Contacts of the helix formed by residues 118 - 131 (chain L) in PDB entry 6IY6
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 SER 118 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66L GLY 5.5 0.9 - - - -
67L LEU* 3.4 18.2 - - - +
69L GLY* 5.2 2.0 - - - -
78L ILE* 3.9 16.4 - - - -
113L VAL* 3.6 25.4 + - - +
116L SER* 4.2 3.8 - - - -
117L LEU* 1.3 73.5 - - - +
119L LEU* 1.3 65.3 + - - +
120L ALA* 3.6 10.3 - - - +
121L ASP* 2.8 32.9 + - - +
122L LEU* 3.4 12.2 + - - +
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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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20L ALA* 4.6 4.7 - - + -
55L LEU* 3.3 51.6 - - + +
56L ARG* 3.9 7.2 - - - +
59L ALA* 3.4 28.3 - - + +
67L LEU* 2.9 27.3 + - + +
68L TYR* 4.1 12.6 - - + -
78L ILE* 3.9 14.6 - - + +
82L LEU* 4.5 10.8 - - + -
118L SER* 1.3 67.3 - - - +
120L ALA* 1.3 58.4 - - - +
122L LEU* 3.1 15.1 + - + +
123L CYS* 2.7 39.1 + - + +
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Residues in contact with ALA 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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78L ILE* 4.2 11.4 - - + +
81L TRP* 3.7 35.9 - - + -
112L LEU* 3.7 12.6 - - + -
113L VAL* 4.0 6.7 - - + -
118L SER* 3.6 12.5 - - - +
119L LEU* 1.3 76.4 - - - +
121L ASP* 1.3 63.3 + - - +
123L CYS* 3.9 9.2 - - - -
124L VAL* 3.0 31.2 + - - +
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Residues in contact with ASP 121 (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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111L TYR* 3.5 23.0 - - - +
112L LEU* 2.8 27.8 + - - +
116L SER 3.5 2.9 - - - +
117L LEU* 3.6 14.6 - - + -
118L SER* 2.8 39.0 + - - +
120L ALA* 1.3 77.1 - - - +
122L LEU* 1.3 56.6 + - - +
125L TRP* 3.1 33.6 + - - +
150L TRP* 3.3 24.8 + - - -
154L LEU* 3.9 10.3 - - + -
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Residues in contact with LEU 122 (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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16L GLY* 4.5 10.8 - - - +
19L LEU* 4.3 13.2 - - + +
20L ALA* 3.8 36.3 - - + +
23L HIS* 5.0 3.8 - - + +
55L LEU* 5.7 1.8 - - + -
67L LEU* 4.4 17.0 - - + -
117L LEU* 3.8 26.7 - - + -
118L SER 3.7 10.1 - - - +
119L LEU* 3.1 14.2 + - + +
121L ASP* 1.3 73.0 - - - +
123L CYS* 1.3 57.9 + - - +
125L TRP* 3.2 4.5 + - - +
126L ALA* 2.8 38.0 + - - +
154L LEU* 5.8 0.2 - - + -
158L LEU* 4.1 29.4 - - + -
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Residues in contact with CYS 123 (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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16L GLY* 5.1 2.9 - - - -
52L ASN* 5.3 0.9 - - - +
55L LEU* 4.1 17.2 - - + +
81L TRP 3.6 17.0 - - - -
82L LEU* 3.7 26.0 - - + -
85L SER* 3.4 21.8 - - - +
119L LEU 2.7 18.5 + - - +
120L ALA* 3.4 15.3 - - - -
122L LEU* 1.3 72.3 - - - +
124L VAL* 1.3 62.0 + - - +
126L ALA* 4.0 4.6 - - - +
127L THR* 2.7 32.1 + - - -
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Residues in contact with VAL 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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81L TRP* 4.0 25.8 - - + +
84L PHE* 4.6 2.5 - - + -
85L SER* 4.0 9.9 - - - -
89L LEU* 3.7 17.5 - - + +
102L LEU* 3.8 20.9 - - + -
112L LEU* 3.7 12.1 - - + -
120L ALA 3.0 16.9 + - - +
123L CYS* 1.3 88.0 - - - +
125L TRP* 1.3 54.3 + - - +
127L THR* 3.3 4.0 + - - -
128L LEU* 2.7 37.3 + - + +
150L TRP* 3.5 22.9 - - + -
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Residues in contact with TRP 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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15L LEU* 4.1 17.5 - - + -
19L LEU* 3.7 24.5 - - + -
121L ASP 3.1 21.8 + - - +
122L LEU* 3.8 2.2 - - - +
124L VAL* 1.3 75.6 - - - +
126L ALA* 1.3 57.1 + - - +
128L LEU* 3.3 5.3 + - - +
129L LYS* 2.8 47.8 + - + +
150L TRP* 3.8 10.3 - + + -
151L PHE* 3.2 61.2 + + - -
154L LEU* 3.5 25.3 - - + +
155L GLU* 3.8 29.8 - - + -
158L LEU* 3.7 24.7 - - + -
159L GLU 5.6 3.6 - - - -
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Residues in contact with ALA 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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15L LEU* 3.6 26.1 - - + +
16L GLY* 3.3 35.4 - - - +
19L LEU* 4.5 2.0 - - + -
122L LEU 2.8 21.1 + - - +
123L CYS* 4.0 4.9 - - - +
125L TRP* 1.3 76.3 - - - +
127L THR* 1.3 56.0 + - - +
129L LYS* 3.4 3.3 + - - +
130L GLY* 3.0 24.8 + - - -
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Residues in contact with THR 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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85L SER* 3.3 33.2 + - - +
89L LEU* 3.7 9.0 - - + +
90L SER* 3.6 26.6 + - - +
123L CYS 2.7 21.9 + - - -
124L VAL 3.3 4.1 + - - -
126L ALA* 1.3 76.6 - - - +
128L LEU* 1.3 56.4 + - - +
130L GLY* 3.3 3.2 + - - +
131L ASN* 2.9 27.4 + - - +
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Residues in contact with LEU 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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89L LEU* 3.6 30.5 - - + +
95L PHE* 4.0 6.3 - - + -
99L ILE* 3.8 17.0 - - + -
102L LEU* 4.2 5.6 - - + -
124L VAL* 2.7 21.4 + - + +
125L TRP* 3.5 5.2 - - - +
127L THR* 1.3 71.7 - - - +
129L LYS* 1.3 63.0 + - - +
131L ASN* 3.3 13.6 + - + +
134L TRP* 3.0 43.6 - - + +
147L VAL* 3.9 19.3 - - + -
150L TRP* 3.8 27.6 - - + -
151L PHE* 3.8 13.5 - - + -
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Residues in contact with LYS 129 (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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15L LEU* 4.0 18.4 - - + -
125L TRP* 2.8 35.2 + - + +
126L ALA 3.6 5.4 - - - +
128L LEU* 1.3 70.3 - - - +
130L GLY* 1.3 60.8 + - - +
131L ASN 3.4 8.8 + - - +
134L TRP* 4.4 1.8 - - - -
135L GLN* 3.7 34.3 - - - +
151L PHE* 3.7 26.6 - - + -
155L GLU* 4.2 18.7 + - - -
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Residues in contact with GLY 130 (chain L).
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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15L LEU* 5.0 2.2 - - - +
126L ALA 3.0 14.1 + - - -
127L THR* 3.6 6.1 - - - -
128L LEU 3.3 0.4 - - - -
129L LYS* 1.3 74.2 - - - +
131L ASN* 1.3 61.0 + - - +
132L ALA* 3.9 1.4 + - - +
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Residues in contact with ASN 131 (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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89L LEU 3.0 24.7 + - - +
90L SER 5.1 1.2 + - - -
91L SER 3.8 6.1 + - - -
92L CYS* 4.1 10.4 - - - +
95L PHE* 3.3 26.8 - - + -
127L THR 2.9 13.2 + - - +
128L LEU* 3.4 18.2 - - - +
129L LYS 3.2 10.5 - - - +
130L GLY* 1.3 76.7 - - - +
132L ALA* 1.3 62.7 + - - +
133L ALA* 2.7 33.5 + - - +
134L TRP* 2.9 12.3 + - + -
135L GLN* 4.0 11.3 + - - +
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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