Contacts of the helix formed by residues 107 - 124 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ALA 5.5 0.4 - - - -
90B ILE* 3.7 29.4 - - + -
93B VAL* 3.9 29.2 - - + -
94B LEU* 3.6 33.4 - - + -
105B GLY 5.2 2.5 - - - +
106B HIS* 1.3 79.4 - - - +
108B ALA* 1.3 68.1 + - - +
109B SER 3.3 2.3 + - - -
110B PHE* 3.4 8.9 + - - +
111B GLN* 3.3 24.8 + - - +
396B MET* 4.2 17.7 - - + -
400B ALA 5.7 1.8 - - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B MET* 1.3 78.9 - - - +
109B SER* 1.3 61.1 + - - +
111B GLN* 3.4 7.8 + - - +
112B SER 3.4 1.9 + - - -
392B LYS* 2.5 43.0 - - + +
396B MET* 3.6 12.9 - - - -
400B ALA 3.6 31.1 + - - +
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A TPP 3.0 28.7 + - - -
106B HIS* 5.2 3.5 - - - +
107B MET 3.3 1.8 - - - +
108B ALA* 1.3 76.3 - - - +
110B PHE* 1.3 65.1 + - - +
112B SER* 2.7 25.0 + - - -
113B SER* 3.3 8.5 + - - -
140B GLN* 3.6 2.4 + - - -
142B HIS* 3.0 37.3 + - - -
143B ILE* 3.4 9.9 - - - +
258B ASN* 4.7 0.2 + - - -
392B LYS* 4.7 6.7 - - - +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 4.2 18.4 - - + -
86B ARG* 4.7 4.5 - - - -
89B ALA* 4.2 11.7 - - + -
106B HIS 5.6 2.4 - - - +
107B MET* 3.4 10.0 + - - +
109B SER* 1.3 78.9 - - - +
111B GLN* 1.3 69.4 + - - +
113B SER* 3.7 5.8 - - - -
114B ALA* 2.7 63.7 + - + +
117B TYR* 4.1 18.8 - + + -
142B HIS 5.3 1.1 + - - +
143B ILE* 3.5 41.3 - - + +
145B PRO* 5.7 1.3 - - + -
146B GLY* 3.4 40.8 - - - +
147B VAL* 4.9 0.9 - - + -
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 3.8 39.6 + - - +
89B ALA* 5.4 0.4 - - - +
90B ILE* 3.7 23.7 - - + +
107B MET 3.3 14.7 + - - +
108B ALA 3.5 10.8 - - - +
109B SER 3.1 0.6 - - - -
110B PHE* 1.3 93.0 - - - +
112B SER* 1.3 60.5 + - - +
113B SER 3.6 0.2 + - - -
114B ALA* 3.9 9.7 + - - +
364B HIS* 4.1 0.5 + - - -
392B LYS 4.2 5.2 - - - +
394B TYR* 3.5 27.8 - - + -
395B GLY 4.2 2.2 + - - +
396B MET* 3.8 25.4 - - + -
420B ILE* 4.7 1.6 - - - +
424B PHE* 3.8 20.8 - - - -
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 3.4 1.9 + - - -
109B SER 2.7 20.8 + - - -
111B GLN* 1.3 80.7 - - - +
113B SER* 1.3 56.4 + - - +
114B ALA 3.6 0.2 - - - -
258B ASN* 3.0 14.8 + - - -
260B ASN* 3.5 8.0 + - - -
363B GLY 4.5 2.1 - - - +
364B HIS* 3.4 12.4 + - - -
390B THR* 3.1 39.4 - - - +
391B ILE 2.9 30.7 - - - -
392B LYS* 3.6 8.4 + - - -
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B SER 3.3 10.7 + - - -
110B PHE* 3.3 8.3 + - - -
112B SER* 1.3 77.7 + - - +
114B ALA* 1.3 67.0 + - - +
115B THR 3.3 2.5 - - - -
116B ILE* 3.0 27.2 + - - +
117B TYR* 3.2 36.9 + - - -
140B GLN* 4.5 2.8 + - - -
143B ILE* 3.9 5.7 - - - +
227B PHE* 6.1 1.1 - - - -
258B ASN* 3.5 22.9 - - - -
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG* 4.3 5.2 - - + +
86B ARG* 3.7 33.4 - - + +
110B PHE* 2.7 49.1 + - + +
111B GLN* 4.0 2.9 - - - +
112B SER 3.6 1.4 - - - -
113B SER* 1.3 74.1 - - - +
115B THR* 1.3 58.1 + - - +
117B TYR* 3.3 3.6 + - - +
118B ASP* 2.9 27.5 + - - +
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG* 3.8 25.3 + - - +
86B ARG* 3.1 20.8 + - - +
111B GLN 5.3 0.2 + - - -
112B SER 5.3 0.6 + - - -
113B SER 3.3 0.8 - - - -
114B ALA* 1.3 73.8 - - - +
116B ILE* 1.3 67.7 + - - +
118B ASP* 3.6 0.5 - - - +
119B VAL* 3.0 24.1 + - + +
363B GLY 4.0 8.5 - - - -
364B HIS* 3.8 25.6 + - - +
366B PRO* 3.9 21.3 - - + -
369B ILE* 3.5 20.2 - - + -
394B TYR* 5.1 0.2 - - - -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B SER* 3.0 24.3 + - - +
115B THR* 1.3 79.2 - - - +
117B TYR* 1.3 62.2 + - + +
119B VAL* 3.5 2.8 + - - +
120B CYS* 3.3 22.3 + - - -
227B PHE* 3.8 26.0 - - + -
256B VAL* 4.1 7.4 - - + -
258B ASN* 4.7 6.7 - - - +
363B GLY 3.7 14.4 - - - +
369B ILE* 3.9 14.7 - - + +
373B PHE* 3.9 22.2 - - + -
388B ALA* 3.6 29.8 - - + -
390B THR* 4.0 18.4 - - + -
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 4.1 17.0 - + + -
113B SER* 3.2 45.2 + - - -
114B ALA 3.7 5.4 - - - +
116B ILE* 1.3 77.0 - - - +
118B ASP* 1.3 61.0 + - - +
120B CYS* 3.2 5.7 + - - +
121B PHE* 2.8 46.3 + + + -
125B PHE* 4.3 4.7 - + - -
139B PHE* 3.4 34.3 - + - -
140B GLN* 3.2 21.5 + - - +
143B ILE* 3.6 20.6 - - + +
147B VAL* 5.7 0.9 - - + -
227B PHE* 3.2 54.6 - + - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 3.6 5.8 - - - +
81B ILE* 5.0 2.6 - - - +
82B ARG* 2.7 58.1 + - + +
85B ILE* 4.4 1.4 - - - +
114B ALA 2.9 17.2 + - - +
115B THR 3.6 5.4 - - - +
116B ILE 3.3 0.2 - - - -
117B TYR* 1.3 76.3 - - - +
119B VAL* 1.3 57.3 + - - +
121B PHE* 3.2 1.6 + - - +
122B ASN* 2.9 50.5 + - - -
150B ARG* 2.6 33.7 + - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.8 22.7 - - - +
78B GLU* 5.4 0.2 - - - +
82B ARG* 5.7 1.6 - - - +
115B THR* 3.0 19.7 + - + +
116B ILE 3.9 0.4 - - - +
118B ASP* 1.3 75.5 - - + +
120B CYS* 1.3 58.9 + - - +
122B ASN* 3.3 1.2 + - - +
123B HIS* 2.8 32.9 + - - +
124B PHE* 3.9 14.1 - - + -
366B PRO* 3.8 28.5 - - + +
369B ILE* 3.7 27.1 - - + -
370B TYR* 4.0 25.6 - - + -
373B PHE* 5.2 0.7 - - + -
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Residues in contact with CYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE 3.3 14.1 + - - +
117B TYR* 3.2 7.8 + - - +
118B ASP 3.2 0.6 - - - -
119B VAL* 1.3 80.0 - - - +
121B PHE* 1.3 57.8 + - - +
124B PHE* 2.8 19.0 + - - -
125B PHE* 2.7 62.9 + - + -
227B PHE* 4.0 5.2 - - - -
373B PHE* 3.5 45.8 - - - -
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Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TYR* 2.8 40.1 + + + +
118B ASP 3.7 0.2 - - - +
120B CYS* 1.3 73.6 - - - +
122B ASN* 1.3 62.1 + - - +
125B PHE* 3.8 12.8 - + - -
139B PHE* 3.7 32.3 - + - -
147B VAL* 5.2 11.0 - - + -
150B ARG* 3.2 55.4 - - + +
154B GLU* 4.9 0.9 - - - -
454B GLN* 4.7 1.2 - - - +
455B ARG* 2.7 40.8 + - - +
458B LEU* 3.7 1.7 - - - +
462B LEU* 3.3 44.9 - - + -
463B PRO* 4.9 2.0 - - + -
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Residues in contact with ASN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 3.6 26.9 + - - +
81B ILE* 5.7 5.0 - - - +
118B ASP* 2.9 43.6 + - - +
119B VAL* 4.4 0.8 - - - +
121B PHE* 1.3 81.6 - - - +
123B HIS* 1.3 78.4 + - + +
150B ARG* 4.7 8.6 + - - -
450B TYR* 3.9 8.2 - - - -
451B LEU* 5.2 4.9 - - - +
454B GLN* 3.0 47.2 - - + +
455B ARG* 6.0 0.2 - - - -
458B LEU* 3.8 7.0 - - - +
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Residues in contact with HIS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.3 26.0 + + - -
72B PRO* 3.8 18.6 - - + -
73B GLY* 3.4 16.5 + - - -
78B GLU* 2.8 30.3 + - - -
119B VAL* 2.8 18.9 + - - +
122B ASN* 1.3 90.9 - - + +
124B PHE* 1.3 73.6 + - + +
370B TYR* 3.9 18.9 - + + -
374B LYS* 5.8 1.4 + - - -
377B GLN* 5.5 0.7 - - - +
454B GLN* 3.7 12.5 + - - -
458B LEU* 3.8 14.1 - - - +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 3.9 19.5 - - + -
120B CYS* 2.8 27.4 + - + +
123B HIS* 1.3 81.1 - - + +
125B PHE* 1.3 66.2 + - - +
126B ARG* 3.2 7.3 + - - +
135B ASP* 3.3 9.8 - - - +
225B TYR* 3.8 21.6 + - + +
370B TYR* 3.6 39.7 - + - -
373B PHE* 3.5 46.7 - + + -
374B LYS* 3.5 26.2 - - + -
377B GLN* 3.8 20.4 - - - +
458B LEU* 3.6 10.1 - - - +
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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
------------------------------------------------------------
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