Contacts of the helix formed by residues 143 - 162 (chain G) in PDB entry 4D1Q
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 143 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G PRO* 1.3 76.6 - - - +
144G PRO* 1.3 66.3 - - - +
145G ILE* 3.6 14.5 - - - +
146G THR* 2.7 34.5 + - - -
147G LEU* 3.1 11.3 + - - +
112H VAL* 4.2 1.1 - - - -
6L G 3.1 42.2 + - - -
7L T 4.8 7.2 - - - -
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Residues in contact with PRO 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G SER* 1.3 87.0 - - - +
145G ILE* 1.3 56.2 + - - +
147G LEU* 3.5 2.9 + - + +
148G SER* 3.0 23.6 + - - -
109H PHE* 3.3 40.8 - - + +
110H SER* 3.5 16.4 - - - +
112H VAL* 3.2 24.2 - - + -
113H SER* 3.5 22.0 - - - +
6K A 4.8 1.1 - - - +
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Residues in contact with ILE 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G SER* 3.0 14.2 - - - +
144G PRO* 1.3 77.9 - - - +
146G THR* 1.3 64.1 + - - +
148G SER* 3.8 9.2 - - - -
149G ARG* 3.0 65.4 + - + +
7K C 4.2 26.0 - - + +
8K A 3.6 38.1 - - - +
9K A 4.2 4.3 - - - +
6L G 4.2 4.0 - - - +
7L T 4.1 17.5 - - + +
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Residues in contact with THR 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G PRO* 3.7 22.0 - - + -
143G SER* 2.7 15.1 + - - -
145G ILE* 1.3 76.6 - - - +
147G LEU* 1.3 54.1 - - + +
149G ARG* 2.8 37.4 + - - +
150G LYS* 2.8 18.0 + - + +
95H ILE* 4.1 26.7 - - + -
5L T 3.7 18.6 + - - +
6L G 2.7 22.9 + - - +
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Residues in contact with LEU 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G PRO* 3.4 32.1 - - + -
143G SER 3.1 12.5 + - - +
144G PRO* 3.6 11.0 - - + +
146G THR* 1.3 78.7 - - + +
148G SER* 1.3 56.2 + - - +
150G LYS* 3.1 6.9 + - - +
151G VAL* 2.9 32.2 + - - +
95H ILE* 4.1 16.8 - - + +
98H CYS* 3.9 17.0 - - + -
99H ALA* 3.9 10.1 - - + +
101H TRP* 5.6 0.4 - - + -
102H VAL* 3.6 29.4 - - + -
109H PHE* 3.8 13.0 - - + +
112H VAL* 4.3 18.2 - - + -
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Residues in contact with SER 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G PRO 3.0 14.8 + - - -
145G ILE* 4.0 10.5 - - - -
147G LEU* 1.3 79.9 - - - +
149G ARG* 1.3 59.9 + - - +
151G VAL* 3.7 2.5 + - - +
152G THR* 3.1 25.6 + - - +
593G THR* 3.8 7.8 + - - +
109H PHE* 3.1 32.1 - - - -
6K A 5.6 1.1 - - - -
7K C 2.9 26.3 + - - -
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Residues in contact with ARG 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G ILE* 3.0 54.6 + - + +
146G THR* 2.8 19.9 + - - +
148G SER* 1.3 77.2 - - - +
150G LYS* 1.3 59.9 + - - -
152G THR* 2.9 18.2 + - - +
153G SER* 3.2 15.1 + - - -
9K A 4.6 3.6 + - - +
5L T 3.5 31.5 + - - +
6L G 3.3 36.8 + - - -
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Residues in contact with LYS 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G THR* 2.8 11.8 + - + +
147G LEU* 3.1 6.3 + - - +
149G ARG* 1.3 74.2 - - - +
151G VAL* 1.3 58.4 + - - +
152G THR 3.0 0.2 + - - -
153G SER* 3.0 15.4 + - - -
154G ASP* 2.7 67.0 + - - +
157G GLU* 5.3 2.6 + - - -
92H LYS* 5.3 4.0 - - - -
95H ILE* 3.3 35.0 - - + -
96H GLU* 3.8 28.2 + - + +
99H ALA* 3.7 24.2 - - + -
100H GLN* 6.3 0.2 - - + -
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Residues in contact with VAL 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G LEU 2.9 18.6 + - - +
148G SER 4.1 4.9 - - - +
149G ARG 3.4 0.2 - - - -
150G LYS* 1.3 77.9 - - + +
152G THR* 1.3 58.4 + - - +
154G ASP* 4.0 4.9 - - + -
155G ALA 3.4 10.7 + - - -
593G THR* 4.8 2.9 - - + +
596G SER* 3.0 26.5 - - - -
597G LEU* 3.4 29.8 - - + +
600G LEU* 3.8 6.8 - - + +
99H ALA* 4.0 17.7 - - + +
102H VAL* 5.1 0.7 - - + -
103H VAL* 3.5 27.6 - - + -
109H PHE* 4.3 14.4 - - + -
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Residues in contact with THR 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G SER 3.1 10.5 + - - +
149G ARG* 2.9 20.6 + - - +
151G VAL* 1.3 75.5 - - - +
153G SER* 1.3 62.6 + - - +
154G ASP 3.3 0.7 - - - -
155G ALA* 3.4 4.0 + - - +
156G LYS* 3.4 26.7 + - - +
592G GLN* 4.3 13.9 - - + +
593G THR* 3.7 32.8 - - + +
596G SER* 3.6 16.8 + - - +
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Residues in contact with SER 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G ARG 3.2 12.5 + - - -
150G LYS* 3.0 28.4 + - - -
152G THR* 1.3 77.1 + - - +
154G ASP* 1.3 60.2 + - - +
156G LYS* 3.8 10.8 + - - +
157G GLU* 3.3 33.7 + - - +
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Residues in contact with ASP 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G LYS* 2.7 54.1 + - - +
151G VAL* 4.2 4.5 - - - +
153G SER* 1.3 72.0 + - - +
155G ALA* 1.3 69.8 + - - +
157G GLU* 3.7 12.9 - - - +
158G LYS* 2.8 41.2 + - - +
600G LEU* 3.7 15.7 - - + +
604G TYR* 3.6 19.6 + - - -
96H GLU* 5.3 5.3 - - - +
100H GLN* 5.6 1.6 + - - +
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Residues in contact with ALA 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G VAL 3.4 3.4 + - - -
152G THR 3.5 6.3 - - - +
153G SER 3.4 0.2 - - - -
154G ASP* 1.3 79.3 - - - +
156G LYS* 1.3 56.0 + - - +
159G LYS* 2.7 57.2 + - + +
596G SER* 3.2 32.1 - - - +
599G PHE* 4.4 1.3 - - + -
600G LEU* 3.2 22.8 - - + +
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Residues in contact with LYS 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G THR* 3.4 13.7 + - - +
153G SER* 3.9 12.1 - - - +
154G ASP 3.3 0.6 - - - -
155G ALA* 1.3 78.6 - - - +
157G GLU* 1.3 62.0 + - + +
159G LYS* 4.4 9.1 - - - +
160G ALA* 3.3 23.7 + - - +
592G GLN* 5.3 6.3 + - - -
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Residues in contact with GLU 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G LYS* 5.3 1.9 + - - -
153G SER* 3.3 24.3 + - - +
154G ASP* 3.2 18.8 + - - +
156G LYS* 1.3 80.6 - - + +
158G LYS* 1.3 69.1 + - + +
160G ALA* 3.8 3.6 - - - +
161G LEU* 2.9 27.0 + - - +
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Residues in contact with LYS 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ASP* 2.8 33.5 + - - +
157G GLU* 1.3 77.8 - - - +
159G LYS* 1.3 65.5 + - - +
160G ALA 3.1 2.0 - - - -
161G LEU* 3.6 20.9 - - + +
162G ILE* 3.0 26.5 + - - +
599G PHE* 3.9 10.8 - - + -
600G LEU* 4.2 12.1 - - + -
603G PHE* 3.4 49.4 - - + -
604G TYR* 4.3 15.4 + - - -
100H GLN* 6.1 0.6 - - - +
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Residues in contact with LYS 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ALA* 2.7 47.9 + - - +
156G LYS* 4.4 8.3 - - - +
158G LYS* 1.3 71.9 - - - +
160G ALA* 1.3 61.5 + - - +
162G ILE* 3.8 1.7 + - - +
163G GLY* 3.5 11.1 + - - -
209G LEU 4.4 2.2 - - - +
234G GLN* 3.0 52.2 - - + +
235G PHE* 3.3 40.8 - - + -
595G ASP* 3.2 20.5 + - - +
596G SER* 5.1 0.6 + - - -
599G PHE* 3.2 39.5 - - + -
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Residues in contact with ALA 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G LYS 3.3 18.3 + - - +
157G GLU* 3.8 3.8 - - - +
158G LYS 3.1 0.4 - - - -
159G LYS* 1.3 77.0 - - - +
161G LEU* 1.3 60.8 + - - +
162G ILE 3.2 0.2 - - - -
163G GLY* 2.8 22.2 + - - +
164G ARG 4.5 0.7 + - - -
234G GLN 5.0 6.7 - - - +
236G ASN* 6.4 0.2 - - - +
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Residues in contact with LEU 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G GLU 2.9 17.6 + - - +
158G LYS* 3.6 27.8 - - + +
160G ALA* 1.3 77.4 - - - +
162G ILE* 1.3 77.7 + - + +
163G GLY 3.5 0.3 + - - -
164G ARG* 4.4 9.0 + - - +
603G PHE* 4.7 8.1 - - + -
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Residues in contact with ILE 162 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G LYS 3.0 17.2 + - - +
159G LYS* 4.1 8.1 - - - +
161G LEU* 1.3 94.6 - - + +
163G GLY* 1.3 67.9 + - - +
164G ARG 3.1 3.3 + - - -
165G GLU* 3.3 13.8 + - + +
166G ILE* 3.1 48.4 + - + +
207G LEU* 3.9 10.3 - - + -
235G PHE* 5.0 1.6 - - + -
599G PHE* 4.7 12.1 - - + -
603G PHE* 4.1 5.2 - - + -
607G PHE* 3.0 56.8 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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