Contacts of the helix formed by residues 102 - 113 (chain I) in PDB entry 5A15
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 GLU 102 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81I LEU* 3.5 11.8 - - + +
100I PHE* 3.1 27.3 - - + -
101I PRO* 1.3 97.6 - - + +
103I LYS* 1.3 63.9 + - - +
104I GLY 3.3 2.9 - - - +
105I ARG* 3.0 42.5 + - + +
106I LEU 3.0 15.2 + - - -
83J ARG* 2.6 35.9 + - - -
84J TYR* 4.4 0.3 + - - -
97J PRO* 4.3 14.1 - - + +
98J ASP* 5.3 0.2 - - - -
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Residues in contact with LYS 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I LEU* 4.1 25.6 - - + -
99I HIS* 6.3 0.2 - - - +
100I PHE* 4.0 26.9 - - + +
101I PRO 3.8 2.4 + - - -
102I GLU* 1.3 76.1 - - - +
104I GLY* 1.3 57.9 + - - +
106I LEU* 3.3 4.0 + - - +
107I LYS* 2.9 28.8 + - - +
122I LEU* 4.3 20.2 - - + +
98J ASP* 4.2 8.5 + - - +
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Residues in contact with GLY 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I GLU* 3.3 0.8 - - - +
103I LYS* 1.3 80.6 - - - +
105I ARG* 1.3 59.6 + - - +
107I LYS* 3.3 14.0 - - - +
108I ARG* 3.1 17.2 + - - +
122I LEU 6.0 0.4 - - - -
95J VAL* 3.7 19.1 - - - +
96J LEU 5.8 0.7 - - - -
98J ASP* 5.1 7.3 + - - -
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Residues in contact with ARG 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I ASP* 4.2 5.1 + - - +
81I LEU* 3.7 22.0 - - + +
102I GLU* 3.0 29.6 + - + +
103I LYS 3.3 0.4 - - - -
104I GLY* 1.3 75.5 - - - +
106I LEU* 1.3 64.4 + - - +
108I ARG* 3.0 16.4 + - - +
109I GLU* 3.0 19.3 + - - +
83J ARG* 2.9 43.8 - - - +
84J TYR* 4.0 13.0 - - - -
87J ASP* 2.1 40.4 + - - +
95J VAL* 3.1 36.9 + - + +
96J LEU 4.0 7.2 + - - +
97J PRO* 4.1 12.6 - - - -
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Residues in contact with LEU 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I LEU* 3.8 37.1 - - + +
84I TYR* 4.0 23.6 - - + -
85I ILE* 3.8 19.7 - - + -
94I VAL* 5.3 1.3 - - + -
96I LEU* 4.3 16.4 - - + -
100I PHE* 4.2 16.2 - - + -
102I GLU 3.0 19.1 + - - +
103I LYS 3.7 4.7 - - - +
105I ARG* 1.3 76.0 - - - +
107I LYS* 1.3 62.3 + - - +
109I GLU* 3.3 2.2 + - + +
110I ALA* 3.0 21.5 + - - +
118I LEU* 5.3 4.9 - - + -
122I LEU* 3.6 24.9 - - + -
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Residues in contact with LYS 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I LYS 2.9 13.8 + - - +
104I GLY* 3.3 15.9 - - - +
106I LEU* 1.3 78.5 - - - +
108I ARG* 1.3 56.7 + - - +
110I ALA* 3.2 4.4 + - - +
111I GLU* 3.0 49.3 + - - +
119I VAL* 4.1 10.3 - - + +
122I LEU* 3.4 31.1 - - + +
123I THR* 3.3 34.6 - - + +
124I PRO* 5.5 3.4 - - + +
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Residues in contact with ARG 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I ARG* 4.0 6.1 - - - +
104I GLY 3.1 9.0 + - - +
105I ARG* 3.0 11.7 + - - +
107I LYS* 1.3 77.4 - - - +
109I GLU* 1.3 66.6 + - - +
111I GLU* 3.2 41.9 + - - +
112I TYR* 3.0 39.7 + - - +
91J ASP* 3.2 43.2 + - - +
93J GLN* 4.5 24.6 - - + +
95J VAL* 4.2 20.4 - - + -
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Residues in contact with GLU 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I ARG* 2.8 53.6 + - - +
78I ASP* 4.3 16.5 + - - +
81I LEU* 3.8 26.7 - - + +
85I ILE* 4.1 17.7 - - + -
105I ARG* 3.0 20.7 + - - +
106I LEU* 3.3 7.2 + - - +
108I ARG* 1.3 73.7 - - - +
110I ALA* 1.3 61.4 + - - +
112I TYR* 3.1 3.4 + - - +
113I PHE* 2.9 45.9 + - + -
87J ASP* 4.7 5.5 - - - +
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Residues in contact with ALA 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I ILE* 4.0 7.3 - - - +
106I LEU 3.0 13.0 + - - +
107I LYS 3.2 9.8 + - - +
109I GLU* 1.3 78.0 - - - +
111I GLU* 1.3 61.2 + - - +
113I PHE 3.6 0.7 + - - -
114I GLN 3.0 17.3 + - - -
115I LEU* 3.0 18.6 + - - +
118I LEU* 3.8 31.6 - - + -
119I VAL* 3.4 19.1 - - + +
122I LEU* 4.2 2.5 - - + -
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Residues in contact with GLU 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I LYS* 3.0 44.5 + - - +
108I ARG* 3.2 38.3 + - - +
109I GLU 3.2 0.4 - - - -
110I ALA* 1.3 77.5 - - - +
112I TYR* 1.3 62.2 + - - +
114I GLN* 3.2 18.4 + - - +
119I VAL* 3.8 22.3 - - + +
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Residues in contact with TYR 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I LEU* 3.2 38.9 - - + +
54I MET* 6.0 1.2 - - - -
75I ILE* 4.9 5.0 - - + +
76I ASP* 5.3 4.2 + - - +
77I ARG* 3.6 60.3 - - + +
108I ARG* 3.0 30.1 + - - +
109I GLU 3.1 6.0 + - - +
111I GLU* 1.3 79.0 - - - +
113I PHE* 1.3 77.7 + + - +
114I GLN* 3.1 10.3 + - - +
91J ASP* 4.9 0.4 - - - -
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Residues in contact with PHE 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I SER* 3.8 3.6 - - - -
50I LEU* 3.0 30.6 + - + -
51I LEU* 3.8 30.8 + - + -
54I MET* 6.2 0.2 - - - -
75I ILE* 4.0 26.9 - - + -
77I ARG* 4.0 10.3 - - + -
82I PHE* 3.7 35.7 - + + -
85I ILE* 4.0 19.5 - - + -
109I GLU* 2.9 51.5 + - + +
112I TYR* 1.3 83.0 - + - +
114I GLN* 1.3 67.7 + - - +
115I LEU* 3.9 20.5 - - + +
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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