Contacts of the helix formed by residues 102 - 115 (chain F) in PDB entry 1R4N
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 PRO 102 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81F ASP 4.1 6.3 - - - +
82F THR* 4.4 1.3 - - - -
100F GLY 4.6 0.9 - - - +
101F ARG* 1.3 87.9 - - + +
103F LYS* 1.3 68.9 + - - +
104F ALA 3.2 0.9 - - - +
105F GLU* 2.9 50.0 + - + +
106F VAL* 2.9 14.7 + - - +
124F PHE* 3.3 44.2 - - + -
121H VAL* 6.3 0.2 - - + -
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Residues in contact with LYS 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ATP 2.7 60.4 + - - +
56F ALA* 3.3 13.7 - - - +
79F ASP* 4.0 9.2 - - - +
81F ASP* 3.1 23.4 + - + +
82F THR 4.2 5.2 - - - -
83F ILE* 3.6 20.2 - - - +
87F ASN* 3.2 27.2 + - - +
91F GLN* 3.6 13.9 + - - +
94F PHE* 3.5 23.1 - - + -
101F ARG 3.3 2.8 + - - -
102F PRO* 1.3 70.2 - - - +
104F ALA* 1.3 65.6 + - - +
107F ALA* 2.8 27.3 + - - +
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F ALA* 4.6 3.1 - - - -
77F VAL* 4.2 8.3 - - + +
78F ILE 4.5 0.2 - - - -
79F ASP* 3.9 33.7 + - + +
102F PRO* 3.2 1.3 - - + -
103F LYS* 1.3 78.8 - - - +
105F GLU* 1.3 63.4 + - - +
107F ALA* 3.5 7.2 - - - +
108F ALA* 3.2 13.9 + - - +
122F PRO* 3.1 14.5 - - + +
123F HIS 3.9 30.3 - - - +
124F PHE* 4.3 3.8 - - + +
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Residues in contact with GLU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F ARG* 3.3 24.9 + - - +
102F PRO* 2.9 44.0 + - + +
104F ALA* 1.3 75.8 - - - +
106F VAL* 1.3 55.8 + - - +
108F ALA* 3.1 6.2 + - - +
109F GLU* 2.8 34.9 + - + +
122F PRO* 3.8 15.3 - - + +
124F PHE* 5.7 1.4 - - + +
120H VAL 5.6 0.3 - - - +
122H PRO* 4.5 20.6 - - - +
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Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ILE* 3.5 22.7 - - + -
93F LEU 3.7 15.7 - - - +
94F PHE* 3.9 5.6 - - + -
98F ASP* 3.5 27.6 - - + +
101F ARG* 3.6 33.0 - - + +
102F PRO 2.9 14.7 + - - +
103F LYS 3.9 0.4 - - - +
105F GLU* 1.3 72.0 - - + +
107F ALA* 1.3 69.4 + - - +
109F GLU* 2.9 17.1 + - - +
110F PHE* 2.8 27.1 + - + +
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Residues in contact with ALA 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F ALA* 4.4 10.1 - - + -
61F CYS* 5.7 0.4 - - - -
64F LEU* 4.0 21.3 - - + -
77F VAL* 4.9 1.6 - - + -
93F LEU* 4.0 16.1 - - + +
94F PHE* 3.8 14.3 - - + -
103F LYS 2.8 23.7 + - - +
104F ALA* 3.5 8.5 - - - +
106F VAL* 1.3 76.1 - - - +
108F ALA* 1.3 60.7 + - - +
110F PHE* 3.4 2.4 + - - +
111F LEU* 3.0 24.1 + - - +
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Residues in contact with ALA 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F VAL* 5.4 0.4 - - + +
104F ALA 3.2 5.1 + - - +
105F GLU 3.1 8.7 + - - +
107F ALA* 1.3 76.3 - - - +
109F GLU* 1.3 68.4 + - - +
111F LEU* 4.6 1.3 - - - +
112F ASN* 2.8 40.6 + - - +
120F VAL* 3.3 32.3 - - + +
122F PRO* 3.6 24.9 - - + -
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Residues in contact with GLU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F ASP* 4.3 2.4 - - - +
101F ARG* 2.9 41.5 + - - +
105F GLU* 2.8 19.0 + - + +
106F VAL* 3.2 18.7 - - - +
108F ALA* 1.3 76.4 - - - +
110F PHE* 1.3 66.5 + - - +
112F ASN* 3.5 4.3 + - - +
113F ASP* 3.4 16.5 + - + +
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Residues in contact with PHE 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E PHE* 3.7 19.3 - + - -
75E PHE* 6.4 0.2 - + - -
96E LEU* 6.2 0.7 - - + -
92F PHE* 3.8 19.3 - + - -
93F LEU* 3.3 35.7 - - + +
95F ARG* 4.1 18.4 - - + -
98F ASP* 6.0 0.2 - - - -
106F VAL* 2.8 19.8 + - + +
107F ALA 3.8 2.7 - - - +
109F GLU* 1.3 74.6 - - - +
111F LEU* 1.3 60.3 + - - +
113F ASP* 2.7 24.6 + - + +
114F ARG* 2.9 69.3 + - + -
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Residues in contact with LEU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E PHE* 4.2 11.9 - - + -
64F LEU* 3.1 53.2 - - + +
65F LYS* 3.6 6.3 - - + +
68F ALA* 3.6 15.5 - - + -
93F LEU* 4.5 8.7 - - + +
107F ALA 3.0 18.0 + - - +
108F ALA 4.0 1.3 - - - +
110F PHE* 1.3 81.9 - - - +
112F ASN* 1.3 57.7 + - - +
113F ASP 2.9 5.5 + - - -
114F ARG* 4.5 1.1 - - - +
115F VAL* 3.1 42.5 + - + +
118F CYS* 4.1 10.8 - - - -
120F VAL* 4.6 8.7 - - + -
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Residues in contact with ASN 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ALA* 2.8 34.3 + - - +
109F GLU* 3.9 4.4 - - - +
111F LEU* 1.3 70.4 - - - +
113F ASP* 1.3 59.0 + - - +
115F VAL 4.1 2.3 - - - +
116F PRO 4.0 15.8 - - - +
118F CYS* 3.0 27.9 - - - +
119F ASN* 3.1 2.1 - - - -
120F VAL* 2.5 57.8 + - - +
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Residues in contact with ASP 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E GLN* 3.8 15.6 - - - +
109F GLU 3.4 9.8 + - - +
110F PHE* 2.7 13.6 + - + +
111F LEU 2.8 0.2 - - - -
112F ASN* 1.3 81.2 - - - +
114F ARG* 1.3 69.4 + - - +
115F VAL 3.2 1.7 + - - -
116F PRO* 4.1 8.1 - - - +
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Residues in contact with ARG 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ASN 5.8 0.2 - - - +
74E PHE* 3.2 52.2 + - + +
75E PHE* 4.6 9.0 - - - +
76E LEU 5.4 2.5 - - - +
77E GLN* 3.7 33.7 + - - +
92E PHE* 3.5 46.9 + - - +
95E GLU* 5.0 11.9 + - - +
95F ARG* 5.1 6.3 - - - +
110F PHE* 2.9 59.0 + - + +
111F LEU 4.3 1.1 - - - +
113F ASP* 1.3 79.4 + - - +
115F VAL* 1.3 58.4 + - + +
116F PRO* 3.3 10.0 - - - +
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E PHE* 3.9 18.4 - - + -
16F ARG* 3.6 18.4 - - - +
17F TRP* 5.5 0.9 - - + -
68F ALA* 4.1 15.3 - - + +
69F LEU* 4.0 28.3 - - + -
111F LEU* 3.1 34.7 + - + +
112F ASN 4.1 1.9 - - - +
113F ASP 4.1 2.0 - - - -
114F ARG* 1.3 81.7 - - - +
116F PRO* 1.3 70.8 - - + +
118F CYS* 3.0 26.9 + - + +
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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