Contacts of the helix formed by residues 27 - 42 (chain X) 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 THR 27 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88 TYR* 5.9 2.7 - - + -
118 ASN* 2.3 44.8 + - - +
128 GLN* 5.3 5.4 - - + +
158 TYR* 5.3 0.7 - - - -
26X LEU* 1.3 92.1 + - - +
28X THR* 1.3 63.0 + - - +
29X PHE* 3.4 26.0 - - + +
30X SER* 3.4 18.5 + - - +
31X LEU 3.0 20.8 + - - -
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Residues in contact with THR 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76U PHE* 6.3 0.4 - - - -
80U MET* 3.7 36.1 - - + -
84U PHE* 4.5 15.7 - - + -
26X LEU* 4.3 4.0 - - + +
27X THR* 1.3 73.0 - - - +
29X PHE* 1.3 60.7 + - - +
31X LEU* 3.3 11.9 + - + +
32X TYR* 2.9 48.0 + - - -
109X PHE* 4.7 12.4 - - - +
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Residues in contact with PHE 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128 GLN* 3.6 57.0 - - + +
158 TYR* 5.9 1.6 - - + -
168 GLY 5.3 0.7 - - - -
27X THR* 3.2 12.9 - - + +
28X THR* 1.3 80.2 + - - +
30X SER* 1.3 62.4 + - - +
32X TYR* 3.1 16.9 + + + +
33X THR* 3.0 40.9 + - + +
95X PHE* 5.9 2.2 - + - -
109X PHE* 5.8 4.3 - - + -
110X ALA 4.2 12.6 - - - -
111X LEU* 3.2 36.8 - - + -
114X HIS* 4.3 10.8 - + - +
117X PHE* 4.2 25.4 - + - -
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Residues in contact with SER 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118 ASN* 5.0 0.4 - - - -
158 TYR* 3.5 38.9 - - - -
26X LEU* 6.1 1.1 - - - -
27X THR* 3.4 25.2 + - - +
29X PHE* 1.3 77.9 - - - +
31X LEU* 1.3 60.8 + - - +
33X THR* 2.3 31.7 + - - -
34X ILE* 3.0 24.4 + - - +
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Residues in contact with LEU 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76U PHE* 3.5 40.4 - - + -
80U MET* 4.9 8.5 - - + -
26X LEU* 4.4 17.9 - - + -
27X THR 3.0 14.0 + - - +
28X THR* 3.4 11.9 - - + +
29X PHE 3.2 0.2 - - - -
30X SER* 1.3 77.2 - - - +
32X TYR* 1.3 57.6 + - + +
34X ILE* 3.2 15.9 + - + +
35X ILE* 2.9 51.8 + - + +
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Residues in contact with TYR 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76U PHE* 4.8 16.9 - + - -
80U MET* 5.7 3.8 - - - -
28X THR* 2.9 29.9 + - - -
29X PHE* 3.1 22.9 + + + +
31X LEU* 1.3 78.1 - - + +
33X THR* 1.3 57.6 + - + +
35X ILE* 3.2 25.0 + - + +
36X VAL* 2.9 32.4 + - - +
102X ILE* 4.8 4.9 - - + +
108X SER* 3.6 12.5 + - - -
109X PHE* 2.8 59.9 + + + +
110X ALA 4.5 1.3 - - - -
111X LEU* 3.7 32.3 - - + -
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Residues in contact with THR 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158 TYR* 4.8 18.5 + - + +
168 GLY* 5.0 4.7 - - - -
198 LEU* 3.2 35.1 - - + +
29X PHE* 3.0 30.4 + - + +
30X SER* 2.3 36.2 + - - -
32X TYR* 1.3 74.9 - - + +
34X ILE* 1.3 61.6 + - - +
36X VAL* 3.2 7.1 + - - +
37X LEU* 3.0 24.4 + - - +
95X PHE* 5.7 5.8 - - + -
117X PHE* 6.5 0.2 - - + -
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Residues in contact with ILE 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30X SER* 3.0 36.0 + - - +
31X LEU* 3.2 17.9 + - + +
33X THR* 1.3 79.6 + - - +
35X ILE* 1.3 58.7 + - + +
37X LEU* 3.3 7.8 + - + +
38X LEU* 2.9 48.3 + - + +
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Residues in contact with ILE 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U PHE* 4.3 23.6 - - + -
73U ILE* 5.6 10.5 - - + -
76U PHE* 5.0 10.3 - - + -
31X LEU* 2.9 39.5 + - + +
32X TYR* 3.2 26.4 + - + +
34X ILE* 1.3 78.4 - - + +
36X VAL* 1.3 59.0 + - - +
38X LEU* 3.7 9.0 - - + +
39X VAL* 2.9 32.0 + - + +
102X ILE* 4.4 22.4 - - + -
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Residues in contact with VAL 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198 LEU* 4.4 18.6 - - + -
238 LEU* 4.7 0.2 - - + -
32X TYR 2.9 20.1 + - - +
33X THR* 3.2 13.2 + - + +
35X ILE* 1.3 75.5 - - - +
37X LEU* 1.3 57.8 + - - +
39X VAL* 3.3 2.8 + - - +
40X ILE* 2.9 47.6 + - + +
95X PHE* 4.5 15.3 - - + -
98X ILE* 4.3 17.6 - - + +
99X ALA* 4.8 8.5 - - + -
102X ILE* 3.7 20.4 - - + -
111X LEU* 4.6 8.1 - - + -
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Residues in contact with LEU 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198 LEU* 4.4 9.2 - - + -
228 THR* 4.2 16.6 - - + -
238 LEU* 3.7 26.7 - - + -
268 LEU* 3.8 20.6 - - + -
33X THR 3.0 15.2 + - - +
34X ILE* 3.8 7.9 - - + +
36X VAL* 1.3 78.3 - - - +
38X LEU* 1.3 59.7 + - + +
40X ILE* 3.4 8.4 + - + +
41X THR* 2.9 35.7 + - - +
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Residues in contact with LEU 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U PHE* 6.5 0.9 - - + -
34X ILE* 2.9 39.4 + - + +
35X ILE* 3.7 9.4 - - + +
37X LEU* 1.3 77.0 - - + +
39X VAL* 1.3 61.2 + - + +
41X THR* 3.4 12.1 + - + +
42X SER* 2.8 26.3 + - - -
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Residues in contact with VAL 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U PHE* 3.6 38.1 - - + -
35X ILE* 2.9 25.0 + - + +
36X VAL 3.9 3.4 - - - +
38X LEU* 1.3 75.7 - - + +
40X ILE* 1.3 59.8 + - - +
42X SER* 2.8 27.6 + - - +
43X LEU* 2.9 27.6 + - + +
98X ILE* 4.5 24.7 - - + -
102X ILE* 5.5 3.6 - - + -
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Residues in contact with ILE 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238 LEU* 3.7 29.6 - - + -
268 LEU* 4.1 15.9 - - + -
278 PHE* 3.6 35.2 - - + -
318 PHE* 4.4 6.2 - - + -
36X VAL* 2.9 37.9 + - + +
37X LEU* 3.6 8.3 - - + +
39X VAL* 1.3 73.0 - - - +
41X THR* 1.3 65.1 + - - +
43X LEU* 3.3 17.5 + - + -
44X TYR* 3.4 17.5 - - + -
94X MET* 5.5 5.6 - - + +
95X PHE 5.6 0.9 - - - +
98X ILE* 4.6 18.6 - - + -
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Residues in contact with THR 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268 LEU* 6.1 0.9 - - - +
318 PHE* 4.9 9.1 - - + -
37X LEU* 2.9 20.2 + - - +
38X LEU* 3.5 17.4 - - + +
40X ILE* 1.3 77.5 - - - +
42X SER* 1.3 57.5 + - - +
43X LEU 3.2 4.4 + - - -
45X THR* 3.3 43.9 + - + +
46X LEU* 4.2 4.3 + - + +
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Residues in contact with SER 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56U PHE* 5.2 2.8 - - - -
38X LEU 2.8 13.9 + - - -
39X VAL* 2.8 27.0 + - - +
41X THR* 1.3 70.2 - - - +
43X LEU* 1.3 61.3 + - - +
46X LEU* 3.3 43.0 - - - +
47X THR* 4.0 1.7 + - - -
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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
------------------------------------------------------------
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