Contacts of the helix formed by residues 31 - 51 (chain R) in PDB entry 6XOX
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 31 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R VAL 1.3 68.1 - - - -
32R LEU* 1.3 57.5 + - - +
33R TRP 3.3 5.0 + - - -
34R GLU* 2.2 46.6 + - - +
35R THR* 2.5 35.4 + - - -
90R PRO* 5.7 1.8 - - - -
136R SER* 3.6 11.0 - - - -
137R PRO* 3.7 17.0 - - - +
138R GLU 5.8 0.2 - - - -
205R TYR* 3.6 7.6 + - - -
501R V6G 3.3 24.4 - - - +
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Residues in contact with LEU 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R SER* 1.3 76.6 - - - +
33R TRP* 1.3 60.1 + - - +
35R THR* 3.4 12.1 - - + -
36R VAL* 2.9 35.6 + - + +
90R PRO* 5.6 8.3 - - + -
136R SER* 4.8 10.8 - - - +
138R GLU* 6.4 1.6 - - + -
205R TYR* 3.5 31.7 + - + +
208R ALA* 4.6 18.8 - - + +
209R ALA* 5.1 8.5 - - + -
214R TRP* 5.0 14.6 - - + +
217R LEU* 5.7 3.6 - - + -
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Residues in contact with TRP 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R SER* 3.3 6.6 + - - +
32R LEU* 1.3 78.9 - - - +
34R GLU* 1.3 69.3 + - + +
36R VAL* 3.2 9.8 - - - +
37R GLN* 3.1 28.7 + - + +
201R LEU* 4.8 12.6 - - + -
204R MET* 4.4 14.4 - - + -
205R TYR* 3.5 20.9 + + - +
217R LEU* 5.4 6.7 - - + -
220R TYR* 4.5 0.2 - + - -
221R GLN* 3.1 46.2 - - + -
226R CYS* 4.1 9.0 - - - -
295R GLY 4.0 9.3 + - - -
296R CYS* 4.3 4.9 - - + -
298R THR* 3.5 18.9 + - - -
299R ARG* 6.4 1.5 - - - +
501R V6G 3.6 76.1 - + + -
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Residues in contact with GLU 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R THR 4.4 1.6 - - - +
30R VAL* 3.1 20.8 - - + -
31R SER* 2.2 55.9 + - - +
33R TRP* 1.3 78.6 - - + +
35R THR* 1.3 59.2 + - - +
37R GLN* 3.3 13.9 - - + +
38R LYS* 2.9 41.1 + - - +
137R PRO* 5.1 0.5 - - - +
299R ARG* 5.9 8.1 - - - +
501R V6G 3.9 18.8 - - - +
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Residues in contact with THR 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R VAL* 4.0 8.7 - - - +
31R SER 2.5 26.2 + - - -
32R LEU* 3.4 13.9 - - + +
33R TRP 3.2 1.0 - - - -
34R GLU* 1.3 77.0 - - - +
36R VAL* 1.3 58.4 + - + +
38R LYS* 3.1 8.7 + - - +
39R TRP* 2.8 24.6 + - - +
88R TYR* 3.3 23.2 + - + +
90R PRO* 3.8 26.8 - - + +
214R TRP* 4.1 24.0 - - + -
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Residues in contact with VAL 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R LEU* 2.9 22.1 + - + +
33R TRP* 3.2 15.9 - - - +
35R THR* 1.3 72.9 - - - +
37R GLN* 1.3 61.6 + - - +
39R TRP* 3.6 9.3 - - + +
40R ARG* 3.0 27.4 + - - +
214R TRP* 3.6 47.8 - - + +
217R LEU* 4.3 22.9 - - + -
218R LEU* 4.4 8.7 - - + +
221R GLN* 3.7 24.0 - - - +
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Residues in contact with GLN 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R TRP* 3.1 23.5 + - + +
34R GLU* 3.3 16.8 - - + +
35R THR 3.2 0.2 - - - -
36R VAL* 1.3 77.8 - - - +
38R LYS* 1.3 57.6 + - + +
40R ARG* 3.2 27.5 + - - +
41R GLU* 3.0 26.2 + - - +
221R GLN* 3.1 34.9 + - - +
294R GLU* 3.9 5.7 + - - +
295R GLY* 3.3 36.2 - - - +
299R ARG* 4.5 20.0 - - - +
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Residues in contact with LYS 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R VAL* 4.7 15.0 - - + +
34R GLU* 2.9 28.5 + - + +
35R THR* 3.5 9.4 - - - +
37R GLN* 1.3 76.6 - - + +
39R TRP* 1.3 57.2 + - - +
41R GLU* 3.7 7.9 - - - +
42R TYR* 2.8 30.1 + - - +
87R TRP* 3.7 42.5 + - + +
88R TYR* 3.8 15.9 - - + +
89R LEU 5.6 1.1 - - - +
299R ARG* 6.2 2.5 - - - +
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Residues in contact with TRP 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35R THR 2.8 15.2 + - - +
36R VAL* 3.6 6.3 - - + +
37R GLN 3.2 0.4 - - - -
38R LYS* 1.3 75.8 - - - +
40R ARG* 1.3 58.5 + - - +
42R TYR* 3.5 7.8 - + - +
43R ARG* 2.9 47.3 + - + +
66R PHE* 5.2 1.8 - - - -
68R GLU* 2.8 62.5 + - + +
88R TYR* 3.4 37.4 - + + +
212R HIS* 4.7 4.5 - + - -
213R GLN* 3.6 26.7 - - - -
214R TRP* 3.6 36.3 - + + -
215R ASP* 5.5 3.1 - - - -
218R LEU* 3.7 24.0 - - + -
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Residues in contact with ARG 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R VAL 3.0 13.1 + - - +
37R GLN* 3.2 33.4 + - - +
39R TRP* 1.3 77.8 - - - +
41R GLU* 1.3 57.3 + - - +
43R ARG* 3.3 9.6 + - - +
44R ARG* 3.0 75.8 + - - +
218R LEU* 2.4 69.7 + - + +
221R GLN* 4.2 9.8 + - - +
222R ASP* 3.6 21.0 + - - +
294R GLU* 5.1 8.2 - - - +
295R GLY 4.9 6.5 - - - +
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Residues in contact with GLU 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R GLN 3.0 15.6 + - - +
38R LYS* 3.7 8.7 - - - +
39R TRP 3.4 0.2 - - - -
40R ARG* 1.3 77.3 - - - +
42R TYR* 1.3 57.3 + - - +
44R ARG* 3.4 10.9 + - - +
45R GLN* 2.8 64.2 + - - +
87R TRP* 4.2 17.7 - - + -
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Residues in contact with TYR 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R LYS 2.8 18.7 + - - +
39R TRP* 3.5 12.8 - + - +
41R GLU* 1.3 73.2 - - - +
43R ARG* 1.3 60.3 + - - +
45R GLN* 4.4 2.1 - - - +
46R CYS* 2.9 34.2 + - + +
66R PHE* 3.6 28.5 - + - -
69R TYR 4.7 0.7 - - - -
70R ALA* 4.6 3.4 - - - -
71R CYS* 3.1 38.9 + - - +
86R PRO* 3.3 37.6 - - + +
87R TRP* 3.7 33.8 - + + +
88R TYR* 4.1 24.7 - + + -
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Residues in contact with ARG 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R TRP* 2.9 41.0 + - + +
40R ARG* 3.3 14.8 + - - +
42R TYR* 1.3 76.4 - - - +
44R ARG* 1.3 70.1 + - + +
46R CYS* 4.1 0.3 - - - +
47R GLN* 2.8 40.5 + - + +
66R PHE* 3.6 28.8 - - + -
68R GLU* 3.3 22.4 - - - +
218R LEU* 3.4 47.0 - - - +
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Residues in contact with ARG 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R ARG* 3.0 61.0 + - - +
41R GLU* 3.9 12.6 + - - +
43R ARG* 1.3 89.3 - - + +
45R GLN* 1.3 60.7 + - + +
47R GLN* 3.4 4.9 + - - +
48R ARG* 2.9 30.0 + - - +
218R LEU* 5.2 2.4 - - - +
222R ASP* 5.1 7.9 + - - -
294R GLU* 6.2 2.4 - - - +
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Residues in contact with GLN 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R GLU* 2.8 48.5 + - - +
42R TYR* 4.4 1.8 - - - +
44R ARG* 1.3 74.1 - - + +
46R CYS* 1.3 62.5 + - - +
48R ARG* 3.4 6.2 + - - +
49R SER* 2.9 28.9 + - - -
87R TRP* 4.7 13.0 + - - -
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Residues in contact with CYS 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R TYR* 2.9 20.4 + - + +
43R ARG 4.1 0.2 - - - +
45R GLN* 1.3 76.9 - - - +
47R GLN* 1.3 56.4 + - - +
49R SER* 2.7 20.9 + - - -
50R LEU* 2.9 33.3 + - - +
66R PHE* 3.6 21.1 - - + -
71R CYS* 2.0 51.6 - - - -
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Residues in contact with GLN 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R ARG* 2.8 27.8 + - + +
44R ARG* 3.7 5.4 - - - +
46R CYS* 1.3 77.5 - - - +
48R ARG* 1.3 57.9 + - - +
49R SER 3.1 0.2 - - - -
50R LEU* 4.9 5.4 - - - +
51R THR* 2.9 42.9 + - + +
66R PHE* 5.4 14.4 - - + +
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Residues in contact with ARG 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R ARG 2.9 18.5 + - - +
45R GLN* 3.6 5.8 - - - +
47R GLN* 1.3 76.2 - - - +
49R SER* 1.3 56.5 + - - +
51R THR* 3.9 8.3 - - - -
52R GLU* 2.8 21.0 - - - +
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Residues in contact with SER 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R GLN 2.9 14.8 + - - -
46R CYS* 2.7 26.4 + - - -
48R ARG* 1.3 77.0 - - - +
50R LEU* 1.3 65.9 + - - +
51R THR 3.2 2.0 - - - -
52R GLU* 3.2 26.2 + - - +
53R ASP* 3.8 1.6 + - - +
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Residues in contact with LEU 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R CYS* 2.9 42.9 + - - +
47R GLN* 4.3 7.6 - - - +
49R SER* 1.3 75.0 + - - +
51R THR* 1.3 56.6 + - - +
52R GLU 3.2 5.6 - - - -
53R ASP* 3.0 40.5 - - + +
64R ARG* 4.6 13.8 - - + +
65R THR 4.9 0.7 - - - +
66R PHE* 4.7 13.9 - - + -
71R CYS* 5.7 0.7 - - + -
72R TRP 3.3 34.5 - - - +
73R PRO* 4.2 11.4 - - + -
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Residues in contact with THR 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R GLN* 2.9 29.8 + - + +
48R ARG* 3.9 9.6 - - - -
50R LEU* 1.3 76.9 - - - +
52R GLU* 1.3 83.9 + - - +
53R ASP* 3.7 2.0 - - - -
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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
------------------------------------------------------------
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