Contacts of the helix formed by residues 49 - 66 (chain D) in PDB entry 3J9X
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 VAL 49 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198 A 3.9 28.0 - - + +
10C TYR* 3.8 10.1 - - + -
13C ARG* 3.7 26.6 + - - +
45D PHE* 3.0 64.7 + - + +
48D ASN* 1.3 70.6 - - - +
50D PRO* 1.4 60.6 - - + +
51D LYS 3.0 4.5 - - - -
52D PHE* 2.8 30.5 + - - +
53D THR 3.2 6.4 + - - -
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Residues in contact with PRO 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 3.5 38.3 - - + -
46D GLN 3.1 25.1 - - - +
47D THR 3.7 6.3 - - - +
48D ASN 3.4 2.2 - - - -
49D VAL* 1.4 96.2 - - + +
51D LYS* 1.3 65.5 + - + +
53D THR* 3.7 5.1 - - - +
54D SER* 3.1 24.3 + - - -
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Residues in contact with LYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR* 3.4 28.1 + - - +
48D ASN* 3.0 33.9 + - - +
49D VAL 2.9 0.2 + - - -
50D PRO* 1.3 80.8 - - + +
52D PHE* 1.3 62.3 + - + +
54D SER* 2.9 20.0 + - - -
55D VAL* 3.4 12.5 - - - +
84D ALA* 5.7 0.6 - - - +
88D ASN* 3.8 29.3 + - - +
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Residues in contact with PHE 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188 T 3.6 24.0 - - + +
198 A 3.5 29.6 - - - +
13C ARG* 4.6 6.3 - - - +
48D ASN* 3.1 29.2 - - + -
49D VAL* 2.8 7.1 + - + +
51D LYS* 1.3 76.3 - - + +
53D THR* 1.3 66.8 + - - +
54D SER 3.2 0.4 - - - -
55D VAL* 3.1 8.0 + - - +
56D ASN* 3.0 26.5 + - - -
81D LEU* 3.5 46.4 - - + +
84D ALA* 3.6 12.8 - - + -
85D ARG* 3.5 14.4 - - - -
88D ASN* 3.4 28.7 - - - -
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Residues in contact with THR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG 4.8 2.9 - - - +
9C SER* 4.3 5.2 - - - -
10C TYR* 3.5 42.7 - - + +
13C ARG* 2.8 36.5 + - - +
49D VAL 3.2 7.8 + - - -
50D PRO* 3.3 7.6 + - - -
52D PHE* 1.3 77.9 - - - +
54D SER* 1.3 62.2 + - - +
56D ASN* 3.1 19.0 + - + +
57D GLU* 3.1 13.1 + - + +
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Residues in contact with SER 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PRO 3.1 12.2 + - - -
51D LYS* 2.9 21.8 + - - -
53D THR* 1.3 77.0 - - - +
55D VAL* 1.3 62.6 + - - +
57D GLU* 3.4 10.7 + - - +
58D ASN* 3.2 29.7 + - - +
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Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LYS 3.4 17.3 - - - +
52D PHE* 3.1 14.3 + - - +
54D SER* 1.3 84.8 + - - +
56D ASN* 1.3 59.0 + - - +
58D ASN* 3.3 3.9 + - - +
59D VAL* 2.8 52.6 + - + +
77D GLN* 5.4 0.9 - - - +
80D GLY 4.5 8.3 - - - +
81D LEU* 4.5 12.6 - - + +
84D ALA* 4.2 17.7 - - + -
124D ILE* 6.1 1.8 - - + -
125D ILE* 4.0 25.4 - - + -
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Residues in contact with ASN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3327 T 5.2 4.6 + - - +
3337 A 4.4 31.6 + - - +
13C ARG* 4.3 14.1 - - - +
52D PHE* 3.0 17.1 + - - +
53D THR* 3.1 15.8 + - + +
55D VAL* 1.3 76.9 - - - +
57D GLU* 1.3 57.3 + - - +
60D SER* 2.9 33.1 + - - -
77D GLN* 3.4 21.8 + - - +
81D LEU* 3.4 31.0 - - - +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D THR* 3.1 12.0 + - + +
54D SER* 3.7 11.2 - - - +
55D VAL 3.2 0.2 - - - -
56D ASN* 1.3 77.8 - - - +
58D ASN* 1.3 72.0 + - - +
60D SER* 3.6 4.5 - - - -
61D ALA* 3.0 22.4 + - + +
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Residues in contact with ASN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D SER* 3.2 17.4 + - - +
55D VAL* 4.0 2.6 - - - +
57D GLU* 1.3 85.2 - - - +
59D VAL* 1.3 66.2 + - - +
61D ALA* 3.2 9.0 + - - +
62D VAL* 3.1 26.3 + - - +
124D ILE* 3.6 28.8 - - + +
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Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D VAL* 2.8 41.5 + - + +
58D ASN* 1.3 71.8 - - - +
60D SER* 1.3 63.4 + - - +
62D VAL* 3.1 9.6 + - - +
63D LEU* 3.0 30.6 + - + +
76D TYR 4.4 7.0 - - - +
77D GLN* 3.3 28.0 - - - +
80D GLY* 5.0 1.6 - - - -
121D VAL* 4.1 37.5 - - + +
124D ILE* 4.9 8.3 - - + -
125D ILE* 4.6 7.0 - - + -
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3337 A 4.8 1.1 - - - -
3347 T 2.9 19.4 + - - -
89B ARG 4.5 4.3 + - - -
90B ILE 4.9 1.6 + - - -
56D ASN 2.9 22.3 + - - -
57D GLU* 3.6 5.6 - - - -
59D VAL* 1.3 77.5 - - - +
61D ALA* 1.3 61.7 + - - +
63D LEU* 3.1 3.6 + - - -
64D THR* 3.0 10.7 + - - -
73D ARG* 2.7 41.7 + - - +
77D GLN* 3.5 9.6 - - - +
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE 5.8 0.9 - - - -
57D GLU* 3.0 14.5 + - + +
58D ASN* 3.4 13.0 - - - +
60D SER* 1.3 77.1 - - - +
62D VAL* 1.3 62.6 + - + +
64D THR* 3.2 9.7 + - - -
65D GLN* 3.1 25.8 + - + +
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ASN 3.1 13.7 + - - +
59D VAL* 3.3 10.5 - - + +
61D ALA* 1.3 76.1 - - + +
63D LEU* 1.3 62.7 + - + +
65D GLN* 2.9 10.7 + - - +
66D TYR* 2.9 50.9 + - + -
117D VAL* 5.5 0.2 - - + -
120D ALA* 3.8 18.4 - - + +
121D VAL* 5.0 4.5 - - + +
124D ILE* 3.7 33.0 - - + -
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D VAL* 3.0 34.5 + - + +
60D SER* 3.1 8.3 + - - +
62D VAL* 1.3 76.3 - - + +
64D THR* 1.3 60.4 + - - +
66D TYR* 3.2 3.0 + - - +
67D GLY 3.0 4.3 + - - -
68D ILE* 2.9 38.8 + - + -
73D ARG* 3.5 47.3 - - + +
76D TYR* 3.6 32.3 - - + -
77D GLN* 4.0 10.5 - - - +
117D VAL* 3.6 19.1 - - + -
121D VAL* 5.0 3.1 - - + -
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ILE* 2.6 28.5 + - + +
91B GLY 3.6 13.5 - - - +
92B SER 3.4 27.6 - - - +
93B GLY* 4.5 1.8 - - - -
94B PRO* 3.3 4.4 - - + +
95B ALA* 3.2 19.8 + - + +
60D SER 3.0 5.4 + - - -
61D ALA* 3.4 11.6 - - - -
62D VAL 3.1 0.2 - - - -
63D LEU* 1.3 77.4 - - - +
65D GLN* 1.3 62.6 + - - +
67D GLY 3.1 9.9 + - - -
73D ARG* 2.9 23.4 + - - +
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Residues in contact with GLN 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B SER 4.9 8.3 + - - -
93B GLY* 5.3 1.4 - - - -
94B PRO* 3.4 31.9 - - - +
61D ALA* 3.1 17.9 + - + +
62D VAL* 2.9 12.2 + - - +
64D THR* 1.3 77.9 - - - +
66D TYR* 1.3 64.1 + - + +
67D GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B PRO* 4.7 0.4 - - - -
62D VAL* 2.9 33.2 + - + +
63D LEU* 3.2 6.4 + - - +
65D GLN* 1.3 80.6 - - + +
67D GLY* 1.3 63.3 + - - +
68D ILE* 3.4 19.5 + - + +
116D GLN* 3.2 41.7 + - + -
117D VAL* 3.9 18.6 - - + -
120D ALA* 3.5 30.5 - - + +
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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