Contacts of the helix formed by residues 94 - 113 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PRO 4.4 2.4 + - - -
92A THR 4.3 0.8 + - - -
93A ALA* 1.3 68.9 - - - +
95A ASN* 1.3 68.4 + - - +
96A MET 3.0 3.1 - - - -
97A ALA* 2.7 42.9 + - + +
98A ARG* 3.0 20.2 + - + +
283A TYR 6.0 2.0 - - - +
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Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.2 40.4 - - + +
49A PRO* 3.9 13.5 - - + +
52A ALA* 3.6 8.0 - - + +
93A ALA* 3.3 1.4 - - + +
94A VAL* 1.3 86.2 + - - +
96A MET* 1.3 56.7 + - - +
98A ARG* 4.1 7.9 - - - +
99A ALA* 3.1 28.9 + - - +
283A TYR* 3.5 42.2 - - - +
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Residues in contact with MET 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 5.8 1.8 - - - -
48A ALA 5.4 0.2 - - - +
51A ILE* 3.9 25.1 - - + +
52A ALA* 3.6 35.2 - - - +
55A GLY* 4.6 2.5 - - - -
56A CYS* 4.3 14.4 - - - -
83A LEU* 5.3 1.1 - - + -
86A LEU* 3.7 45.5 - - + +
87A VAL* 4.3 14.4 - - + +
89A ALA* 6.1 0.2 - - - -
90A ARG 5.7 3.4 - - - +
91A PRO* 6.5 0.2 - - + -
93A ALA 4.0 9.7 + - - +
94A VAL 3.0 0.6 - - - -
95A ASN* 1.3 77.0 - - - +
97A ALA* 1.3 60.6 + - - +
99A ALA* 3.2 1.0 + - + -
100A ALA* 2.8 35.4 + - + +
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.9 24.1 - - + +
93A ALA 4.9 0.2 + - - -
94A VAL* 2.7 30.5 + - + +
96A MET* 1.3 74.5 - - - +
98A ARG* 1.3 61.4 + - - +
100A ALA* 3.1 3.8 + - - +
101A ARG* 3.0 25.3 + - - +
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 3.0 21.0 + - + +
95A ASN* 4.2 7.6 - - - +
97A ALA* 1.3 76.1 - - - +
99A ALA* 1.3 64.8 + - - +
101A ARG* 3.2 28.2 + - - +
102A ASP* 2.8 59.3 + - - +
132A MET* 5.6 5.8 - - - +
283A TYR* 6.5 1.3 - - + -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 4.3 6.5 - - + -
56A CYS* 3.9 16.6 - - - -
95A ASN 3.1 20.8 + - - +
96A MET* 3.4 7.9 - - - +
98A ARG* 1.3 84.4 + - - +
100A ALA* 1.3 60.9 + - - +
102A ASP* 3.7 0.3 + - - +
103A LEU* 3.0 27.7 + - - +
132A MET* 3.8 28.4 - - + +
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.4 46.0 - - + +
87A VAL* 4.3 7.9 - - + -
96A MET* 2.8 21.7 + - + +
97A ALA 3.4 5.6 - - - +
99A ALA* 1.3 74.4 - - - +
101A ARG* 1.3 54.3 + - - +
104A ALA* 2.8 37.7 + - - +
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA 3.0 16.2 + - - +
98A ARG* 3.2 33.3 + - - +
99A ALA 3.4 0.2 - - - -
100A ALA* 1.3 78.1 - - - +
102A ASP* 1.3 82.8 + - - +
104A ALA* 3.6 4.7 - - - +
105A ASP* 2.8 47.2 + - - +
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ARG* 2.8 42.6 + - - +
99A ALA 4.5 0.2 - - - +
100A ALA 3.3 0.2 - - - -
101A ARG* 1.3 110.8 + - - +
103A LEU* 1.3 56.9 + - - +
104A ALA 3.0 1.8 - - - -
105A ASP* 3.4 9.9 - - - +
106A VAL* 2.6 42.2 + - + +
128A CYS* 6.0 0.2 - - - -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A CYS* 4.4 9.4 - - + -
59A LEU* 4.1 12.8 - - + -
79A VAL* 4.5 2.1 - - + +
83A LEU* 3.8 33.0 - - + -
99A ALA 3.0 20.4 + - - +
102A ASP* 1.3 77.0 - - - +
104A ALA* 1.3 57.7 + - - +
106A VAL* 3.7 5.8 - - + +
107A ALA* 3.1 26.0 + - - +
125A VAL* 4.1 16.7 - - + +
128A CYS* 3.8 32.5 - - + -
129A THR* 3.8 31.9 - - + -
132A MET* 4.6 6.7 - - - -
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 5.6 1.0 - - - +
79A VAL* 4.9 2.0 - - - -
80A ARG* 4.0 35.1 + - + +
83A LEU* 3.9 11.3 - - + +
100A ALA 2.8 19.1 + - - +
101A ARG* 3.6 7.4 - - - +
103A LEU* 1.3 76.5 - - - +
105A ASP* 1.3 53.8 + - - +
107A ALA* 3.0 8.9 + - - +
108A ALA* 2.7 34.5 + - - +
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 5.3 3.1 + - - -
101A ARG* 2.8 41.6 + - - +
102A ASP* 3.0 12.0 + - + +
104A ALA* 1.3 76.4 - - - +
106A VAL* 1.3 61.0 + - - +
108A ALA* 3.4 8.9 - - - +
109A ARG* 2.9 30.0 + - - +
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASP* 2.6 26.8 + - + +
103A LEU* 3.7 8.7 - - + +
105A ASP* 1.3 73.2 - - - +
107A ALA* 1.3 65.7 + - - +
108A ALA 3.1 0.9 + - - -
109A ARG* 3.4 3.8 + - - +
110A GLU* 3.2 24.3 + - - +
124A ARG* 4.0 44.0 - - + +
125A VAL* 5.0 4.0 - - - -
128A CYS* 3.9 30.7 - - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 3.4 21.9 - - + +
79A VAL* 4.4 15.0 - - + -
80A ARG* 6.1 0.4 - - + -
103A LEU 3.1 14.7 + - - +
104A ALA* 3.0 12.4 + - - +
106A VAL* 1.3 76.6 - - - +
108A ALA* 1.3 57.0 + - - +
111A ALA* 3.0 26.6 + - - +
121A VAL* 4.0 7.4 - - + +
124A ARG* 6.5 0.2 - - - -
125A VAL* 4.1 23.8 - - + -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 5.2 5.8 - - + -
80A ARG* 6.1 2.5 - - - +
104A ALA 2.7 13.1 + - - +
105A ASP* 3.4 14.8 - - - +
106A VAL 3.0 0.4 - - - -
107A ALA* 1.3 75.6 - - - +
109A ARG* 1.3 61.0 + - - +
111A ALA* 2.9 8.1 + - - +
112A GLU* 2.8 42.7 + - - +
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Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASP 2.9 19.2 + - - +
106A VAL* 4.2 4.0 - - - +
108A ALA* 1.3 72.5 - - - +
110A GLU* 1.3 58.0 - - - +
112A GLU* 3.0 28.4 + - + +
113A ARG* 3.0 12.9 + - + +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL 3.2 14.4 + - - +
107A ALA* 4.3 0.4 - - - -
109A ARG* 1.3 77.0 - - - +
111A ALA* 1.3 62.3 + - - +
113A ARG* 3.5 45.8 + - - +
116A ALA* 3.5 10.8 - - - +
117A THR 4.7 1.2 + - - +
120A ALA* 3.6 24.5 - - - +
121A VAL* 3.0 38.5 + - + +
124A ARG* 3.8 29.1 - - + +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.0 25.0 - - + +
76A VAL* 3.7 19.3 - - + -
107A ALA 3.0 23.2 + - - +
108A ALA* 2.9 8.6 + - - +
110A GLU* 1.3 78.9 - - - +
112A GLU* 1.3 57.6 + - + +
113A ARG 3.1 1.6 - - - -
116A ALA* 3.2 17.9 - - - +
121A VAL* 4.6 0.9 - - + -
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA* 2.8 27.1 + - - +
109A ARG* 3.0 13.1 + - + +
111A ALA* 1.3 77.4 - - + +
113A ARG* 1.3 62.3 + - - +
114A GLU* 3.5 3.5 + - - +
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ARG 3.0 10.2 + - - +
110A GLU* 3.5 46.3 + - - +
111A ALA 3.1 1.8 - - - +
112A GLU* 1.3 77.9 - - - +
114A GLU* 1.3 67.3 + - + +
115A GLY 3.2 0.5 + - - -
116A ALA* 2.8 37.3 + - - +
120A ALA* 5.9 1.2 - - - +
124A ARG* 6.1 1.4 - - - +
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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
------------------------------------------------------------
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