Contacts of the helix formed by residues 104 - 119 (chain A) in PDB entry 5L0T
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 PHE 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A CYS* 3.2 6.7 - - - -
103A MET* 1.3 101.3 - - + +
105A PRO* 1.3 67.8 - - - +
106A SER 3.2 2.9 - - - -
107A ARG* 2.9 62.7 + - + -
108A CYS 3.1 9.5 + - - -
131A VAL* 3.8 23.5 - - + +
132A ARG* 4.3 12.8 - - + -
133A ASP* 5.4 0.9 - - - -
407A CL 3.3 8.7 - - + -
4B GLU* 3.6 31.4 - - + -
9B PRO* 4.0 12.1 - - + -
23B TYR* 3.6 27.4 - + - -
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Residues in contact with PRO 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ARG* 5.6 0.6 + - - +
102A CYS* 3.8 20.6 - - + +
103A MET 3.5 8.3 - - - +
104A PHE* 1.3 87.3 - - - +
106A SER* 1.3 55.8 + - - +
108A CYS* 3.4 3.0 + - + +
109A SER* 2.9 32.0 + - - -
407A CL 3.7 4.5 - - + -
23B TYR* 4.2 0.2 - - - +
34B PRO* 5.2 10.8 - - + -
35B ASN* 3.4 26.2 - - - +
37B GLU* 5.9 2.7 - - - +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE 3.1 0.2 + - - -
105A PRO* 1.3 75.6 - - - +
107A ARG* 1.3 59.6 + - - +
109A SER* 4.2 5.6 - - - -
110A GLY* 2.9 22.5 + - - -
168A GLU* 3.4 21.6 + - - +
169A GLY* 3.6 21.7 - - - -
407A CL 3.2 16.1 - - - +
11B GLN* 3.3 25.7 + - - -
35B ASN* 5.5 1.8 + - - +
37B GLU* 5.6 1.2 - - - +
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Residues in contact with ARG 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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104A PHE* 2.9 56.6 + - + +
106A SER* 1.3 75.4 - - - +
108A CYS* 1.3 65.7 + - - +
110A GLY 3.1 1.0 + - - -
111A VAL* 3.0 23.4 + - - +
131A VAL* 2.8 45.6 + - + -
133A ASP* 3.0 32.0 + - - +
164A TRP* 3.3 52.6 - - + +
169A GLY 3.8 11.2 + - - +
170A GLY 6.3 0.2 - - - -
407A CL 4.4 2.5 - - + -
408A GOL 3.6 3.4 + - - -
7B SER* 3.6 26.3 + - - -
9B PRO* 5.3 2.8 - - - +
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Residues in contact with CYS 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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87A THR* 4.0 18.6 - - - -
89A TYR* 3.4 20.0 - - - +
98A ARG* 3.7 8.1 - - - +
102A CYS* 2.1 47.8 - - - -
104A PHE 3.1 6.3 + - - -
105A PRO 3.8 3.6 - - - +
107A ARG* 1.3 76.0 - - - +
109A SER* 1.3 58.0 + - - +
111A VAL* 3.3 4.7 + - - +
112A GLU* 2.8 41.8 + - - +
131A VAL* 4.2 13.0 - - - -
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO* 2.9 19.4 + - - +
106A SER* 3.6 2.2 - - - -
107A ARG 3.2 0.2 - - - -
108A CYS* 1.3 76.0 - - - +
110A GLY* 1.3 56.3 + - - +
112A GLU* 3.3 15.1 + - - +
113A HIS* 2.9 26.2 + - - +
168A GLU* 3.2 29.9 - - - +
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Residues in contact with GLY 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 SER 2.9 12.4 + - - -
107A ARG 3.1 3.3 + - - -
109A SER* 1.3 74.5 - - - +
111A VAL* 1.3 62.5 + - - +
113A HIS* 3.3 9.4 + - - +
114A PHE* 3.2 22.9 - - - -
164A TRP* 3.9 20.2 - - - -
167A TRP* 4.4 4.5 - - - -
168A GLU* 3.5 19.0 + - - -
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Residues in contact with VAL 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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89A TYR* 4.5 9.2 - - + +
107A ARG 3.0 16.5 + - - +
108A CYS* 3.6 9.0 - - - +
110A GLY* 1.3 76.2 - - - +
112A GLU* 1.3 64.6 + - - +
114A PHE* 3.1 7.9 + - - +
115A ILE* 3.1 41.9 + - + +
129A ILE* 4.0 17.3 - - + -
131A VAL* 4.3 5.8 - - + -
161A TYR* 3.7 35.0 - - + +
164A TRP* 4.2 9.1 - - + +
359A TRP* 3.8 18.9 - - + -
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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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89A TYR* 2.6 36.5 + - + +
96A LEU* 4.1 4.5 - - + -
98A ARG* 3.0 29.0 + - - -
108A CYS* 2.8 19.5 + - - +
109A SER* 3.7 15.7 + - - +
111A VAL* 1.3 73.2 - - - +
113A HIS* 1.3 66.1 + - - +
115A ILE* 4.5 6.3 - - - +
116A LEU* 2.9 33.5 + - + +
383A ILE* 3.6 33.7 - - + +
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Residues in contact with HIS 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 SER 2.9 14.1 + - - +
110A GLY 3.4 10.3 - - - +
111A VAL 3.2 0.2 - - - -
112A GLU* 1.3 78.0 - - - +
114A PHE* 1.3 87.3 + + - +
116A LEU* 4.0 5.9 - - - +
117A GLU* 3.2 36.9 + - - +
167A TRP* 3.3 69.1 + + + +
352A MET* 5.0 1.4 - - - +
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Residues in contact with PHE 114 (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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110A GLY 3.2 19.7 - - - -
111A VAL* 3.1 3.8 + - - +
113A HIS* 1.3 92.0 - + - +
115A ILE* 1.3 68.3 + - - +
117A GLU* 3.1 16.1 + - - +
118A VAL* 3.4 16.6 + - - +
162A PRO 5.4 0.2 - - - -
163A ALA 4.7 4.3 - - - -
164A TRP* 4.4 3.4 - - - -
166A PHE* 3.8 17.7 - - + -
167A TRP* 3.7 29.6 - - + -
352A MET* 4.0 18.6 - - + -
355A ILE* 3.6 24.9 - - + -
356A THR* 3.6 25.7 - - - +
359A TRP* 3.3 38.8 - + + +
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Residues in contact with ILE 115 (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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89A TYR* 5.0 3.6 - - + -
91A ILE* 4.1 17.5 - - + -
96A LEU* 4.0 33.2 - - + -
111A VAL* 3.1 37.3 + - + +
112A GLU* 4.0 2.9 - - - +
114A PHE* 1.3 75.8 - - - +
116A LEU* 1.3 57.6 + - - +
118A VAL* 3.1 9.1 + - - +
119A ILE* 2.9 30.6 + - + +
122A LEU* 4.5 5.8 - - + -
127A MET* 4.1 12.6 - - + -
129A ILE* 3.9 17.3 - - + -
359A TRP* 4.1 22.4 - - + -
363A LEU* 4.2 3.8 - - + -
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Residues in contact with LEU 116 (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 LEU* 4.1 23.8 - - + +
112A GLU* 2.9 25.8 + - + +
113A HIS* 4.0 4.9 - - - +
115A ILE* 1.3 75.7 - - - +
117A GLU* 1.3 63.2 + - - +
118A VAL 3.3 0.5 + - - -
119A ILE* 3.6 25.7 + - + +
120A GLY 5.1 0.3 + - - -
383A ILE* 3.8 30.5 - - + +
384A ILE 4.0 7.2 - - - +
385A PRO* 3.9 45.4 - - + +
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Residues in contact with GLU 117 (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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113A HIS* 3.2 36.1 + - - +
114A PHE* 3.1 11.6 + - - +
116A LEU* 1.3 79.6 - - - +
118A VAL* 1.3 57.9 + - + +
119A ILE 4.0 0.2 + - - -
120A GLY 5.2 0.9 + - - -
121A ARG* 4.3 11.3 + - - +
353A ASP* 5.5 2.9 - - - +
356A THR* 3.9 31.6 + - + +
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Residues in contact with VAL 118 (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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114A PHE 3.6 8.7 - - - +
115A ILE* 3.1 13.0 + - - +
117A GLU* 1.3 77.6 - - + +
119A ILE* 1.3 65.3 + - - +
120A GLY 3.2 3.1 - - - -
121A ARG* 2.9 36.5 + - - +
122A LEU* 3.6 23.2 - - + +
356A THR* 3.3 40.8 - - + +
359A TRP* 4.9 3.8 - - + -
360A GLU* 3.7 33.2 - - + +
363A LEU* 5.5 0.4 - - + -
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Residues in contact with ILE 119 (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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91A ILE* 3.9 25.6 - - + -
94A ASN* 2.9 39.7 + - - +
95A ARG 3.6 9.4 - - - +
96A LEU* 3.5 41.3 - - + +
115A ILE* 2.9 17.4 + - + +
116A LEU* 3.6 27.1 - - + +
117A GLU 3.6 0.8 - - - -
118A VAL* 1.3 77.2 - - - +
120A GLY* 1.3 61.4 + - - +
121A ARG 3.0 0.4 - - - -
122A LEU* 3.0 16.5 + - + +
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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