* 2.8 62.7 + - + +
210C ARG* 5.5 0.4 - - - -
216C SER 4.6 2.2 - - - -
217C HIS* 3.8 25.4 - + + -
220C ARG* 3.3 52.3 - - + +
222C TRP* 6.3 0.2 - - - -
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LEU* 2.9 30.0 + - + +
106C MET* 3.9 16.8 - - + +
108C PHE* 1.3 86.9 - - + +
110C ALA* 1.3 57.4 + - - +
112C GLU* 3.0 10.0 + - - +
113C ARG* 2.8 50.9 + - + +
118C VAL* 4.7 4.9 - - + -
208C THR* 4.1 31.4 - - + +
217C HIS* 4.7 2.2 - - + +
222C TRP* 4.3 3.4 - - + +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C MET 2.9 18.7 + - - +
107C GLY* 3.8 5.8 - - - +
109C VAL* 1.3 73.5 - - - +
111C GLU* 1.3 65.3 + - - +
113C ARG* 3.3 17.1 + - - +
114C LYS* 3.4 22.4 + - - +
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Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B MET* 6.0 1.8 - - - -
107C GLY 2.9 21.2 + - - +
108C PHE* 3.6 7.2 - - + +
110C ALA* 1.3 72.3 - - - +
112C GLU* 1.3 64.5 + - + +
114C LYS* 3.0 36.4 + - - +
115C HIS* 2.8 50.2 + - + +
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ILE* 4.0 9.5 - - - +
99B MET* 5.1 3.5 - - - +
108C PHE* 2.8 40.2 + - + +
109C VAL* 3.0 13.7 + - - +
111C GLU* 1.3 76.2 - - + +
113C ARG* 1.3 51.0 + - - +
115C HIS* 3.1 5.2 + - - -
116C TYR* 2.8 46.1 + - - +
118C VAL* 4.0 14.1 - - + -
210C ARG* 2.7 50.6 + - - +
217C HIS* 2.8 28.7 + - + +
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Residues in contact with ARG 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 2.8 30.2 + - + +
110C ALA* 3.7 9.4 - - - +
111C GLU 3.1 0.4 - - - -
112C GLU* 1.3 76.5 - - - +
114C LYS* 1.3 60.1 + - + +
116C TYR 3.5 15.3 - - - +
118C VAL* 2.9 51.9 + - + +
120C PRO 3.0 20.4 + - - -
121C PRO* 3.9 0.8 - - - +
122C PRO* 3.6 33.9 - - - +
125C VAL* 3.5 20.2 - - - +
208C THR* 4.2 4.6 - - - +
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Residues in contact with LYS 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ALA* 3.4 19.0 + - - +
111C GLU* 3.0 34.2 + - - +
113C ARG* 1.3 79.5 - - - +
115C HIS* 1.3 69.4 + - + +
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Residues in contact with HIS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B MET* 3.8 32.9 - - + +
111C GLU* 2.8 54.5 + - + +
112C GLU* 3.1 4.6 + - - -
114C LYS* 1.3 85.1 + - + +
116C TYR* 1.3 89.0 + + + +
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Residues in contact with TYR 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B MET* 3.4 31.7 - - + +
100B PRO* 3.4 14.9 - - - +
112C GLU* 2.8 29.7 + - - +
113C ARG* 3.5 15.9 - - - +
114C LYS 3.6 0.6 - - - -
115C HIS* 1.3 102.5 - - + +
117C THR* 1.3 70.5 + - - +
118C VAL* 3.3 4.1 + - + +
210C ARG* 3.5 54.9 + - + -
211C ALA 5.6 1.3 - - - +
213C GLN* 4.4 11.0 - - - -
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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