Contacts of the helix formed by residues 47 - 65 (chain A) in PDB entry 3OTC
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 ASP 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE* 3.5 11.2 - - + -
43A ALA* 2.8 37.3 + - - +
46A ASN* 1.3 74.9 - - - +
48A SER* 1.3 63.1 + - - +
49A ARG* 2.8 64.8 + - - +
50A ALA* 3.2 17.4 + - + +
51A LEU* 3.2 28.8 + - - +
116A PHE* 4.7 1.1 - - - -
206A TYR* 4.7 0.4 - - - -
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASN 4.3 0.2 + - - -
47A ASP* 1.3 70.6 + - - +
49A ARG* 1.3 68.3 + - - +
51A LEU* 4.6 4.9 - - - +
52A GLN* 2.9 44.5 + - - +
203A LEU* 6.1 1.8 - - - -
205A MET* 5.3 4.3 - - - -
206A TYR* 3.5 25.0 + - - -
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS 4.2 2.6 + - - -
41A ASN* 3.1 24.2 + - - +
43A ALA* 4.6 1.2 - - - +
47A ASP* 2.8 35.5 + - - +
48A SER* 1.3 76.2 - - - +
50A ALA* 1.3 59.8 + - - +
52A GLN* 5.0 2.0 - - - -
53A LEU* 3.2 21.5 + - - +
115A TYR* 3.5 33.5 - - - +
116A PHE* 3.4 43.0 - - + +
117A GLU 5.7 0.2 - - - +
118A ASP* 5.9 2.2 - - - +
119A GLN* 3.9 17.4 - - - +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 3.3 41.7 - - + -
47A ASP* 3.2 13.6 + - + +
48A SER 3.2 0.2 - - - -
49A ARG* 1.3 81.5 - - - +
51A LEU* 1.3 65.8 + - + +
53A LEU* 3.2 4.7 + - - +
54A MET* 3.1 27.5 + - + +
76A ASP* 5.8 1.6 - - - +
108A TYR* 5.2 4.0 + - - +
116A PHE* 3.5 9.8 - - + -
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASN* 4.5 7.6 - - + +
47A ASP 3.2 23.1 + - - +
48A SER 4.1 2.0 - - - +
50A ALA* 1.3 77.2 - - + +
52A GLN* 1.3 62.4 + - - +
54A MET* 3.4 7.5 + - + +
55A THR* 3.0 25.3 + - - -
73A GLY 5.8 0.9 - - - +
74A GLN* 4.8 1.8 - - - -
75A SER* 3.8 39.9 - - - +
78A TYR* 5.1 0.3 - - - -
205A MET* 4.3 25.1 - - + +
206A TYR* 3.7 33.9 - - + -
210A THR* 5.3 3.3 + - - +
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Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A SER* 2.9 31.3 + - - +
49A ARG* 5.3 0.5 - - - -
51A LEU* 1.3 74.8 - - - +
53A LEU* 1.3 64.2 + - - +
55A THR* 3.3 9.0 + - - -
56A LYS* 3.0 21.7 + - - +
115A TYR* 3.5 34.5 + - + -
205A MET* 4.3 29.5 - - + +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ARG 3.2 17.8 + - - +
50A ALA 3.2 4.2 + - - +
51A LEU 3.2 0.2 - - - -
52A GLN* 1.3 75.1 - - - +
54A MET* 1.3 66.2 + - - +
56A LYS* 3.0 12.7 + - + +
57A CYS* 3.0 20.1 + - - -
108A TYR* 3.3 48.5 - - + +
111A TYR* 3.6 38.8 - - + +
112A TRP* 3.6 26.2 - - + -
115A TYR* 3.8 16.8 - - + -
116A PHE* 4.1 7.2 - - + -
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Residues in contact with MET 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 6.2 1.8 - - + -
33A PHE* 5.0 6.5 - - + -
50A ALA* 3.1 18.3 + - + +
51A LEU* 3.6 10.1 - - + +
52A GLN 3.3 0.2 - - - -
53A LEU* 1.3 78.2 - - - +
55A THR* 1.3 57.8 + - - +
57A CYS* 3.3 2.6 + - - -
58A ALA* 3.0 24.6 + - - +
75A SER 4.0 13.0 - - - +
76A ASP* 3.6 12.1 - - - +
77A GLU* 3.6 40.2 - - - +
78A TYR* 3.7 12.1 - - + +
104A PHE* 3.5 41.5 - - + -
108A TYR* 3.9 17.9 - - + +
127A PHE* 4.5 9.6 - - + -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU 3.0 14.1 + - - -
52A GLN* 3.6 11.0 - - - -
53A LEU 3.1 0.6 - - - -
54A MET* 1.3 75.9 - - - +
56A LYS* 1.3 60.5 + - - +
58A ALA* 3.2 1.6 + - - +
59A GLN* 2.8 37.6 + - + +
78A TYR* 2.9 28.4 + - - +
205A MET* 5.8 1.9 - - - +
210A THR* 3.8 21.0 + - + +
212A LEU* 3.8 23.6 - - + -
247A PRO* 4.1 12.3 - - + -
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLN 3.0 6.8 + - - +
53A LEU* 3.0 9.7 + - + +
55A THR* 1.3 76.4 - - - +
57A CYS* 1.3 60.4 + - - +
59A GLN* 3.3 22.9 + - + +
60A THR* 2.9 29.6 + - - -
63A GLU* 6.0 0.4 + - - -
111A TYR* 3.8 49.8 - - + -
114A ASP* 5.3 2.7 - - - -
115A TYR* 3.5 34.3 - - + +
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Residues in contact with CYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.0 22.0 + - - -
54A MET 3.6 2.7 - - - +
56A LYS* 1.3 73.2 - - - +
58A ALA* 1.3 65.9 + - - +
60A THR* 3.1 4.9 + - - -
61A VAL* 3.0 24.9 + - - +
104A PHE* 3.5 30.1 - - + -
107A SER* 3.6 16.9 + - - -
108A TYR* 3.2 52.7 - - - -
111A TYR* 5.3 0.4 - - - -
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A MET 3.0 14.1 + - - +
55A THR 3.5 5.4 - - - +
57A CYS* 1.3 77.8 - - - +
59A GLN* 1.3 61.9 + - - +
61A VAL* 3.2 3.8 + - - +
62A MET* 3.0 26.3 + - - +
78A TYR* 3.5 38.8 - - + -
80A PHE* 3.6 20.0 - - + -
104A PHE* 3.5 2.2 - - + -
212A LEU* 3.7 8.1 - - + -
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Residues in contact with GLN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 2.8 21.9 + - - +
56A LYS* 3.6 32.6 + - + +
57A CYS 3.2 0.2 - - - -
58A ALA* 1.3 76.0 - - - +
60A THR* 1.3 61.3 + - - +
62A MET* 3.1 10.7 + - - +
63A GLU* 2.8 29.8 + - - +
212A LEU* 3.9 19.3 - - + +
245A PRO* 2.7 39.2 + - + +
247A PRO* 3.6 20.0 - - - +
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Residues in contact with THR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS* 2.9 17.6 + - - +
57A CYS 3.1 4.7 + - - -
59A GLN* 1.3 78.3 - - - +
61A VAL* 1.3 61.2 + - - +
63A GLU* 3.4 12.4 + - - +
64A GLU* 3.1 34.0 + - + +
103A GLN* 3.9 16.6 - - + +
107A SER* 3.0 28.4 + - - +
111A TYR* 3.5 19.5 + - + +
124B PRO* 4.5 9.0 - - + -
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A CYS 3.0 17.2 + - - +
58A ALA 3.2 7.2 + - - +
60A THR* 1.3 75.2 - - - +
62A MET* 1.3 59.0 + - - +
65A LEU* 3.1 50.9 + - + +
68A ILE* 3.9 4.4 - - + +
80A PHE* 3.7 25.1 - - + -
100A VAL* 3.9 15.7 - - + +
103A GLN* 4.0 12.8 - - + -
104A PHE* 3.7 38.8 - - + +
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Residues in contact with MET 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ALA 3.0 11.8 + - - +
59A GLN* 3.1 9.6 + - - +
61A VAL* 1.3 79.0 - - - +
63A GLU* 1.3 58.1 + - - +
65A LEU 3.4 12.3 - - - +
66A GLU* 5.3 0.5 - - - -
68A ILE* 3.7 36.6 + - + +
69A VAL 4.3 4.5 - - - +
71A ALA* 3.7 22.2 - - + -
80A PHE* 4.4 4.7 - - + -
212A LEU* 3.8 36.3 - - - +
213A ILE* 4.9 0.2 - - - -
214A TRP* 3.4 55.0 - - + +
245A PRO* 4.0 15.9 - - + -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS* 6.0 0.3 + - - -
59A GLN* 2.8 23.2 + - - +
60A THR* 4.0 14.2 + - - +
62A MET* 1.3 74.0 - - - +
64A GLU* 1.3 75.2 + - - +
65A LEU 3.8 3.5 - - - +
214A TRP* 4.4 7.4 - - + -
244A LYS* 5.2 10.4 + - - +
245A PRO* 4.1 22.3 - - + +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 3.1 27.1 + - + +
61A VAL 4.3 0.2 - - - +
63A GLU* 1.3 89.6 - - + +
65A LEU* 1.3 61.2 + - + +
66A GLU* 4.7 2.6 - - - +
103A GLN* 3.9 35.1 + - + +
31B ARG* 3.2 27.3 + - - +
123B TYR* 5.7 7.3 - - - -
124B PRO 5.7 1.3 - - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.1 29.8 + - + +
62A MET 3.4 16.7 - - - +
63A GLU 3.8 3.6 - - - +
64A GLU* 1.3 82.2 - - + +
66A GLU* 1.3 67.1 + - - +
68A ILE* 4.2 8.7 - - + -
82A PHE* 4.4 5.8 - - + -
88A TRP* 3.7 27.1 - - + -
99A HIS* 3.8 19.7 - - + +
100A VAL* 3.6 41.5 - - + +
103A GLN* 5.2 4.7 - - + +
31B ARG* 3.4 23.3 - - - +
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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