Contacts of the helix formed by residues 95 - 112 (chain A) in PDB entry 4L8E
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 ASP 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A SER* 3.0 11.3 + - - +
94A LYS* 1.3 76.5 - - - +
96A THR* 1.3 68.5 + - - +
97A ARG* 3.2 15.3 + - - +
98A GLU* 3.0 40.5 + - - +
99A ARG* 2.8 24.8 + - - +
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Residues in contact with THR 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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94A LYS 3.5 5.2 + - - -
95A ASP* 1.3 73.3 + - - +
97A ARG* 1.3 62.7 + - + +
99A ARG* 3.8 7.9 - - - +
100A THR* 2.7 45.5 + - - +
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Residues in contact with ARG 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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95A ASP* 3.3 15.4 + - - +
96A THR* 1.3 83.2 - - + +
98A GLU* 1.3 64.9 + - + +
100A THR* 3.3 4.7 + - - -
101A GLU* 3.1 22.3 + - - +
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Residues in contact with GLU 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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93A SER* 2.9 28.2 + - - +
95A ASP* 3.0 23.7 + - - +
97A ARG* 1.3 77.0 - - + +
99A ARG* 1.3 63.4 + - - +
101A GLU* 3.3 7.1 + - - +
102A GLN* 3.0 34.0 + - - +
160A GLY 4.5 1.8 - - - +
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Residues in contact with ARG 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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82A LEU* 4.2 0.6 - - - +
86A ASN* 2.8 27.9 + - - +
92A LEU* 3.5 25.7 + - + +
93A SER* 3.0 35.6 + - - +
94A LYS* 4.4 16.8 - - - +
95A ASP 2.8 18.9 + - - +
96A THR* 3.8 7.4 - - - +
98A GLU* 1.3 77.6 - - - +
100A THR* 1.3 57.9 + - - +
102A GLN* 3.3 13.1 + - - +
103A LEU* 2.9 50.9 + - + +
304A CL 3.3 26.3 - - - +
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Residues in contact with THR 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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96A THR* 2.7 33.5 + - - +
97A ARG* 3.8 4.7 - - - -
99A ARG* 1.3 77.8 - - - +
101A GLU* 1.3 58.2 + - - +
103A LEU* 3.8 8.7 - - + +
104A GLN* 2.9 32.9 + - + +
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Residues in contact with GLU 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 ARG 3.1 13.4 + - - +
98A GLU* 3.7 9.2 - - - +
99A ARG 3.3 0.2 - - - -
100A THR* 1.3 78.0 - - - +
102A GLN* 1.3 60.8 + - - +
104A GLN* 3.2 25.3 + - - +
105A TRP* 3.0 48.6 + - - -
152A GLN* 4.4 9.2 + - - +
160A GLY* 3.3 28.4 - - - +
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Residues in contact with GLN 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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92A LEU* 3.3 16.6 - - + +
93A SER* 2.8 40.7 + - - +
98A GLU* 3.0 20.9 + - - +
99A ARG* 3.6 5.0 - - - +
101A GLU* 1.3 76.2 - - - +
103A LEU* 1.3 56.9 + - - +
105A TRP 3.3 2.1 + - - -
106A LEU* 3.0 23.8 + - - +
159A LEU 4.8 1.8 - - - +
160A GLY 3.9 16.3 + - - +
161A GLY* 5.3 4.4 - - - -
163A GLU* 4.6 13.3 + - - +
165A SER* 3.7 33.4 - - - +
166A ILE* 5.7 0.7 - - + -
167A ALA* 3.5 15.3 - - + +
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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
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82A LEU* 4.0 30.7 - - + -
92A LEU* 4.0 15.7 - - + -
99A ARG* 2.9 45.1 + - + +
100A THR* 3.9 7.0 - - + +
101A GLU 3.3 0.2 - - - -
102A GLN* 1.3 73.1 - - - +
104A GLN* 1.3 66.8 + - - +
106A LEU* 3.2 22.5 + - + +
107A PHE* 2.9 43.8 + - + -
166A ILE* 4.6 0.9 - - + -
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Residues in contact with GLN 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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100A THR* 2.9 21.4 + - + +
101A GLU* 3.2 35.4 + - - +
103A LEU* 1.3 76.7 - - - +
105A TRP* 1.3 72.5 + - + +
107A PHE* 3.4 7.6 + - - +
108A TRP* 2.9 26.9 + - + +
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Residues in contact with TRP 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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101A GLU* 3.0 40.6 + - - -
102A GLN 3.3 7.4 + - - +
103A LEU 3.2 0.4 - - - -
104A GLN* 1.3 90.7 + - + +
106A LEU* 1.3 64.0 + - - +
108A TRP* 3.3 46.0 + + + +
109A GLN* 3.0 23.0 + - - +
148A VAL* 3.9 26.5 - - + -
149A LEU* 5.4 0.2 - - - -
152A GLN* 3.5 35.7 + - + -
159A LEU* 3.7 33.0 - - + +
160A GLY* 3.6 21.5 - - - +
167A ALA* 4.0 8.5 - - + -
171A VAL* 4.9 0.3 - - - +
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Residues in contact with LEU 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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78A GLY* 4.0 30.1 - - - +
81A LEU* 4.2 12.1 - - + -
82A LEU* 4.9 3.4 - - + -
102A GLN 3.0 13.3 + - - +
103A LEU* 3.2 23.1 + - + +
105A TRP* 1.3 75.1 - - - +
107A PHE* 1.3 70.3 + - + +
109A GLN* 3.2 6.6 + - - +
110A VAL* 3.0 24.3 + - + +
166A ILE* 3.9 32.1 - - + +
167A ALA* 4.0 11.5 - - - +
170A ALA* 3.7 26.0 - - + -
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Residues in contact with PHE 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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82A LEU* 5.8 8.3 - - + -
103A LEU* 2.9 48.1 + - + +
104A GLN* 3.7 5.8 - - - +
106A LEU* 1.3 80.7 - - + +
108A TRP* 1.3 62.7 + - - +
110A VAL* 3.3 15.4 + - + +
111A ALA* 2.9 32.1 + - + +
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Residues in contact with TRP 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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104A GLN* 2.9 16.2 + - + +
105A TRP* 3.5 40.4 - + + +
106A LEU 3.2 0.2 - - - -
107A PHE* 1.3 74.1 - - - +
109A GLN* 1.3 72.1 + - + +
111A ALA* 5.0 1.8 - - - -
112A GLY* 2.9 27.8 + - - +
113A PHE* 3.3 37.7 + + + -
144A ARG* 5.2 3.6 - - - +
145A LEU* 3.7 47.8 - - + +
148A VAL* 3.9 20.2 - - + +
149A LEU* 4.0 22.2 - - + -
159A LEU* 4.4 3.1 - - + -
171A VAL* 4.1 15.0 - - + -
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LYS* 2.8 26.8 + - - +
105A TRP 3.0 12.7 + - - +
106A LEU* 3.2 8.0 + - - +
108A TRP* 1.3 78.7 - - - +
110A VAL* 1.3 70.7 + - - +
113A PHE* 3.2 15.6 + - + +
114A GLY* 2.9 41.1 + - - +
170A ALA* 3.4 26.7 - - + +
171A VAL* 3.6 25.4 - - + -
174A TRP* 3.3 30.7 - - - -
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Residues in contact with VAL 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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19A LYS* 4.2 8.1 - - - +
76A GLU* 5.6 3.1 - - - +
77A SER* 4.4 1.3 - - - +
78A GLY* 4.0 30.7 - - - +
81A LEU* 6.4 0.2 - - + -
106A LEU* 3.0 17.6 + - + +
107A PHE* 3.4 25.8 - - + +
109A GLN* 1.3 94.0 - - - +
111A ALA* 1.3 59.9 + - + +
112A GLY 3.6 0.2 - - - -
115A PRO* 3.0 20.4 - - - +
170A ALA* 5.3 0.4 - - + -
301A GSH 4.4 2.9 - - - +
302A GSH 4.7 12.6 + - - +
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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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107A PHE* 2.9 20.1 + - + +
108A TRP* 4.4 2.0 - - - +
110A VAL* 1.3 83.0 - - + +
112A GLY* 1.3 58.0 + - - +
115A PRO* 3.6 13.4 - - - +
116A MET* 5.5 2.4 - - - +
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Residues in contact with GLY 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 TRP* 2.9 14.4 + - - -
110A VAL 3.6 0.6 - - - -
111A ALA* 1.3 80.7 - - - +
113A PHE* 1.3 63.8 + - - +
114A GLY 3.4 0.9 - - - -
115A PRO* 3.6 1.3 - - - -
116A MET* 3.0 36.0 + - - +
141A GLU* 5.8 0.4 - - - -
144A ARG* 6.2 0.4 - - - -
145A LEU* 4.2 12.3 - - - -
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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