Contacts of the helix formed by residues 101 - 119 (chain A) in PDB entry 5L26
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A PHE* 4.2 11.4 - - + -
97A PHE* 3.0 55.8 + - + +
100A ARG* 1.3 82.1 - - - +
102A LEU* 1.3 65.4 + - + +
103A PRO 3.3 1.6 - - - -
104A MET* 2.8 31.7 + - - +
105A ILE* 3.7 6.2 + - + +
191A GLY* 3.6 35.6 - - - +
194A GLN* 4.4 2.0 - - + -
195A MET* 3.8 7.0 - - + -
333A PHE* 4.1 12.3 - - + -
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Residues in contact with LEU 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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97A PHE* 3.7 20.6 + - + +
98A ALA* 3.7 32.1 - - + +
101A VAL* 1.3 76.9 - - + +
103A PRO* 1.3 68.9 - - + +
105A ILE* 3.1 37.7 + - + +
106A VAL* 3.5 2.6 + - - +
260A ALA* 3.5 40.6 - - + +
261A ILE* 5.5 0.9 - - - -
263A VAL* 4.5 6.3 - - + -
264A GLY* 3.9 22.0 - - - +
333A PHE* 5.9 0.4 - - + -
77B LEU* 4.5 5.4 - - + -
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Residues in contact with PRO 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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74A VAL* 3.7 15.0 - - + -
78A PHE* 3.9 22.7 - - + -
98A ALA 3.3 17.0 - - - +
99A LEU 3.5 22.7 - - - +
100A ARG 4.3 0.4 - - - -
101A VAL 3.4 4.0 - - - +
102A LEU* 1.3 90.1 - - + +
104A MET* 1.3 62.7 + - + +
106A VAL* 3.1 22.4 + - + +
107A PHE* 3.1 11.6 + - - +
268C LEU* 3.6 27.0 - - + +
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Residues in contact with MET 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.7 32.5 - - + +
70A GLY* 4.6 4.5 - - - -
71A ASN* 3.7 21.8 - - - +
74A VAL* 4.6 11.7 - - - -
100A ARG 3.7 15.7 - - - +
101A VAL* 2.8 20.9 + - - +
103A PRO* 1.3 69.2 - - + +
105A ILE* 1.3 63.2 + - - +
107A PHE* 4.3 9.6 - - + +
108A PHE* 3.1 60.3 + - + +
187A SER 4.1 5.2 - - - +
190A ALA* 3.9 18.4 - - + +
191A GLY 4.5 0.2 - - - +
194A GLN* 4.1 12.3 - - + -
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Residues in contact with ILE 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 VAL* 4.3 5.2 - - + +
102A LEU* 3.3 37.0 - - + +
104A MET* 1.3 79.4 - - - +
106A VAL* 1.3 57.4 + - - +
109A SER* 2.5 40.7 + - - +
187A SER* 3.8 26.7 - - - +
188A VAL* 4.1 24.7 - - + -
191A GLY* 6.0 0.2 - - - -
256A GLY 3.6 14.8 - - - +
259A ILE* 3.9 19.7 - - + -
260A ALA* 4.1 11.0 - - + +
263A VAL* 4.6 14.1 - - + -
333A PHE* 5.0 4.0 - - + -
505A URI 6.4 0.2 - - + -
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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 LEU 3.8 11.7 - - - +
103A PRO* 3.1 13.8 + - + +
105A ILE* 1.3 77.0 - - - +
107A PHE* 1.3 63.3 + - - +
109A SER* 3.4 3.6 + - - -
110A SER* 3.1 21.3 + - - -
253A ALA* 3.4 23.0 - - + +
256A GLY 3.6 21.3 - - - +
257A ALA* 3.6 13.5 - - + -
260A ALA* 4.3 3.8 - - + -
265C ALA* 3.9 29.4 - - + +
268C LEU* 3.9 13.7 - - + -
269C ALA* 5.2 0.2 - - + -
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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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66A VAL* 3.5 45.3 - - + -
69A TYR* 4.7 2.7 - - + -
70A GLY* 3.8 20.0 - - - +
74A VAL* 6.5 0.2 - - + -
103A PRO 3.1 12.3 + - - +
104A MET* 4.1 6.3 - - + +
105A ILE 3.4 0.2 - - - -
106A VAL* 1.3 79.0 - - - +
108A PHE* 1.3 78.2 + + - +
110A SER* 2.5 27.0 + - - -
111A LEU* 2.8 22.1 + - + +
268C LEU* 3.9 14.3 - - + +
269C ALA* 4.4 5.8 - - - +
272C ALA* 3.5 28.5 - - + -
273C LEU* 3.7 22.2 - - + -
276C MET* 4.4 10.1 - - - -
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Residues in contact with PHE 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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63A ILE* 4.6 7.4 - - + -
66A VAL* 3.7 26.2 - - + -
67A ILE* 4.0 11.2 - - + -
104A MET* 3.1 37.8 + - + +
107A PHE* 1.3 93.2 - + - +
109A SER* 1.3 61.7 + - - +
111A LEU* 3.7 15.2 - - + +
112A MET* 2.9 41.3 + - + +
186A GLY* 3.6 20.0 - - - -
187A SER* 3.6 18.6 - - - +
190A ALA* 3.5 26.5 - - + -
501A 6ZL 4.3 23.1 - - + -
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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
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105A ILE* 2.5 30.4 + - - +
106A VAL 3.7 1.3 - - - -
107A PHE 3.3 0.2 - - - -
108A PHE* 1.3 77.1 - - - +
110A SER* 1.3 60.6 + - - +
112A MET* 4.2 4.5 - - - +
113A ALA* 3.3 20.6 + - - +
156A GLU* 5.5 3.5 + - - -
187A SER* 4.2 7.5 + - - -
252A GLY* 3.3 21.5 - - - -
255A THR* 5.6 1.6 - - - -
256A GLY* 3.5 17.7 - - - -
259A ILE* 5.0 5.4 - - - +
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Residues in contact with SER 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 3.1 8.5 + - - -
107A PHE* 2.5 25.8 + - - -
109A SER* 1.3 76.6 - - - +
111A LEU* 1.3 62.4 + - - +
113A ALA* 3.3 3.5 + - - +
114A VAL* 3.1 27.8 + - - +
249A ALA* 3.3 26.0 - - - -
252A GLY* 3.7 8.7 + - - -
253A ALA 3.6 7.9 - - - -
269C ALA* 3.3 25.5 - - - +
273C LEU* 4.5 4.2 - - - +
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Residues in contact with LEU 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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66A VAL* 3.8 28.9 - - + -
107A PHE* 2.8 23.7 + - + +
108A PHE* 3.3 21.3 + - + +
110A SER* 1.3 75.1 + - - +
112A MET* 1.3 61.5 + - - +
114A VAL* 3.0 10.5 + - + +
115A LEU* 3.0 48.9 + - + +
501A 6ZL 4.5 15.9 - - + -
273C LEU* 4.1 18.6 - - + -
276C MET* 3.9 27.4 - - + -
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Residues in contact with MET 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 PHE* 2.9 27.6 + - + +
109A SER* 4.2 4.9 - - - +
111A LEU* 1.3 76.9 - - + +
113A ALA* 1.3 56.7 + - - +
115A LEU* 3.8 9.8 - - - +
116A TYR* 2.9 45.0 + - + -
121A MET* 3.6 47.8 - - + -
151A PHE* 4.0 15.3 - - + +
152A VAL* 3.6 31.4 - - + -
156A GLU* 6.0 1.1 - - - +
186A GLY* 5.9 3.1 - - - -
187A SER 6.0 1.1 - - - +
501A 6ZL 4.4 14.1 - - - -
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Residues in contact with ALA 113 (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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109A SER 3.3 14.5 + - - +
110A SER 3.3 11.4 + - - +
111A LEU 3.1 0.6 - - - -
112A MET* 1.3 80.0 - - - +
114A VAL* 1.3 61.5 + - - +
116A TYR* 3.7 6.4 + - - +
117A TYR* 3.2 21.3 + - - +
248A ALA* 3.3 28.4 - - + +
252A GLY* 3.9 9.0 - - - -
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Residues in contact with VAL 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 SER 3.2 15.5 - - - +
111A LEU* 3.0 13.4 + - + +
113A ALA* 1.3 76.3 - - - +
115A LEU* 1.3 62.0 + - + +
117A TYR* 3.0 7.7 + - - +
118A ILE* 2.9 46.8 + - + +
245A VAL* 4.0 14.6 - - + +
248A ALA* 4.9 1.6 - - - -
249A ALA* 3.8 26.7 - - + +
503A 6ZL 4.0 22.2 - - + -
273C LEU* 4.3 12.3 - - + -
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Residues in contact with LEU 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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111A LEU* 3.0 37.5 + - + +
112A MET* 3.8 13.5 - - - +
114A VAL* 1.3 79.5 - - + +
116A TYR* 1.3 57.7 + - - +
118A ILE* 4.3 10.3 - - + +
119A GLY 3.3 2.8 + - - -
120A VAL* 3.0 49.7 + - + -
121A MET* 3.4 43.4 + - + -
501A 6ZL 3.9 31.9 - - + -
276C MET* 6.2 0.2 - - + -
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Residues in contact with TYR 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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112A MET* 2.9 38.5 + - + +
113A ALA* 4.0 6.5 - - - +
115A LEU* 1.3 76.4 - - - +
117A TYR* 1.3 62.1 + - - +
119A GLY* 3.7 2.1 + - - -
121A MET* 4.0 16.6 - - + -
122A GLN* 2.6 49.8 + - + +
125A ILE* 3.5 20.9 - - + +
148A ALA* 4.7 0.7 - - - +
152A VAL* 3.6 40.9 - - + +
156A GLU 4.9 5.4 + - - -
157A ALA* 5.3 0.2 - - - -
160A VAL* 4.1 23.3 - - + +
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Residues in contact with TYR 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 ALA 3.2 15.5 + - - +
114A VAL* 3.0 11.1 + - - +
116A TYR* 1.3 76.6 - - - +
118A ILE* 1.3 67.9 + - + +
119A GLY* 3.5 0.5 + - - -
242A PRO* 3.8 32.1 - - + -
243A THR 3.5 5.7 + - - -
244A ASN* 3.3 26.9 - - - +
245A VAL* 3.6 31.4 + - + -
248A ALA* 4.1 14.8 - - + -
503A 6ZL 3.6 52.4 + - - +
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Residues in contact with ILE 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 VAL* 2.9 39.4 + - + +
115A LEU* 3.7 7.4 + - + +
117A TYR* 1.3 79.1 - - + +
119A GLY* 1.3 58.1 + - - +
120A VAL* 4.0 23.3 - - + -
245A VAL* 5.3 0.4 - - + -
503A 6ZL 3.0 86.5 + - + +
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Residues in contact with GLY 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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115A LEU 3.3 2.4 + - - -
116A TYR 3.7 1.3 + - - -
117A TYR 3.2 3.7 - - - -
118A ILE* 1.3 80.2 - - - +
120A VAL* 1.3 65.9 + - - +
122A GLN* 3.2 25.0 - - - +
123A LEU* 3.6 18.9 + - - +
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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