Contacts of the helix formed by residues 107 - 124 (chain A) in PDB entry 1L8A
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 MET 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA 4.9 1.1 - - - +
90A ILE* 4.1 23.1 - - + -
93A VAL* 3.9 25.1 - - + -
94A LEU* 3.2 35.0 - - + -
105A GLY 5.3 0.2 - - - +
106A HIS* 1.4 80.8 - - - +
108A ALA* 1.3 68.8 + - - +
109A SER 3.3 1.5 + - - -
110A PHE* 3.4 8.0 + - - +
111A GLN* 3.1 26.3 + - - +
396A MET* 3.4 26.2 - - + -
399A ALA* 5.6 4.0 - - + -
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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
----------------------------------------------------------
106A HIS* 5.0 0.6 - - + +
107A MET* 1.3 78.5 - - - +
109A SER* 1.3 63.3 + - - +
111A GLN* 3.3 2.9 + - - +
112A SER* 3.3 11.4 + - - -
392A LYS* 4.5 14.8 - - + +
393A GLY* 3.0 24.4 + - - +
396A MET* 3.6 14.1 - - - +
400A ALA 3.7 29.2 - - - -
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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
----------------------------------------------------------
106A HIS* 5.3 3.9 - - - +
107A MET 3.3 1.6 - - - +
108A ALA* 1.3 76.5 - - - +
110A PHE* 1.3 65.8 + - - +
112A SER* 2.9 25.2 + - - -
113A SER* 3.2 7.6 + - - -
140A GLN* 3.8 2.6 + - - -
142A HIS* 3.4 31.5 + - - -
143A ILE* 3.7 10.1 - - - +
258A ASN* 4.3 0.5 + - - -
392A LYS* 4.8 6.9 - - - +
887B TPP 3.0 31.4 + - - -
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Residues in contact with PHE 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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85A ILE* 4.0 22.2 - - + -
86A ARG* 4.4 8.7 - - - -
89A ALA* 4.1 12.6 - - + -
106A HIS 5.4 3.1 - - - +
107A MET* 3.4 10.4 + - - +
109A SER* 1.3 78.4 - - - +
111A GLN* 1.3 71.7 + - - +
113A SER* 3.9 3.8 - - - -
114A ALA* 2.8 62.2 + - + +
117A TYR* 4.4 15.9 - + + -
142A HIS 5.2 1.5 + - - +
143A ILE* 3.7 40.1 - - + +
145A PRO* 5.7 1.6 - - + -
146A GLY* 3.5 35.4 - - - +
147A VAL* 4.9 0.7 - - + -
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Residues in contact with GLN 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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86A ARG* 3.0 65.2 + - - +
89A ALA* 5.2 0.8 - - - +
90A ILE* 3.7 25.4 - - + +
107A MET* 3.1 18.6 + - - +
108A ALA 3.4 9.9 - - - +
109A SER 3.1 0.6 - - - -
110A PHE* 1.3 94.7 - - - +
112A SER* 1.3 60.5 + - - +
113A SER 3.6 0.3 + - - -
114A ALA 4.1 1.4 + - - -
364A HIS* 4.3 0.9 + - - -
394A TYR* 3.5 40.5 - - - +
396A MET* 3.8 20.4 - - + -
424A PHE* 4.3 6.6 - - - -
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Residues in contact with SER 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 3.3 2.1 + - - -
109A SER* 2.9 17.1 + - - -
111A GLN* 1.3 82.2 - - - +
113A SER* 1.3 55.5 + - - +
114A ALA 3.7 0.2 - - - -
115A THR 5.4 0.6 + - - -
258A ASN* 2.9 18.2 + - - -
260A ASN* 3.4 9.1 + - - -
363A GLY 4.6 1.9 - - - +
364A HIS* 3.6 10.9 + - - -
390A THR* 3.2 30.1 - - - +
391A ILE 3.0 33.4 - - - -
392A LYS* 3.7 9.6 - - - -
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Residues in contact with SER 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 3.2 11.2 + - - -
110A PHE* 3.8 2.6 + - - -
112A SER* 1.3 77.9 - - - +
114A ALA* 1.3 65.6 + - - +
115A THR 3.3 2.9 - - - -
116A ILE* 3.0 26.7 + - - +
117A TYR* 3.1 37.0 + - - -
140A GLN* 4.5 2.0 + - - -
143A ILE* 3.8 11.4 - - - +
227A PHE* 6.1 0.4 - - - -
258A ASN* 3.5 25.5 + - - -
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Residues in contact with ALA 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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82A ARG* 4.3 6.2 - - + +
86A ARG* 3.6 30.5 - - + +
110A PHE* 2.8 53.6 + - + +
111A GLN 4.1 0.6 + - - -
112A SER 3.7 1.2 - - - -
113A SER* 1.3 72.5 + - - +
115A THR* 1.3 52.0 + - - +
117A TYR* 3.2 3.9 + - - +
118A ASP* 2.7 35.8 + - - +
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Residues in contact with THR 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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82A ARG* 3.5 25.2 + - - +
86A ARG* 3.0 22.4 + - - +
112A SER 5.4 0.6 + - - -
113A SER 3.3 0.8 - - - -
114A ALA* 1.3 75.4 - - - +
116A ILE* 1.3 65.1 + - - +
118A ASP* 3.6 0.4 - - - +
119A VAL* 3.0 25.2 + - + +
363A GLY 4.2 7.6 - - - -
364A HIS* 4.0 20.1 + - - +
366A PRO* 3.8 26.5 - - + -
369A ILE* 3.8 19.1 - - + -
394A TYR* 5.3 0.2 - - - -
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Residues in contact with ILE 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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113A SER* 3.0 23.6 + - - +
115A THR* 1.3 79.3 - - - +
117A TYR* 1.3 64.5 + - - +
119A VAL* 3.6 3.1 + - - +
120A CYS* 3.4 21.7 + - - -
227A PHE* 3.7 26.2 - - + -
256A VAL* 4.0 7.4 - - + -
258A ASN* 4.5 7.0 - - + +
363A GLY 3.7 15.0 - - - +
369A ILE* 4.2 14.8 - - + +
373A PHE* 4.0 20.4 - - + -
388A ALA* 3.5 30.5 - - + -
390A THR* 4.0 17.3 - - + -
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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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110A PHE* 4.4 14.6 - + + -
113A SER* 3.1 45.2 + - - -
114A ALA* 3.6 5.6 - - - +
116A ILE* 1.3 79.1 - - - +
118A ASP* 1.3 60.4 + - - +
120A CYS* 3.1 6.8 + - - +
121A PHE* 2.9 44.8 + + + -
125A PHE* 4.4 4.7 - + - -
139A PHE* 3.4 35.0 - + - -
140A GLN* 3.2 23.3 + - - +
143A ILE* 3.6 17.6 - - + +
147A VAL* 5.8 0.7 - - + -
227A PHE* 3.1 56.8 - + - +
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Residues in contact with ASP 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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78A GLU* 3.7 5.9 - - - +
81A ILE* 5.0 2.4 - - - +
82A ARG* 2.5 55.3 + - + +
85A ILE* 4.3 5.5 - - - +
114A ALA 2.7 20.8 + - - +
115A THR* 3.6 5.8 - - - +
116A ILE 3.3 0.2 - - - -
117A TYR* 1.3 73.5 - - - +
119A VAL* 1.3 63.2 + - - +
121A PHE* 3.2 6.3 + - - +
122A ASN* 3.0 44.0 + - - -
150A ARG* 3.8 17.9 + - - +
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Residues in contact with VAL 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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71A TYR* 3.9 11.9 - - - +
82A ARG* 5.8 0.9 - - - +
115A THR* 3.0 19.1 + - + +
116A ILE 3.9 0.7 - - - +
118A ASP* 1.3 77.1 - - + +
120A CYS* 1.3 57.6 + - - +
122A ASN* 3.3 1.3 + - - +
123A HIS* 2.8 41.8 + - - +
124A PHE* 3.9 21.9 + - + -
366A PRO* 3.8 30.3 - - + -
369A ILE* 3.8 24.2 - - + -
370A TYR* 4.1 14.4 - - + -
373A PHE* 5.2 1.3 - - + -
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Residues in contact with CYS 120 (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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116A ILE 3.4 13.2 + - - +
117A TYR 3.1 7.9 + - - +
119A VAL* 1.3 80.4 - - - +
121A PHE* 1.3 57.4 + - - +
124A PHE* 2.8 20.5 + - - -
125A PHE* 2.7 65.1 + - + -
225A TYR* 5.1 0.2 - - - -
227A PHE* 4.0 4.0 - - - -
373A PHE* 3.5 44.0 - - - -
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Residues in contact with PHE 121 (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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117A TYR* 2.9 40.8 + + + +
118A ASP* 3.8 2.9 - - - +
120A CYS* 1.3 73.3 - - - +
122A ASN* 1.3 61.2 + - - +
125A PHE* 3.9 10.3 - + - -
139A PHE* 3.6 34.8 - + - -
147A VAL* 5.3 8.1 - - + -
150A ARG* 3.4 55.1 + - + +
154A GLU* 5.0 0.7 - - - -
454A GLN* 4.6 1.7 - - - +
455A ARG* 2.6 39.4 + - - +
458A LEU* 3.6 2.3 - - - +
462A LEU* 3.2 46.2 - - + -
463A PRO* 4.8 2.7 - - + -
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Residues in contact with ASN 122 (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 GLU* 3.5 29.7 + - - +
81A ILE* 5.5 5.6 - - - +
118A ASP* 3.0 38.8 + - - +
119A VAL* 4.5 0.6 - - - +
121A PHE* 1.3 80.4 - - - +
123A HIS* 1.3 77.1 + - + +
150A ARG* 4.4 11.6 + - - +
450A TYR* 4.0 8.3 - - - -
451A LEU* 5.2 3.3 - - - +
454A GLN* 3.1 46.8 - - + +
457A LYS* 5.7 0.3 - - - -
458A LEU* 3.8 6.8 - - - +
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Residues in contact with HIS 123 (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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71A TYR* 2.9 42.2 + + - -
72A PRO* 3.9 16.2 - - + -
73A GLY* 3.5 15.5 + - - -
78A GLU* 2.9 21.9 + - - -
119A VAL* 2.8 23.4 + - - +
122A ASN* 1.3 89.6 + - + +
124A PHE* 1.3 74.8 + - + +
370A TYR* 4.1 15.2 - + + -
374A LYS* 5.3 2.8 + - - -
450A TYR* 3.9 3.6 + - - -
454A GLN* 3.9 7.1 + - - -
458A LEU* 3.9 13.5 - - - +
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Residues in contact with PHE 124 (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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119A VAL* 3.9 20.4 - - + -
120A CYS* 2.8 25.7 + - + +
123A HIS* 1.3 79.5 - - + +
125A PHE* 1.3 66.0 + - - +
126A ARG* 3.0 6.1 + - - +
135A ASP* 3.3 8.3 - - - +
225A TYR* 3.9 17.2 + - + +
370A TYR* 3.6 39.7 - + - -
373A PHE* 3.5 46.0 - + + -
374A LYS* 3.5 31.2 - - - -
377A GLN* 3.8 19.7 + - - +
458A LEU* 3.8 10.8 - - - +
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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