Contacts of the helix formed by residues 102 - 115 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D ASP 6.1 0.2 - - - +
81D ASP 4.1 5.8 - - - +
82D THR* 4.4 1.8 - - - +
100D GLY 4.6 0.9 - - - +
101D ARG* 1.3 87.9 - - + +
103D LYS* 1.3 68.1 + - - +
104D ALA 3.2 1.3 - - - +
105D GLU* 2.9 48.5 + - + +
106D VAL* 2.9 15.9 + - - +
124D PHE* 3.3 44.9 - - + -
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Residues in contact with LYS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ATP 3.0 54.6 + - - +
56D ALA* 3.3 20.9 - - - +
79D ASP* 4.0 9.6 - - - +
81D ASP* 3.1 25.0 + - + +
82D THR 4.3 5.2 - - - -
83D ILE* 3.5 20.2 - - - +
87D ASN* 3.3 28.6 - - - +
91D GLN* 3.6 9.5 + - - -
94D PHE* 3.5 24.3 - - + -
101D ARG 3.3 2.8 + - - -
102D PRO* 1.3 70.6 - - - +
104D ALA* 1.3 66.5 + - - +
106D VAL 3.3 0.2 + - - -
107D ALA* 2.8 27.5 + - - +
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ALA* 4.6 3.1 - - - -
77D VAL* 4.2 7.1 - - + +
78D ILE 4.6 0.4 - - - -
79D ASP* 3.9 32.3 - - + +
81D ASP 4.5 1.2 + - - -
102D PRO* 5.0 0.9 - - + -
103D LYS* 1.3 78.6 - - - +
105D GLU* 1.3 62.9 + - - +
107D ALA* 3.4 6.9 - - - +
108D ALA* 3.2 13.9 + - - +
122D PRO* 3.2 14.9 - - + +
123D HIS 3.9 30.1 - - - +
124D PHE* 4.3 4.7 - - + +
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Residues in contact with GLU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PRO* 4.6 19.2 - - - +
101D ARG* 3.4 24.5 + - - +
102D PRO* 2.9 42.2 + - + +
104D ALA* 1.3 76.9 - - - +
106D VAL* 1.3 60.6 + - - +
108D ALA* 3.1 5.9 + - - +
109D GLU* 2.8 28.4 + - + +
122D PRO* 3.8 14.7 - - + +
124D PHE* 5.7 1.4 - - + +
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Residues in contact with VAL 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ILE* 3.5 22.7 - - + -
93D LEU 3.7 15.5 - - - +
94D PHE* 4.0 4.9 - - + -
98D ASP* 3.5 27.6 - - - +
101D ARG* 3.6 33.7 - - + +
102D PRO 2.9 15.8 + - - +
103D LYS 3.9 0.7 - - - +
105D GLU* 1.3 72.8 - - + +
107D ALA* 1.3 66.2 + - - +
109D GLU* 2.9 16.6 + - - +
110D PHE* 2.8 27.1 + - + +
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ALA* 4.3 11.0 - - + -
61D CYS* 5.7 0.2 - - - -
64D LEU* 4.0 21.3 - - + -
77D VAL* 4.9 2.0 - - + -
93D LEU* 4.1 15.2 - - + +
94D PHE* 3.8 14.5 - - + -
103D LYS 2.8 24.1 + - - +
104D ALA* 3.4 9.2 - - - +
106D VAL* 1.3 76.8 - - - +
108D ALA* 1.3 61.8 + - - +
110D PHE* 3.8 2.3 - - - +
111D LEU* 3.0 24.1 + - - +
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D VAL* 5.6 0.2 - - - +
104D ALA 3.2 5.5 + - - +
105D GLU 3.1 7.0 + - - +
107D ALA* 1.3 76.9 - - - +
109D GLU* 1.3 69.0 + - - +
111D LEU* 4.6 1.1 - - - -
112D ASN* 2.8 39.8 + - - +
120D VAL* 3.3 32.3 - - + +
122D PRO* 3.6 26.0 - - + -
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASP* 4.3 2.3 - - - +
101D ARG* 2.9 42.5 + - - +
105D GLU* 2.8 19.6 + - + +
106D VAL* 3.2 18.4 - - - +
108D ALA* 1.3 74.0 - - - +
110D PHE* 1.3 69.1 + - - +
112D ASN* 3.6 4.7 + - - +
113D ASP* 3.4 16.5 + - - +
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Residues in contact with PHE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PHE* 3.6 20.6 - + - -
75C PHE* 6.4 0.2 - + - -
96C LEU* 6.2 0.7 - - + -
92D PHE* 3.8 18.6 - + - -
93D LEU* 3.4 35.9 - - + +
95D ARG* 4.1 18.6 - - + -
98D ASP* 6.0 0.4 - - - -
106D VAL* 2.8 20.2 + - + +
107D ALA 3.8 2.7 - - - +
109D GLU* 1.3 75.2 - - - +
111D LEU* 1.3 60.1 + - - +
113D ASP* 2.8 24.2 + - + +
114D ARG* 2.9 66.5 + - + -
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PHE* 4.3 11.4 - - + -
64D LEU* 3.1 53.4 - - + +
65D LYS* 3.6 6.5 - - + +
68D ALA* 3.6 15.5 - - + -
93D LEU* 4.5 8.5 - - + +
107D ALA 3.0 17.2 + - - +
108D ALA 4.0 1.3 - - - +
110D PHE* 1.3 80.8 - - - +
112D ASN* 1.3 59.5 + - - +
113D ASP 2.9 5.4 + - - -
114D ARG* 4.5 1.8 - - - +
115D VAL* 3.1 42.1 + - + +
118D CYS* 4.0 11.0 - - - -
120D VAL* 4.6 9.2 - - + -
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Residues in contact with ASN 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ALA* 2.8 34.1 + - - +
109D GLU* 4.0 4.0 - - - +
111D LEU* 1.3 70.7 - - - +
113D ASP* 1.3 58.3 + - - +
115D VAL 4.1 2.4 - - - +
116D PRO 4.0 15.2 - - - +
118D CYS* 3.1 26.1 - - - +
119D ASN* 3.2 1.6 - - - -
120D VAL* 2.5 57.7 + - - +
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C GLN* 3.9 15.8 - - - +
109D GLU* 3.4 10.7 + - + +
110D PHE* 2.8 13.9 + - + +
112D ASN* 1.3 80.8 - - - +
114D ARG* 1.3 69.0 + - - +
115D VAL 3.1 2.5 + - - -
116D PRO* 4.0 8.5 - - - +
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Residues in contact with ARG 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ASN 5.8 0.2 - - - +
74C PHE* 3.1 53.3 + - + +
75C PHE* 4.6 9.0 - - - +
76C LEU 5.4 2.4 - - - +
77C GLN* 3.8 33.7 + - - +
92C PHE* 3.6 43.5 + - - +
95C GLU* 5.2 10.7 + - - -
96C LEU* 5.9 0.2 - - - +
95D ARG* 5.1 6.5 - - - +
110D PHE* 2.9 59.0 + - + +
111D LEU 4.3 0.7 - - - +
113D ASP* 1.3 79.6 + - - +
115D VAL* 1.3 57.8 + - - +
116D PRO* 3.2 10.9 - - - +
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PHE* 3.9 17.7 - - + -
16D ARG* 3.6 17.7 - - - +
17D TRP* 5.4 1.3 - - + -
68D ALA* 4.1 15.5 - - + +
69D LEU* 4.0 28.9 - - + -
111D LEU* 3.1 33.6 + - + +
112D ASN 4.1 1.7 - - - +
113D ASP 4.1 2.2 - - - -
114D ARG* 1.3 80.3 - - - +
116D PRO* 1.3 70.0 - - + +
118D CYS* 3.0 28.2 + - + +
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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