Contacts of the helix formed by residues 102 - 115 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B ASP 6.1 0.2 - - - +
81B ASP 4.1 5.4 - - - +
82B THR* 4.4 1.3 - - - +
100B GLY 4.6 1.3 - - - +
101B ARG* 1.3 88.2 - - + +
103B LYS* 1.3 67.3 + - - +
104B ALA 3.2 1.3 - - - +
105B GLU* 2.8 49.5 + - + +
106B VAL* 2.9 15.5 + - - +
124B PHE* 3.3 44.6 - - + -
121D VAL* 6.4 0.2 - - + -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ATP 3.2 54.2 + - - +
56B ALA* 3.3 20.4 - - - +
79B ASP* 4.0 10.3 - - - +
81B ASP* 3.1 25.6 + - + +
82B THR 4.2 5.2 - - - -
83B ILE* 3.6 20.0 - - - +
87B ASN* 3.2 29.2 - - - +
91B GLN* 3.6 8.4 + - - -
94B PHE* 3.5 23.2 - - + -
101B ARG 3.3 3.0 + - - -
102B PRO* 1.3 69.5 - - - +
104B ALA* 1.3 66.4 + - - +
107B ALA* 2.8 26.7 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ALA* 4.6 3.1 - - - -
77B VAL* 4.1 10.2 - - + +
78B ILE 4.6 0.2 - - - -
79B ASP* 3.9 31.3 - - + +
81B ASP 4.5 0.8 + - - -
102B PRO 3.2 1.1 - - - -
103B LYS* 1.3 79.0 - - - +
105B GLU* 1.3 64.4 + - - +
107B ALA* 3.5 6.7 - - - +
108B ALA* 3.2 13.3 + - - +
122B PRO* 3.2 13.6 - - + +
123B HIS 3.9 29.8 - - - +
124B PHE* 4.3 4.7 - - + +
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 3.3 25.3 + - - +
102B PRO* 2.8 42.2 + - + +
104B ALA* 1.3 75.4 - - - +
106B VAL* 1.3 55.2 + - - +
108B ALA* 3.1 5.7 + - - +
109B GLU* 2.8 35.2 + - + +
122B PRO* 3.8 16.6 - - + +
124B PHE* 5.7 1.2 - - + +
120D VAL 5.7 0.3 - - - +
122D PRO* 4.6 19.1 - - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ILE* 3.5 22.7 - - + -
93B LEU 3.7 15.9 - - - +
94B PHE* 3.8 5.6 - - + -
98B ASP* 3.5 27.8 - - - +
101B ARG* 3.5 34.8 - - + +
102B PRO 2.9 16.2 + - - +
103B LYS 3.9 0.7 - - - +
105B GLU* 1.3 73.1 - - + +
107B ALA* 1.3 65.0 + - - +
109B GLU* 2.9 16.7 + - - +
110B PHE* 2.8 26.3 + - + +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ALA* 4.4 10.8 - - + -
61B CYS* 5.7 0.2 - - - -
64B LEU* 4.0 22.0 - - + -
77B VAL* 4.9 1.8 - - + -
93B LEU* 4.0 16.0 - - + +
94B PHE* 3.8 13.6 - - + -
103B LYS 2.8 24.1 + - - +
104B ALA* 3.5 8.3 - - - +
106B VAL* 1.3 74.9 - - - +
108B ALA* 1.3 62.1 + - - +
110B PHE* 3.8 2.1 - - - +
111B LEU* 3.0 23.6 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA 3.2 5.7 + - - +
105B GLU 3.1 7.7 + - - +
107B ALA* 1.3 77.1 - - - +
109B GLU* 1.3 68.0 - - - +
111B LEU* 4.6 1.1 - - - +
112B ASN* 2.8 39.6 + - - +
120B VAL* 3.4 31.6 - - + +
122B PRO* 3.6 24.9 - - + -
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ASP* 4.3 2.3 - - - +
101B ARG* 2.9 41.9 + - - +
105B GLU* 2.8 19.6 + - + +
106B VAL* 3.2 17.4 - - - +
108B ALA* 1.3 74.2 - - - +
110B PHE* 1.3 67.0 + - - +
112B ASN* 4.0 4.4 - - - +
113B ASP* 3.4 16.1 + - - +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.5 22.2 - + - -
96A LEU* 6.3 0.4 - - + -
92B PHE* 3.8 18.4 - + - -
93B LEU* 3.4 35.7 - - + +
95B ARG* 4.1 18.4 - - + -
98B ASP* 5.9 0.7 - - - -
106B VAL* 2.8 20.2 + - + +
107B ALA 3.8 2.7 - - - +
109B GLU* 1.3 76.1 - - + +
111B LEU* 1.3 60.9 + - - +
113B ASP* 2.8 23.9 + - + +
114B ARG* 2.9 62.3 + - + -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 4.3 12.1 - - + -
64B LEU* 3.1 52.7 - - + +
65B LYS* 3.5 5.4 - - + +
68B ALA* 3.6 15.5 - - + -
93B LEU* 4.5 8.5 - - + +
107B ALA 3.0 17.4 + - - +
108B ALA* 4.0 2.0 - - - +
110B PHE* 1.3 80.3 - - - +
112B ASN* 1.3 57.9 + - - +
113B ASP 2.9 4.9 + - - -
114B ARG* 4.5 1.3 - - - +
115B VAL* 3.1 42.1 + - + +
118B CYS* 4.1 10.3 - - - +
120B VAL* 4.6 9.4 - - + -
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Residues in contact with ASN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA* 2.8 33.1 + - - +
109B GLU* 4.0 4.7 - - - +
111B LEU* 1.3 71.1 - - - +
113B ASP* 1.3 58.1 + - - +
115B VAL 4.1 2.4 - - - +
116B PRO 4.0 15.2 - - - +
118B CYS* 3.1 25.4 - - - +
119B ASN* 3.2 1.7 - - - -
120B VAL* 2.5 57.7 + - - +
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Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLN* 3.9 15.1 - - - +
109B GLU* 3.4 10.5 + - + +
110B PHE* 2.8 13.8 + - + +
112B ASN* 1.3 80.5 - - - +
114B ARG* 1.3 68.4 + - - +
115B VAL 3.2 1.9 + - - -
116B PRO* 4.1 8.7 - - - +
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASN 5.8 0.2 - - - +
74A PHE* 3.1 52.4 + - + +
75A PHE* 4.6 8.4 - - - +
76A LEU 5.4 3.0 - - - +
77A GLN* 3.9 35.2 + - - +
92A PHE* 3.7 42.1 + - - +
95A GLU* 5.2 10.3 + - - -
95B ARG* 5.1 6.7 - - - +
110B PHE* 2.9 59.1 + - + +
111B LEU 4.3 1.1 - - - +
113B ASP* 1.3 79.2 + - - +
115B VAL* 1.3 59.4 + - + +
116B PRO* 3.3 10.7 - - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 4.0 15.7 - - + -
16B ARG* 3.6 17.5 - - - +
17B TRP* 5.4 1.1 - - + -
68B ALA* 4.1 16.4 - - + +
69B LEU* 4.0 30.3 - - + -
111B LEU* 3.1 34.3 + - + +
112B ASN 4.1 1.9 - - - +
113B ASP 4.1 2.5 - - - -
114B ARG* 1.3 80.9 - - + +
116B PRO* 1.3 67.9 - - + +
118B CYS* 3.0 28.3 + - + +
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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