Contacts of the helix formed by residues 113 - 128 (chain L) in PDB entry 1I43
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 ASN 113 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L VAL* 3.0 24.5 + - - +
84L THR 4.6 7.1 + - - -
87L TYR* 3.2 10.4 + - - -
106L PHE* 3.7 10.7 - - - -
109L GLY* 5.2 1.9 - - - +
112L GLY* 1.3 76.6 - - - +
114L PRO* 1.3 72.6 - - - +
115L THR* 2.6 44.1 + - - +
116L THR* 2.9 33.7 + - - +
117L VAL* 3.0 16.5 + - - +
295L LEU 5.8 1.1 - - - +
297L PRO* 3.1 17.2 - - + +
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Residues in contact with PRO 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74K THR* 5.6 3.1 - - + -
75K ASP* 5.8 2.0 - - - +
70L ARG 4.8 3.3 - - - +
71L GLY 6.1 0.9 - - - -
72L ILE* 4.2 29.2 - - + +
82L VAL* 3.6 31.9 - - + -
87L TYR* 3.3 19.5 - - + +
106L PHE* 3.4 17.9 - - + -
113L ASN* 1.3 89.8 - - - +
115L THR* 1.3 56.6 + - - +
117L VAL* 3.1 25.6 - - + +
118L VAL* 3.5 12.6 - - - +
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Residues in contact with THR 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L THR* 3.8 14.2 - - - +
80L PRO 3.2 25.7 + - - -
81L VAL* 4.1 4.2 - - - -
82L VAL 3.5 13.0 - - - +
113L ASN* 2.6 30.6 + - - +
114L PRO* 1.3 74.7 - - - +
116L THR* 1.3 57.8 + - - +
118L VAL* 4.3 2.2 - - - +
297L PRO* 3.2 40.6 + - + -
300L ALA* 3.8 4.4 - - - +
301L TYR* 4.5 8.3 - - - +
304L ILE* 3.5 22.9 - - - +
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Residues in contact with THR 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L GLY* 5.9 1.3 - - - -
113L ASN* 2.9 29.7 + - - +
115L THR* 1.3 78.7 - - - +
117L VAL* 1.3 67.8 + - + +
118L VAL 3.1 1.8 - - - -
119L LEU* 2.9 16.3 + - - +
120L GLU* 3.1 23.6 + - - +
134L LEU* 4.3 11.4 - - + +
295L LEU* 4.2 31.7 + - + +
297L PRO* 4.4 2.9 - - - +
300L ALA* 3.8 17.4 - - + +
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Residues in contact with VAL 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70L ARG 4.8 7.9 - - - +
106L PHE* 3.7 27.1 - - + -
112L GLY* 5.6 1.6 - - - -
113L ASN 3.0 17.1 + - - +
114L PRO* 3.1 25.4 - - + +
116L THR* 1.3 76.2 - - + +
118L VAL* 1.3 55.9 + - + +
120L GLU* 2.9 23.5 + - - +
121L GLU* 2.7 46.7 + - + +
285L ARG* 6.0 0.4 - - - +
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Residues in contact with VAL 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L ALA 4.5 0.9 - - - +
65L GLY* 3.2 21.4 - - - +
66L GLU* 3.6 19.7 - - + +
70L ARG* 3.6 33.9 - - + +
72L ILE* 5.7 0.7 - - + -
79L THR* 3.7 16.4 - - + +
114L PRO 3.5 17.9 - - - +
115L THR 4.3 1.3 - - - +
116L THR 3.1 0.2 - - - -
117L VAL* 1.3 79.5 - - + +
119L LEU* 1.3 53.4 + - - +
121L GLU* 3.2 6.6 + - - +
122L LYS* 2.8 36.5 + - - +
304L ILE* 3.9 17.0 - - + -
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Residues in contact with LEU 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L THR 4.8 0.9 - - - +
116L THR* 2.9 12.0 + - - +
118L VAL* 1.3 79.9 - - - +
120L GLU* 1.3 57.6 + - - +
122L LYS* 3.5 7.8 - - + +
123L ILE* 2.9 33.6 + - + +
134L LEU* 3.5 31.4 - - + -
300L ALA* 3.7 20.4 - - + +
303L ILE* 3.4 41.3 - - + -
304L ILE* 3.7 25.0 - - + +
307L MET* 3.7 18.8 - - - -
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Residues in contact with GLU 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L THR* 3.1 17.3 + - - +
117L VAL* 2.9 29.8 + - - +
119L LEU* 1.3 78.5 - - - +
121L GLU* 1.3 58.7 + - + +
124L SER* 3.0 31.3 + - - -
132L THR* 3.1 35.3 - - - +
133L LEU* 4.5 1.2 - - - +
134L LEU* 3.6 33.8 + - + +
285L ARG* 3.1 29.5 + - - -
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Residues in contact with GLU 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L TYR* 5.2 6.4 - - + -
64L ALA* 4.8 0.5 - - - +
65L GLY* 4.1 22.0 + - - +
69L GLY 5.6 0.5 - - - +
70L ARG* 6.1 0.7 - - - -
117L VAL* 2.7 31.9 + - + +
118L VAL* 3.7 5.1 - - - +
120L GLU* 1.3 71.6 - - + +
122L LYS* 1.3 66.9 + - - +
124L SER* 3.3 8.0 + - - -
125L ALA* 3.1 23.0 + - - +
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Residues in contact with LYS 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L VAL 4.5 0.7 - - - +
61L ALA* 2.9 20.0 + - - +
62L ILE 2.6 27.1 + - - -
64L ALA* 3.1 36.3 + - + +
66L GLU* 2.7 25.7 + - - -
118L VAL* 2.8 19.8 + - - +
119L LEU* 3.5 14.4 - - + +
120L GLU 3.2 0.2 - - - -
121L GLU* 1.3 79.2 - - - +
123L ILE* 1.3 62.6 + - - +
125L ALA* 3.3 11.1 + - - +
126L LEU* 3.3 14.0 + - - +
304L ILE* 4.1 13.6 + - + -
307L MET* 3.9 26.2 - - + -
308L LYS* 3.1 11.9 - - - +
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Residues in contact with ILE 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119L LEU* 2.9 41.7 + - + +
120L GLU 4.1 2.0 - - - +
122L LYS* 1.3 72.6 - - - +
124L SER* 1.3 67.1 + - - +
126L LEU* 3.3 8.7 + - + +
127L GLU* 3.1 29.2 + - + +
132L THR* 3.7 5.8 - - + +
134L LEU* 4.3 7.4 - - + -
242L PRO* 5.9 2.9 - - + -
257L HIS* 6.0 2.2 - - + -
259L ALA* 5.9 0.4 - - + -
263L LEU* 4.4 13.5 - - + -
273L CYS* 3.3 33.2 - - - -
275L SER* 3.6 21.8 - - - +
303L ILE* 5.2 1.6 - - + -
307L MET* 3.9 22.0 - - + -
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Residues in contact with SER 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L GLU 3.0 14.1 + - - -
121L GLU* 3.5 10.5 - - - -
122L LYS 3.2 0.4 - - - -
123L ILE* 1.3 78.2 - - - +
125L ALA* 1.3 56.9 + - - +
127L GLU 3.7 0.2 + - - -
128L GLY* 2.9 5.5 + - - -
129L ALA* 2.7 43.8 + - - +
130L GLU 5.1 1.1 - - - -
131L SER* 3.2 9.7 + - - -
132L THR* 2.9 40.9 + - - -
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Residues in contact with ALA 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L TYR* 4.3 20.4 - - + +
60L VAL* 3.8 19.6 - - + +
64L ALA* 3.8 8.7 - - + -
121L GLU 3.1 12.2 + - - +
122L LYS 3.6 9.6 - - - +
123L ILE 3.2 0.4 - - - -
124L SER* 1.3 76.7 - - - +
126L LEU* 1.3 64.6 + - - +
128L GLY* 3.0 13.6 + - - -
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Residues in contact with LEU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L ASP* 3.4 32.1 - - + +
60L VAL* 3.9 15.3 - - + -
61L ALA* 4.0 7.0 - - + +
122L LYS 3.3 8.6 + - - +
123L ILE* 3.3 10.9 + - - +
125L ALA* 1.3 80.4 - - - +
127L GLU* 1.3 60.5 + - - +
128L GLY 3.2 0.4 + - - -
242L PRO* 4.1 22.7 - - + +
243L LEU* 4.1 14.8 - - + -
246L LYS* 2.7 30.8 + - - +
263L LEU* 5.2 0.4 - - + -
307L MET* 3.5 29.4 - - + -
310L LEU* 3.9 20.2 - - + -
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Residues in contact with GLU 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L ILE* 3.1 19.9 + - + +
126L LEU* 1.3 76.3 - - - +
128L GLY* 1.3 62.6 + - - +
129L ALA 4.3 5.2 - - - +
242L PRO* 3.1 28.0 - - + +
245L GLN 4.3 7.8 - - - +
246L LYS* 4.5 18.2 - - - +
247L ALA 4.6 1.9 + - - -
248L LEU* 3.7 29.2 + - + +
249L ALA* 5.3 1.0 + - - +
255L VAL* 3.9 18.1 - - + +
257L HIS* 2.5 35.8 + - + -
275L SER* 4.0 19.1 - - - +
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Residues in contact with GLY 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L SER 2.9 6.9 + - - -
125L ALA* 3.0 14.6 + - - -
126L LEU 3.2 0.6 + - - -
127L GLU* 1.3 79.6 - - - +
129L ALA* 1.3 62.8 + - - +
248L LEU* 4.3 3.7 - - - +
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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