Contacts of the helix formed by residues 147 - 161 (chain L) in PDB entry 3IT8
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 LEU 147 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L PHE* 4.2 22.4 - - + -
71L SER* 6.2 0.2 - - - +
72L LEU* 4.3 25.4 - - + -
75L GLU* 5.3 4.5 - - - +
145L ASN* 2.5 18.6 + - - +
146L THR* 1.3 85.4 - - + +
148L TRP* 1.3 53.6 + - - +
149L LYS* 3.1 3.8 - - - -
150L ASP* 2.7 47.2 + - - +
151L VAL* 3.1 12.0 + - - +
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Residues in contact with TRP 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120L TYR* 4.1 10.1 - + - -
125L LYS 3.6 19.7 + - - -
126L ARG* 4.0 8.5 - - + -
127L PHE* 3.7 30.1 - + - -
140L MET* 3.3 26.0 - - - -
141L LEU 4.5 2.5 - - - -
142L THR 3.6 16.8 - - - +
143L VAL* 3.5 48.7 - - + +
145L ASN* 3.1 21.1 + - + +
146L THR 3.4 0.6 - - - -
147L LEU* 1.3 75.6 - - - +
149L LYS* 1.3 76.1 + - + +
151L VAL* 2.9 19.3 + - + +
152L LYS* 2.9 60.5 + - + +
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Residues in contact with LYS 149 (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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143L VAL* 4.8 7.2 - - - +
146L THR 5.2 7.0 - - - +
147L LEU* 3.0 1.2 + - - -
148L TRP* 1.3 90.6 - - + +
150L ASP* 1.3 63.8 + - - +
152L LYS* 3.5 35.2 + - + +
153L ALA* 3.2 22.9 + - - +
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Residues in contact with ASP 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68L PHE* 3.5 23.2 - - + -
147L LEU* 2.7 40.1 + - - +
149L LYS* 1.3 73.1 - - - +
151L VAL* 1.3 59.4 + - - +
153L ALA* 3.2 5.3 + - - +
154L TYR* 2.8 55.2 + - + +
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Residues in contact with VAL 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68L PHE* 4.4 1.8 - - + -
69L TRP* 4.2 21.1 - - + -
72L LEU* 3.6 30.5 - - + -
120L TYR* 5.2 2.0 - - + -
127L PHE* 4.3 11.2 - - + -
140L MET* 4.3 13.7 - - + +
145L ASN* 6.3 0.2 - - - -
147L LEU 3.1 10.0 + - - +
148L TRP* 2.9 39.8 + - + +
150L ASP* 1.3 75.9 - - - +
152L LYS* 1.3 59.7 + - - +
155L LEU* 2.8 43.9 + - + +
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Residues in contact with LYS 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H SER 5.3 0.3 - - - +
120L TYR* 3.8 22.1 + - - +
125L LYS* 3.9 30.8 - - + +
143L VAL* 5.3 2.2 - - - +
148L TRP* 2.9 47.0 + - + +
149L LYS* 3.5 36.7 - - + +
151L VAL* 1.3 74.7 - - - +
153L ALA* 1.3 58.2 + - - +
156L GLY* 2.9 28.2 + - - +
157L GLY 3.1 3.3 + - - -
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Residues in contact with ALA 153 (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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86H SER 6.0 0.4 - - - -
87H TYR* 5.5 0.9 - - - -
149L LYS 3.2 14.9 + - - +
150L ASP* 3.7 6.7 - - - +
151L VAL 3.2 0.2 - - - -
152L LYS* 1.3 80.6 - - - +
154L TYR* 1.3 73.2 + - + +
157L GLY* 3.2 21.0 + - - +
158L PHE 4.2 0.2 + - - -
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Residues in contact with TYR 154 (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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62L ASN* 4.9 4.3 + - - -
65L ASN* 3.6 37.8 + - - +
68L PHE* 3.7 42.6 - + + -
69L TRP* 3.7 18.4 - - + +
150L ASP* 2.8 40.3 + - + +
153L ALA* 1.3 80.6 - - + +
155L LEU* 1.3 61.2 + - - +
158L PHE* 3.3 24.4 + - - +
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Residues in contact with LEU 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L TRP* 3.9 16.4 - - + -
93L LEU* 4.3 21.5 - - + -
95L THR* 3.7 31.9 - - + +
108L GLY* 4.1 12.3 - - - +
120L TYR* 3.9 22.0 - - + -
127L PHE* 3.6 32.5 - - + -
151L VAL* 2.8 23.5 + - + +
154L TYR* 1.3 73.9 - - - +
156L GLY* 1.3 66.0 + - - +
157L GLY 3.4 0.2 + - - -
158L PHE* 3.4 3.1 + - - +
159L GLU* 3.0 26.1 + - - +
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Residues in contact with GLY 156 (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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86H SER* 4.4 2.2 - - - -
120L TYR* 3.3 31.1 - - - -
122L THR* 4.1 1.9 + - - -
151L VAL 3.4 1.6 + - - -
152L LYS* 2.9 16.4 + - - +
155L LEU* 1.3 78.9 - - - +
157L GLY* 1.3 51.4 + - - +
159L GLU* 3.3 2.3 + - - +
160L TYR* 2.7 38.9 + - - +
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Residues in contact with GLY 157 (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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86H SER 3.2 21.9 + - - -
87H TYR* 3.5 18.6 - - - -
152L LYS 3.1 9.5 + - - -
153L ALA* 3.2 14.6 + - - -
156L GLY* 1.3 75.3 - - - +
158L PHE* 1.3 61.4 + - - +
160L TYR* 3.1 1.0 + - - +
161L MET 3.0 20.6 + - - -
162L GLY 3.2 5.5 + - - -
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Residues in contact with PHE 158 (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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87H TYR* 4.7 1.9 - - - -
3L LEU* 4.6 2.0 - - + -
5L TYR* 3.1 48.9 - + - -
58L HIS 4.1 9.2 - - - -
60L PRO* 4.1 22.9 - - + -
95L THR* 3.8 29.4 - - + -
96L GLY* 4.3 3.8 - - - -
153L ALA 4.2 0.6 + - - -
154L TYR 3.3 21.0 + - - +
155L LEU* 3.4 4.4 + - - +
156L GLY 3.4 0.2 - - - -
157L GLY* 1.3 74.1 - - - +
159L GLU* 1.3 61.2 + - - +
161L MET 3.6 0.5 + - - -
162L GLY* 3.3 9.5 + - - +
163L CYS* 2.7 79.4 + - + +
166L ALA* 4.8 2.2 - - + -
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Residues in contact with GLU 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L THR* 4.7 4.7 - - - +
96L GLY 5.8 0.2 - - - -
106L SER* 2.6 43.6 + - - +
107L TYR* 3.7 21.1 - - - +
108L GLY* 3.4 28.3 + - - -
119L ARG* 6.0 0.3 - - - +
120L TYR* 3.1 41.5 - - - +
122L THR* 4.2 14.3 + - - +
155L LEU* 3.0 18.5 + - - +
156L GLY* 3.7 4.0 - - - +
158L PHE* 1.3 77.1 - - - +
160L TYR* 1.3 63.4 + - - +
161L MET* 3.6 0.3 + - - -
163L CYS* 5.1 0.4 - - - -
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Residues in contact with TYR 160 (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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82H ARG* 3.3 29.9 + - - -
84H ALA* 4.1 5.2 - - + -
86H SER* 3.7 26.5 - - - +
87H TYR* 4.2 4.9 - - + -
125H GLN 5.6 0.2 + - - -
127H GLU* 3.3 42.3 - - + +
122L THR* 3.3 34.7 + - + +
156L GLY 2.7 22.7 + - - +
157L GLY 3.1 4.0 + - - +
159L GLU* 1.3 75.2 - - - +
161L MET* 1.3 78.3 + - + +
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Residues in contact with MET 161 (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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82H ARG* 3.2 33.9 - - - +
84H ALA* 4.9 4.0 - - + -
87H TYR* 4.1 12.1 - - + -
91H VAL* 4.0 22.4 - - + -
33I ALA* 4.9 9.4 - - + +
34I ASN* 3.7 17.7 - - - +
157L GLY 3.0 3.2 + - - -
158L PHE 4.2 0.2 - - - -
159L GLU 3.4 1.4 - - - -
160L TYR* 1.3 99.5 - - + +
162L GLY* 1.3 71.5 + - - +
163L CYS 3.3 2.0 - - - -
164L SER* 2.8 31.5 + - - +
165L LEU* 3.2 31.4 + - + +
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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