Contacts of the helix formed by residues 63 - 76 (chain A) in PDB entry 3ITS
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 LEU 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A CYS* 2.6 51.6 - - + +
26A ASN 2.9 23.1 - - - +
27A GLY* 4.0 2.2 - - - +
51A SER* 5.0 3.9 - - - -
52A GLY 4.2 2.5 - - - +
53A CYS* 3.4 28.5 - - + +
54A SER* 3.6 15.8 + - - +
62A MET* 1.3 96.7 - - + +
64A SER* 1.4 62.8 - - - +
65A GLY 2.9 4.9 - - - -
66A PHE* 3.0 30.6 + - + +
67A CYS* 3.7 9.0 - - - -
92A VAL* 4.1 6.7 - - + -
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Residues in contact with SER 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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54A SER* 3.6 9.0 + - - -
55A ALA* 3.2 21.0 + - - +
57A GLU* 3.0 21.7 + - - +
61A ARG* 3.5 40.4 + - - +
62A MET 3.3 1.4 + - - +
63A LEU* 1.4 76.7 - - - +
65A GLY* 1.4 55.4 + - - +
66A PHE 3.2 0.4 + - - -
67A CYS* 3.4 15.0 + - - +
68A PRO* 3.0 19.6 - - - +
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Residues in contact with GLY 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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12A GLU* 4.6 2.9 - - - +
16A ILE* 4.7 11.6 - - - +
21A LYS* 6.3 0.4 - - - -
61A ARG* 3.8 18.5 - - - +
62A MET 2.9 15.7 + - - -
64A SER* 1.4 75.5 - - - +
66A PHE* 1.3 58.4 + - - +
68A PRO* 3.5 26.7 - - - +
69A HIS* 3.8 5.7 + - - +
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Residues in contact with PHE 66 (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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13A LEU* 5.6 1.3 - - + -
16A ILE* 5.1 4.9 - - + -
27A GLY* 6.2 0.2 - - - -
47A LEU* 4.2 6.5 - - + -
48A ILE 4.1 8.5 - - - -
50A VAL* 3.2 49.6 - - + -
51A SER* 3.6 21.8 - - - -
62A MET 4.7 0.4 - - - +
63A LEU* 3.0 27.5 + - + +
65A GLY* 1.3 76.8 - - - +
67A CYS* 1.3 62.2 + - - +
68A PRO 3.3 0.4 - - - -
69A HIS* 3.6 24.9 - + + +
70A LYS* 2.8 32.1 + - + +
92A VAL* 6.3 2.7 - - + -
95A LEU* 4.1 22.9 - - + -
96A LEU* 4.9 12.1 - - + -
99A LEU* 6.1 0.2 - - + -
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Residues in contact with CYS 67 (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 SER* 5.3 9.0 - - - -
53A CYS 6.0 0.2 - - - -
54A SER* 5.1 8.7 - - - -
63A LEU 3.7 10.3 - - - -
64A SER* 3.5 17.0 - - - +
66A PHE* 1.3 79.0 - - - +
68A PRO* 1.4 69.5 - - + +
70A LYS* 3.1 9.3 + - + +
71A VAL* 2.8 37.5 + - + +
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Residues in contact with PRO 68 (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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12A GLU* 2.9 17.9 - - + +
61A ARG* 5.6 5.4 - - - +
64A SER 3.0 16.2 - - - +
65A GLY* 3.5 20.2 - - - +
67A CYS* 1.4 87.8 - - + +
69A HIS* 1.3 54.6 + - - +
71A VAL* 2.8 7.6 + - + -
72A SER* 2.6 39.0 + - - +
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Residues in contact with HIS 69 (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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9A LEU* 3.1 42.2 + - + +
12A GLU* 2.8 21.5 + - + +
13A LEU* 3.7 31.1 + - + +
16A ILE* 5.7 3.2 - - + +
47A LEU* 3.7 37.0 - - + +
65A GLY 3.8 3.3 + - - +
66A PHE* 3.3 39.6 + + + +
68A PRO* 1.3 75.7 - - - +
70A LYS* 1.3 52.0 - - - +
72A SER* 3.9 0.7 - - - -
73A ALA* 2.7 40.5 + - - +
99A LEU* 4.1 4.7 - - + +
103A PHE* 4.5 0.2 - + - -
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Residues in contact with LYS 70 (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 ILE* 3.2 51.4 - - + +
49A ASN* 4.7 7.8 + - - +
51A SER* 3.9 21.0 + - - +
66A PHE* 2.8 23.1 + - + +
67A CYS* 3.3 9.9 - - + +
69A HIS* 1.3 80.5 - - - +
71A VAL* 1.3 68.9 + - + +
73A ALA* 3.5 4.7 - - - -
74A GLY* 2.9 19.4 + - - -
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Residues in contact with VAL 71 (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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67A CYS* 2.8 30.9 + - + +
68A PRO* 2.8 3.5 + - + +
70A LYS* 1.3 90.1 - - + +
72A SER* 1.3 69.4 + - - +
74A GLY* 2.9 14.9 + - - +
75A GLN* 3.8 7.8 + - - +
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Residues in contact with SER 72 (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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5A ALA* 5.5 0.9 - - - +
8A GLU* 2.9 33.7 + - - +
9A LEU* 4.6 3.4 - - - +
12A GLU* 2.6 31.8 + - - -
68A PRO* 2.6 21.9 + - - +
69A HIS 3.9 2.0 - - - -
71A VAL* 1.3 74.3 - - - +
73A ALA* 1.3 57.1 + - - -
74A GLY 2.9 5.2 + - - -
75A GLN* 3.0 21.0 + - - +
76A PHE* 4.4 1.4 + - - +
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Residues in contact with ALA 73 (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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9A LEU* 3.7 22.1 - - + +
47A LEU* 3.3 31.2 - - + -
48A ILE* 4.0 2.2 - - + -
69A HIS 2.7 26.6 + - - +
70A LYS 3.5 5.2 - - - +
72A SER* 1.3 70.3 - - - +
74A GLY* 1.3 64.6 + - - +
75A GLN 3.2 0.2 - - - -
76A PHE 3.9 2.2 - - - +
77A SER* 2.8 33.6 + - - +
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Residues in contact with GLY 74 (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 ILE* 3.9 10.5 - - - +
70A LYS 2.9 15.0 + - - -
71A VAL* 2.9 13.3 + - - -
73A ALA* 1.3 79.4 - - - +
75A GLN* 1.3 56.4 + - - +
76A PHE 3.0 7.1 + - - -
77A SER 4.0 8.5 + - - +
78A SER* 4.9 1.6 + - - -
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Residues in contact with GLN 75 (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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5A ALA* 4.6 12.1 - - + +
8A GLU* 2.7 41.4 + - - -
71A VAL 4.1 7.0 - - - +
72A SER* 3.0 8.6 + - - +
74A GLY* 1.3 74.0 - - - +
76A PHE* 1.3 58.9 + - + +
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Residues in contact with PHE 76 (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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3A SER* 4.2 21.5 - - - -
5A ALA* 3.8 25.4 - - + +
6A LEU* 3.6 37.9 - - + -
9A LEU* 3.9 24.7 - - + -
44A LEU* 4.1 18.4 - - + -
72A SER 5.0 0.2 - - - +
73A ALA* 4.1 3.6 - - - +
74A GLY 3.0 1.8 + - - -
75A GLN* 1.3 81.7 - - + +
77A SER* 1.3 60.1 + - - +
78A SER* 2.7 25.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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