Contacts of the helix formed by residues 8 - 30 (chain 8) in PDB entry 6CP3
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 TYR 8 (chain 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78 PHE* 1.3 97.1 - + + +
98 PHE* 1.3 66.9 + - - +
108 MET* 3.3 2.5 - - - +
118 ASN* 3.6 33.4 - - + +
128 GLN* 3.2 38.3 + - + +
27X THR* 5.9 1.8 - - + -
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Residues in contact with PHE 9 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78 PHE 3.3 17.6 + - - +
88 TYR* 1.3 79.8 - - - +
108 MET* 1.3 61.5 + - + +
128 GLN* 4.3 8.7 - - - +
138 LEU* 2.9 36.5 + - - +
27J MET* 4.5 22.7 - - + -
31J ALA* 5.5 9.2 - - + -
34J SER* 6.0 2.5 - - - -
114X HIS* 6.3 1.6 - - - -
116X VAL* 3.6 48.8 - - + +
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Residues in contact with MET 10 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78 PHE 4.6 5.0 + - - +
88 TYR 3.3 0.8 - - - -
98 PHE* 1.3 78.4 - - - +
118 ASN* 1.3 54.7 + - - +
138 LEU* 4.5 2.2 - - - -
148 THR* 2.7 37.8 + - - +
24J TYR* 4.0 31.6 - - + +
27J MET* 3.4 48.7 - - + +
28J SER* 3.5 13.9 - - - +
31J ALA* 4.3 14.4 - - + -
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Residues in contact with ASN 11 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 TYR* 3.5 41.8 + - + +
98 PHE 3.3 0.6 - - - -
108 MET* 1.3 78.5 - - - +
128 GLN* 1.3 64.3 + - + +
148 THR* 5.0 0.2 - - - -
158 TYR* 3.1 58.8 + - - +
27X THR* 2.3 42.7 + - - +
30X SER* 5.0 0.2 - - - -
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Residues in contact with GLN 12 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 TYR* 3.2 27.7 + - + +
98 PHE* 4.3 9.7 - - - +
118 ASN* 1.3 75.3 - - + +
138 LEU* 1.3 58.1 + - - +
158 TYR* 4.2 0.6 - - - -
168 GLY* 2.9 27.5 + - - -
27X THR* 5.3 4.1 - - + +
29X PHE* 3.6 39.7 - - + +
109X PHE* 5.6 0.8 - - - -
114X HIS* 3.2 56.5 + - - +
116X VAL* 5.7 1.4 - - - +
117X PHE* 3.6 17.1 + - + +
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Residues in contact with LEU 13 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 PHE* 2.9 20.5 + - + +
108 MET* 4.1 2.9 - - - +
128 GLN* 1.3 78.1 - - - +
148 THR* 1.3 58.8 + - - +
168 GLY 3.8 0.5 - - - -
178 PHE* 2.9 61.3 + - + -
23J VAL* 4.9 2.2 - - + -
24J TYR* 3.6 32.3 - - + -
27J MET* 3.8 38.4 - - + -
116X VAL* 5.8 2.7 - - + -
117X PHE* 3.9 13.6 - - + -
120X SER* 3.4 25.8 - - - +
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Residues in contact with THR 14 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108 MET* 2.7 27.1 + - - +
118 ASN* 4.1 1.3 - - - -
138 LEU* 1.3 77.5 - - - +
158 TYR* 1.3 68.7 + - + +
178 PHE* 3.3 6.2 + - + +
188 LEU* 3.0 47.8 + - + +
24J TYR* 3.5 31.2 + - + +
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Residues in contact with TYR 15 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118 ASN* 3.1 49.7 + - - +
128 GLN* 4.4 1.8 - - - +
148 THR* 1.3 82.3 - - + +
168 GLY* 1.3 58.0 + - - +
188 LEU* 3.5 19.8 + - + +
198 LEU* 3.0 28.2 + - - +
27X THR* 5.3 0.4 - - - -
29X PHE* 5.9 1.1 - - + -
30X SER* 3.5 35.0 - - - +
33X THR* 4.8 9.4 - - + +
34X ILE* 6.4 0.2 - - + -
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Residues in contact with GLY 16 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128 GLN 2.9 19.4 + - - -
158 TYR* 1.3 77.7 - - - +
178 PHE* 1.3 58.4 + - - +
198 LEU* 3.2 9.5 + - - +
208 MET* 2.8 32.8 + - - +
29X PHE* 5.4 0.7 - - - -
33X THR* 5.0 8.2 - - - +
95X PHE* 6.2 0.7 - - - -
117X PHE* 3.6 20.7 - - - -
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Residues in contact with PHE 17 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 LEU* 2.9 47.1 + - + +
148 THR* 3.8 5.6 - - + +
168 GLY* 1.3 74.0 - - - +
188 LEU* 1.3 62.7 + - + +
208 MET* 3.1 13.8 + - + +
218 ILE* 3.0 40.0 + - + +
20J GLY* 3.8 26.2 - - - -
23J VAL* 4.6 0.9 - - + -
24J TYR* 4.7 9.2 - + + -
117X PHE* 4.9 9.0 - + - -
120X SER* 3.9 17.0 - - - -
121X LEU* 4.9 15.0 - - + -
124X VAL* 3.6 33.2 - - + -
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Residues in contact with LEU 18 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148 THR* 3.0 36.7 + - + +
158 TYR* 3.7 22.4 - - + +
168 GLY 3.3 0.2 - - - -
178 PHE* 1.3 77.3 - - + +
198 LEU* 1.3 58.2 + - - +
218 ILE* 3.5 14.5 + - + +
228 THR* 2.9 32.9 + - - +
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Residues in contact with LEU 19 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158 TYR 3.0 17.5 + - - +
168 GLY* 3.7 7.9 - - - +
188 LEU* 1.3 76.4 - - - +
208 MET* 1.3 59.0 + - - +
228 THR* 4.0 7.4 - - - -
238 LEU* 2.8 52.9 + - + +
33X THR* 3.2 44.6 - - + +
36X VAL* 4.4 7.4 - - + -
37X LEU* 4.4 17.7 - - + -
95X PHE* 3.9 26.7 - - + -
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Residues in contact with MET 20 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168 GLY 2.8 22.2 + - - +
178 PHE* 3.1 21.7 + - + +
198 LEU* 1.3 78.8 - - + +
218 ILE* 1.3 60.0 + - + +
238 LEU* 3.3 5.6 + - - +
248 LEU* 2.9 31.3 + - - +
91X THR* 5.0 7.5 + - - +
92X LEU* 4.7 15.3 - - + -
95X PHE* 3.5 49.8 - - + -
117X PHE* 4.9 5.4 - - + -
121X LEU* 3.7 31.9 - - + -
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Residues in contact with ILE 21 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178 PHE* 3.0 22.9 + - + +
188 LEU* 3.9 16.4 - - + +
208 MET* 1.3 76.6 - - + +
228 THR* 1.3 63.0 + - - +
248 LEU* 3.9 4.8 - - + +
258 ILE* 3.1 46.5 + - + +
17J PHE* 3.6 39.9 - - + -
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Residues in contact with THR 22 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188 LEU* 2.9 21.8 + - - +
198 LEU* 3.6 9.0 - - + +
218 ILE* 1.3 76.4 - - - +
238 LEU* 1.3 52.0 + - - +
258 ILE* 4.1 2.0 - - - +
268 LEU* 2.6 59.0 + - + +
37X LEU* 4.2 23.3 - - + -
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Residues in contact with LEU 23 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198 LEU* 2.8 47.0 + - + +
208 MET* 3.3 6.9 + - - +
228 THR* 1.3 70.6 - - - +
248 LEU* 1.3 61.9 + - - +
268 LEU* 3.7 13.2 - - + -
278 PHE* 2.9 47.5 + - + +
36X VAL* 4.7 0.2 - - + -
37X LEU* 3.7 18.6 - - + -
40X ILE* 3.7 32.8 - - + -
91X THR* 3.4 16.3 + - - +
95X PHE* 4.4 22.2 - - + +
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Residues in contact with LEU 24 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208 MET 2.9 17.9 + - - +
218 ILE* 3.9 5.2 - - + +
238 LEU* 1.3 77.1 - - - +
258 ILE* 1.3 70.7 + - + +
278 PHE* 4.3 0.5 - - - +
288 SER* 3.0 27.0 + - - -
9J ILE* 3.8 22.7 - - + +
13J TYR* 3.6 47.8 - - + -
16J PHE* 6.2 3.1 - - + -
87X PRO* 5.8 1.2 - - + +
88X MET* 4.7 11.0 - - + -
91X THR* 3.8 24.5 + - + -
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Residues in contact with ILE 25 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218 ILE* 3.1 35.8 + - + +
228 THR* 4.4 2.0 - - - +
248 LEU* 1.3 82.6 - - + +
268 LEU* 1.3 57.4 + - - +
298 GLN* 2.9 56.8 + - + +
4J ARG* 5.7 1.1 - - - +
9J ILE* 3.8 39.3 - - + -
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Residues in contact with LEU 26 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228 THR* 2.6 29.8 + - + +
238 LEU* 3.7 12.8 - - + -
258 ILE* 1.3 74.8 - - - +
278 PHE* 1.3 90.1 + - + +
298 GLN* 5.2 0.9 - - - -
308 PHE* 2.9 44.2 + - + +
318 PHE* 3.5 27.5 - - + -
37X LEU* 3.8 24.0 - - + -
40X ILE* 4.1 5.8 - - + -
41X THR* 6.1 0.9 - - - +
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Residues in contact with PHE 27 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238 LEU* 2.9 52.2 + - + +
248 LEU 4.3 1.1 - - - +
268 LEU* 1.3 78.1 - - + +
288 SER* 1.3 60.1 + - - +
318 PHE* 2.9 40.2 + + + -
328 LEU* 3.1 24.1 + - + +
40X ILE* 3.6 32.1 - - + -
44X TYR* 3.6 24.0 - + - -
87X PRO 5.8 0.4 - - - +
90X PHE* 3.5 33.0 - + + -
91X THR* 3.9 17.7 - - - -
94X MET* 4.5 17.5 - - + -
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Residues in contact with SER 28 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1587 TRP* 5.1 4.5 - - - -
248 LEU* 3.0 21.6 + - - -
258 ILE 3.9 0.4 - - - -
278 PHE* 1.3 78.7 - - - +
298 GLN* 1.3 62.5 + - - +
328 LEU* 4.7 6.9 - - - +
338 PRO* 3.3 12.6 - - - +
7J THR* 2.4 44.1 + - - +
8J PRO 4.9 1.6 + - - -
9J ILE* 3.5 19.3 - - - +
13J TYR* 5.9 0.2 - - - -
87X PRO* 4.6 23.3 - - - +
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Residues in contact with GLN 29 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 ILE* 2.9 38.3 + - + +
268 LEU* 4.4 1.1 - - - +
288 SER* 1.3 76.8 - - - +
308 PHE* 1.3 72.7 + - + +
338 PRO* 3.9 8.1 - - - +
3J LYS 4.0 1.9 - - - +
4J ARG* 2.7 48.3 + - + +
5J PHE* 3.3 41.9 + - - +
6J PRO* 4.9 3.8 - - - +
7J THR* 3.6 18.1 + - - +
9J ILE* 5.0 5.2 - - + +
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Residues in contact with PHE 30 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268 LEU* 2.9 21.7 + - + +
288 SER 3.4 0.2 - - - -
298 GLN* 1.3 92.6 - - + +
318 PHE* 1.3 81.6 + + + +
328 LEU 3.5 1.3 - - - -
338 PRO* 3.4 4.0 - - - +
348 MET* 3.1 32.9 + - - +
1J MET* 4.5 20.4 - - + -
2J LEU* 3.7 34.2 - - + +
3J LYS 4.2 6.3 - - - +
4J ARG* 3.6 42.2 - - + -
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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) + - + + + + + -
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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