Contacts of the helix formed by residues 94 - 110 (chain B) in PDB entry 4LDR
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 VAL 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ALA* 1.3 72.7 - - - +
95B ASN* 1.3 76.7 + - - +
96B MET 3.3 2.7 - - - -
97B ALA* 3.0 15.8 + - + -
98B ARG* 2.9 29.2 + - + +
283B TYR 5.0 10.3 - - - +
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Residues in contact with ASN 95 (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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48B ALA* 3.3 41.0 - - + +
49B PRO* 3.8 12.7 - - - +
52B ALA* 3.7 8.1 - - + +
93B ALA* 3.5 2.0 - - - +
94B VAL* 1.3 88.3 + - - +
96B MET* 1.3 58.4 + - - +
98B ARG* 3.3 5.8 + - - +
99B ALA* 2.9 30.3 + - - +
283B TYR* 3.3 43.9 - - - +
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Residues in contact with MET 96 (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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40B ILE* 4.2 5.8 - - + -
48B ALA 4.8 0.6 + - - -
51B ILE* 3.1 44.0 - - + +
52B ALA* 3.6 24.3 - - - +
55B GLY* 3.8 13.2 - - - -
56B CYS* 4.5 10.5 - - - -
83B LEU* 5.8 0.9 - - - -
86B LEU* 3.9 28.7 - - + +
87B VAL* 3.9 29.4 - - + +
90B ARG 5.7 3.6 - - - +
93B ALA 4.3 6.8 + - - +
94B VAL 3.3 0.6 - - - -
95B ASN* 1.3 78.0 - - - +
97B ALA* 1.3 58.4 + - - +
99B ALA* 3.2 2.1 + - - +
100B ALA* 2.8 34.2 + - - +
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Residues in contact with ALA 97 (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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87B VAL* 4.0 28.2 - - + +
93B ALA 4.9 1.9 + - - +
94B VAL* 3.0 21.0 + - + +
96B MET* 1.3 79.0 - - - +
98B ARG* 1.3 61.1 + - - +
100B ALA* 3.3 2.4 + - - +
101B ARG* 3.1 27.3 + - - +
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Residues in contact with ARG 98 (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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94B VAL* 2.9 25.0 + - + +
95B ASN* 3.8 6.5 - - - +
97B ALA* 1.3 77.0 - - - +
99B ALA* 1.3 61.8 + - - +
101B ARG* 3.4 12.8 + - - +
102B ASP* 2.2 66.7 + - - +
105B ASP* 5.5 1.2 + - - -
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Residues in contact with ALA 99 (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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52B ALA* 4.6 9.0 - - + -
53B LEU* 6.3 0.7 - - + -
56B CYS* 3.8 23.3 - - - -
95B ASN 2.9 17.2 + - - +
96B MET 3.8 3.4 - - - +
98B ARG* 1.3 76.5 - - - +
100B ALA* 1.3 62.4 + - - +
102B ASP* 3.4 3.1 + - - -
103B LEU* 3.0 26.0 + - - +
132B MET* 3.6 24.7 - - + +
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Residues in contact with ALA 100 (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 CYS* 4.9 0.6 - - - -
83B LEU* 3.6 35.5 - - + +
87B VAL* 3.8 21.5 - - + -
96B MET* 2.8 19.9 + - + +
97B ALA 3.5 5.4 - - - +
98B ARG 3.2 0.2 - - - -
99B ALA* 1.3 76.2 - - - +
101B ARG* 1.3 59.4 + - - +
104B ALA* 2.9 31.7 + - - +
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Residues in contact with ARG 101 (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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97B ALA 3.1 15.5 + - - +
98B ARG* 3.7 20.9 - - - +
99B ALA 3.3 0.2 - - - -
100B ALA* 1.3 76.6 - - - +
102B ASP* 1.3 53.4 + - - +
104B ALA* 3.1 7.1 + - - +
105B ASP* 2.7 69.1 + - - +
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 2.2 53.1 + - - +
99B ALA* 3.7 8.9 - - - +
101B ARG* 1.3 79.4 - - - +
103B LEU* 1.3 52.5 + - - +
105B ASP* 3.1 9.9 + - - +
106B VAL* 2.7 42.9 + - + +
109B ARG* 5.2 0.2 + - - -
128B CYS* 5.7 2.2 - - - -
132B MET* 4.1 14.0 - - + +
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Residues in contact with LEU 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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56B CYS* 3.4 36.3 - - + +
59B LEU* 5.3 3.1 - - + -
79B VAL* 5.1 0.2 - - - -
83B LEU* 3.8 23.1 - - + -
99B ALA 3.0 10.9 + - - +
102B ASP* 1.3 75.5 - - - +
104B ALA* 1.3 57.9 + - - +
106B VAL* 3.3 4.9 + - + +
107B ALA* 2.9 31.4 + - - +
125B VAL* 3.4 30.4 - - + +
128B CYS* 4.1 16.6 - - + -
129B THR* 3.2 30.1 - - - +
132B MET* 3.5 18.2 - - + -
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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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79B VAL* 4.9 2.0 - - - -
80B ARG* 3.6 34.6 + - + +
83B LEU* 3.8 12.0 - - + +
100B ALA 2.9 20.0 + - - +
101B ARG* 3.4 10.5 - - - +
103B LEU* 1.3 75.5 - - - +
105B ASP* 1.3 60.3 + - - +
107B ALA* 3.4 5.7 + - - +
108B ALA* 2.9 28.9 + - - +
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Residues in contact with ASP 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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80B ARG* 4.9 6.1 + - - -
98B ARG* 5.5 0.9 + - - -
101B ARG* 2.7 56.9 + - - +
102B ASP* 3.5 10.1 + - - +
104B ALA* 1.3 72.9 - - - +
106B VAL* 1.3 55.6 + - - +
108B ALA* 4.3 5.0 - - - +
109B ARG* 2.4 63.8 + - - +
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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
----------------------------------------------------------
102B ASP* 2.7 26.3 + - + +
103B LEU* 3.6 7.2 - - - +
105B ASP* 1.3 71.9 - - - +
107B ALA* 1.3 54.8 + - - +
109B ARG* 3.2 14.8 - - - +
110B GLU* 2.3 39.2 + - + +
124B ARG* 3.7 49.2 + - + +
125B VAL* 4.6 5.4 - - - +
128B CYS* 4.0 28.5 - - + -
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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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76B VAL* 3.8 13.6 - - + +
79B VAL* 4.3 16.6 - - + -
103B LEU 2.9 18.3 + - - +
104B ALA* 3.8 4.0 - - - +
106B VAL* 1.3 76.5 - - - +
108B ALA* 1.3 57.5 + - - +
110B GLU* 2.8 8.8 - - - +
111B ALA* 2.8 28.5 + - - +
121B VAL* 4.3 8.3 - - + -
125B VAL* 3.6 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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76B VAL* 5.0 4.2 - - + +
80B ARG* 3.6 20.9 - - - +
104B ALA 2.9 17.7 + - - +
105B ASP* 3.7 5.4 - - - +
107B ALA* 1.3 74.8 - - - +
109B ARG* 1.3 57.5 + - - +
110B GLU 3.0 4.7 - - - -
111B ALA* 2.9 20.2 + - - +
112B GLU* 3.0 34.9 + - - +
113B ARG* 3.2 0.7 + - - -
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Residues in contact with ARG 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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102B ASP 5.2 0.2 + - - -
105B ASP* 2.4 58.3 + - - +
106B VAL* 3.2 11.7 - - - +
108B ALA* 1.3 64.9 - - - +
110B GLU* 1.3 56.7 + - - +
112B GLU* 4.5 5.4 - - - -
113B ARG* 2.3 27.6 + - - +
124B ARG* 3.8 19.5 + - - +
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Residues in contact with GLU 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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106B VAL 2.3 28.6 + - - +
107B ALA* 2.8 9.7 - - - +
109B ARG* 1.3 72.1 - - - +
111B ALA* 1.3 53.6 + - - +
113B ARG* 2.9 36.2 + - - -
120B ALA* 4.2 14.2 - - + +
121B VAL* 2.9 40.9 - - + +
124B ARG* 2.0 65.5 + - + +
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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