Contacts of the helix formed by residues 147 - 161 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K PHE* 4.2 22.4 - - + +
71K SER* 6.1 0.7 - - - +
72K LEU* 4.3 26.0 - - + -
75K GLU* 5.3 4.3 - - - +
145K ASN* 2.5 18.4 + - - +
146K THR* 1.3 85.3 - - + +
148K TRP* 1.3 64.0 + - - +
149K LYS 3.2 2.9 - - - -
150K ASP* 2.8 36.5 + - - +
151K VAL* 3.1 12.5 + - - +
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Residues in contact with TRP 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120K TYR* 4.1 11.2 - + - -
125K LYS 3.6 19.3 - - - -
126K ARG* 4.0 8.7 - - - -
127K PHE* 3.7 24.7 - + - -
140K MET* 3.4 25.8 - - - -
141K LEU 4.5 1.3 - - - -
142K THR* 3.6 18.8 - - - +
143K VAL* 3.5 48.4 - - + +
145K ASN* 3.1 21.5 + - + +
146K THR 3.4 0.8 - - - -
147K LEU* 1.3 76.9 - - - +
149K LYS* 1.3 76.0 + - + +
151K VAL* 2.9 34.0 + - + +
152K LYS* 2.9 51.5 + - + +
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Residues in contact with LYS 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143K VAL* 4.8 7.2 - - - +
146K THR 5.2 6.3 - - - +
147K LEU 3.1 1.5 + - - -
148K TRP* 1.3 89.6 - - + +
150K ASP* 1.3 65.1 + - - +
152K LYS* 3.5 35.9 + - + +
153K ALA* 3.2 22.2 + - - +
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Residues in contact with ASP 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K PHE* 3.5 25.0 - - + -
147K LEU* 2.8 36.5 + - - +
149K LYS* 1.3 72.2 - - - +
151K VAL* 1.3 60.8 + - - +
153K ALA* 3.2 5.8 + - - +
154K TYR* 2.7 53.6 + - + +
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Residues in contact with VAL 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K PHE* 4.2 0.9 - - + -
69K TRP* 4.2 21.8 - - + -
72K LEU* 3.6 30.7 - - + -
120K TYR* 5.2 2.2 - - + -
127K PHE* 4.3 10.8 - - + -
140K MET* 4.3 13.5 - - + +
145K ASN* 6.4 0.2 - - - -
147K LEU 3.1 10.7 + - - +
148K TRP* 2.9 39.8 + - + +
150K ASP* 1.3 76.0 - - - +
152K LYS* 1.3 59.7 + - - +
155K LEU* 2.8 44.5 + - + +
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Residues in contact with LYS 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G SER* 5.1 1.2 - - - +
120K TYR* 3.8 21.4 + - - +
125K LYS* 3.8 30.0 - - + +
143K VAL* 5.3 2.4 - - - +
148K TRP* 2.9 47.3 + - + +
149K LYS* 3.5 37.6 - - + +
151K VAL* 1.3 77.7 - - - +
153K ALA* 1.3 57.4 + - - +
156K GLY* 2.9 28.2 + - - +
157K GLY 3.1 3.5 + - - -
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Residues in contact with ALA 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G SER 5.8 1.3 - - - -
87G TYR* 5.5 1.0 - - - -
88G GLN* 6.3 0.9 - - - +
149K LYS 3.2 14.5 + - - +
150K ASP* 3.7 7.2 - - - +
152K LYS* 1.3 80.4 - - - +
154K TYR* 1.3 73.0 + - + +
157K GLY* 3.1 20.9 + - - +
158K PHE 4.2 0.2 + - - -
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Residues in contact with TYR 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K ASN* 5.0 4.3 + - - -
65K ASN* 3.5 38.8 + - + +
68K PHE* 3.6 42.2 - + + -
69K TRP* 3.7 18.4 - - + +
150K ASP* 2.7 39.2 + - + +
153K ALA* 1.3 82.7 - - + +
155K LEU* 1.3 61.4 + - - +
158K PHE* 3.3 21.7 + - - +
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Residues in contact with LEU 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69K TRP* 3.9 16.8 - - + -
93K LEU* 4.3 21.1 - - + -
95K THR* 3.7 32.1 - - + +
108K GLY* 4.1 12.8 - - - +
120K TYR* 4.0 21.5 - - + -
127K PHE* 3.6 32.3 - - + -
140K MET* 6.2 0.2 - - - -
151K VAL* 2.8 24.2 + - + +
154K TYR* 1.3 73.7 - - - +
156K GLY* 1.3 66.0 + - - +
158K PHE* 3.4 3.2 + - + +
159K GLU* 3.1 24.4 + - - +
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Residues in contact with GLY 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G SER* 4.1 4.3 - - - -
120K TYR* 3.4 31.0 - - - -
122K THR* 4.1 2.2 + - - -
151K VAL 3.4 1.6 + - - -
152K LYS 2.9 15.8 + - - -
155K LEU* 1.3 79.2 - - - +
157K GLY* 1.3 50.9 + - - +
159K GLU* 3.3 2.3 + - - +
160K TYR* 2.7 37.9 + - - +
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Residues in contact with GLY 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G SER 2.8 23.3 + - - -
87G TYR* 3.5 16.5 - - - -
152K LYS 3.1 10.1 + - - -
153K ALA* 3.1 14.9 + - - -
156K GLY* 1.3 76.0 - - - +
158K PHE* 1.3 61.9 + - - +
160K TYR* 3.2 1.6 + - - +
161K MET 3.1 19.4 + - - -
162K GLY 3.1 6.4 + - - -
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Residues in contact with PHE 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G TYR* 4.6 2.8 - + - -
3K LEU* 4.6 1.8 - - + -
5K TYR* 3.2 49.6 - + - -
58K HIS 4.1 9.0 - - - -
60K PRO* 4.1 22.7 - - + -
95K THR* 3.8 30.1 - - + -
96K GLY* 4.4 4.0 - - - -
153K ALA 4.2 0.6 + - - -
154K TYR 3.3 21.8 + - - +
155K LEU* 3.8 4.0 - - - +
156K GLY 3.3 0.4 - - - -
157K GLY* 1.3 73.7 - - - +
159K GLU* 1.3 62.4 + - - +
161K MET 3.6 0.5 + - - -
162K GLY* 3.3 9.5 + - - +
163K CYS* 2.7 76.0 + - + +
166K ALA* 4.8 2.7 - - + -
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Residues in contact with GLU 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K THR* 4.7 2.7 - - - +
96K GLY 5.8 0.2 - - - -
106K SER* 2.7 42.7 + - - +
107K TYR* 3.6 20.1 - - - +
108K GLY* 3.4 28.6 + - - -
120K TYR* 3.1 40.5 - - - +
122K THR* 4.2 14.3 + - - +
155K LEU* 3.1 17.5 + - - +
156K GLY* 3.7 4.0 - - - +
158K PHE* 1.3 78.5 - - - +
160K TYR* 1.3 64.8 + - - +
161K MET* 4.6 0.2 - - - -
163K CYS* 5.1 0.9 - - - -
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Residues in contact with TYR 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G ARG* 3.2 30.2 + - - -
84G ALA* 4.0 4.7 - - + -
86G SER* 3.5 27.4 - - - +
87G TYR* 4.3 1.8 - - + -
125G GLN 5.2 1.4 + - - -
127G GLU* 3.2 46.9 - - + +
122K THR* 3.4 34.5 + - + +
156K GLY 2.7 21.0 + - - +
157K GLY 3.2 4.5 + - - +
159K GLU* 1.3 76.1 - - - +
161K MET* 1.3 77.0 + - + +
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Residues in contact with MET 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G ARG* 3.0 35.9 - - - +
84G ALA* 4.9 3.6 - - + -
87G TYR* 4.2 14.8 - - + -
91G VAL* 4.2 11.9 - - - -
33H ALA* 4.7 10.3 - - + +
34H ASN* 3.5 25.4 - - - +
157K GLY 3.1 2.8 + - - -
158K PHE 3.8 0.2 - - - -
159K GLU 3.4 2.0 - - - -
160K TYR* 1.3 95.8 - - + +
162K GLY* 1.3 72.0 + - - +
163K CYS 3.2 2.7 - - - -
164K SER* 2.7 30.4 + - - +
165K LEU* 3.1 32.0 + - + +
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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
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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