Contacts of the helix formed by residues 63 - 76 (chain A) in PDB entry 1IN7
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 GLY 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PHE* 3.8 3.0 - - - -
61A GLY 3.4 2.0 - - - -
62A LEU* 1.3 77.5 - - - +
64A LYS* 1.3 60.2 + - - +
66A THR* 3.3 3.9 + - - -
67A LEU* 2.9 34.1 + - - +
177A LEU* 4.3 4.0 - - - -
600A ADP 3.0 40.8 + - - -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.3 43.2 - - + +
58A GLY 2.9 32.8 + - - +
59A PRO 3.0 13.8 + - - +
60A PRO* 3.8 5.3 - - - +
62A LEU 3.7 0.2 - - - -
63A GLY* 1.3 75.9 - - - +
65A THR* 1.3 64.4 + - - +
67A LEU* 3.1 3.5 + - - -
68A ALA* 3.0 19.4 + - - +
107A PHE* 4.8 1.3 - - - -
109A ASP* 5.0 4.3 - - - -
156A ALA* 4.3 10.3 - - + -
157A THR* 3.5 30.7 - - - +
158A THR* 4.7 3.3 - - - +
177A LEU* 4.0 21.1 - - + -
600A ADP 2.8 32.0 + - - +
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Residues in contact with THR 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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20A ARG* 3.4 27.8 - - - +
64A LYS* 1.3 73.2 - - - +
66A THR* 1.3 63.1 + - - +
68A ALA* 3.2 2.8 + - - +
69A HIS* 3.2 34.7 + - + +
81A VAL* 6.5 0.7 - - + -
107A PHE* 3.8 29.4 - - + -
109A ASP* 4.7 6.1 + - - -
600A ADP 2.8 36.6 + - - +
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Residues in contact with THR 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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20A ARG* 3.4 27.7 + - + +
21A PRO* 3.6 37.2 - - + +
27A PHE* 3.6 25.4 - - + -
63A GLY* 3.4 7.4 - - - -
64A LYS 3.2 0.2 - - - -
65A THR* 1.3 77.8 - - - +
67A LEU* 1.3 61.8 + - - +
69A HIS* 3.4 4.7 + - - +
70A ILE* 3.0 28.5 + - + +
600A ADP 2.8 33.2 + - - -
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Residues in contact with LEU 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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24A LEU* 3.8 28.7 - - + -
27A PHE* 3.7 33.4 - - + -
33A VAL* 4.1 25.4 - - + -
34A LYS* 5.4 0.9 - - + -
37A LEU* 4.3 12.8 - - + -
56A LEU* 4.0 23.1 - - + -
63A GLY 2.9 20.5 + - - +
64A LYS* 3.1 4.5 + - - +
66A THR* 1.3 72.6 - - - +
68A ALA* 1.3 67.0 + - - +
70A ILE* 3.1 6.2 + - + +
71A ILE* 2.9 29.2 + - + +
177A LEU* 4.2 14.4 - - + -
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Residues in contact with ALA 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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56A LEU* 4.0 0.6 - - - +
64A LYS 3.0 8.6 + - - +
65A THR 3.4 9.2 - - - +
67A LEU* 1.3 77.6 - - - +
69A HIS* 1.3 61.8 + - - +
71A ILE* 3.3 19.6 + - - +
72A ALA* 3.3 10.0 + - - +
79A ILE* 3.8 13.3 - - + +
105A VAL* 4.5 2.9 - - - +
107A PHE* 3.4 44.6 - - + -
154A VAL* 4.0 11.4 - - + -
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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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20A ARG* 4.1 17.5 + - - -
65A THR* 3.2 38.9 + - + +
66A THR* 3.8 8.5 - - - +
68A ALA* 1.3 76.8 - - + +
70A ILE* 1.3 65.4 + - + +
72A ALA* 3.4 3.7 + - - +
73A SER* 3.0 25.4 + - - -
79A ILE* 3.9 35.4 - - + +
81A VAL* 4.1 21.2 - - + +
107A PHE* 5.3 1.7 - + - -
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Residues in contact with ILE 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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21A PRO 3.6 22.9 - - - +
22A LYS 3.7 3.1 - - - +
23A SER* 3.5 34.3 - - - +
24A LEU* 3.8 32.1 - - + +
27A PHE* 4.0 14.4 - - + -
37A LEU* 5.8 0.4 - - + -
41A LEU* 5.2 2.0 - - + -
66A THR* 3.0 30.0 + - + +
67A LEU* 3.1 13.0 + - + +
69A HIS* 1.3 77.2 - - + +
71A ILE* 1.3 59.4 + - + +
73A SER* 3.4 6.3 + - - -
74A GLU* 2.9 37.5 + - + +
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Residues in contact with ILE 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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37A LEU* 3.8 39.5 - - + -
41A LEU* 4.0 10.2 - - + +
51A LEU* 3.8 14.4 - - + -
54A VAL* 4.7 10.5 - - + -
56A LEU* 5.0 3.6 - - + -
67A LEU* 2.9 23.9 + - + +
68A ALA* 3.4 8.5 - - - +
69A HIS 3.2 0.2 - - - -
70A ILE* 1.3 76.5 - - - +
72A ALA* 1.3 58.3 + - - +
74A GLU* 3.2 2.3 + - - +
75A LEU* 2.9 53.4 + - + +
105A VAL* 4.1 10.3 - - + -
152A THR* 5.2 0.2 - - + -
154A VAL* 4.1 27.4 - - + -
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Residues in contact with ALA 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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68A ALA 3.3 5.9 + - - +
69A HIS 3.9 5.2 - - - +
71A ILE* 1.3 79.2 - - - +
73A SER* 1.3 59.1 + - - +
75A LEU* 3.3 0.9 + - - -
76A GLN 2.9 23.0 + - - -
77A THR* 3.0 30.5 + - - +
79A ILE* 3.7 32.3 - - + +
105A VAL* 3.7 22.2 - - + -
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Residues in contact with SER 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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22A LYS* 4.0 14.5 + - - +
69A HIS 3.0 18.3 + - - -
70A ILE* 3.6 7.4 - - - -
72A ALA* 1.3 78.4 - - - +
74A GLU* 1.3 61.9 + - - +
76A GLN* 3.3 17.9 + - - +
77A THR 5.0 0.9 - - - -
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Residues in contact with GLU 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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22A LYS 5.1 1.0 - - - +
23A SER* 3.9 21.5 - - - -
24A LEU* 5.1 3.1 + - + +
25A ASP* 5.6 0.9 - - - +
41A LEU* 3.5 31.2 - - + -
45A LYS* 2.8 52.1 + - - +
70A ILE* 2.9 29.5 + - + +
71A ILE 3.8 0.9 - - - +
73A SER* 1.3 75.8 + - - +
75A LEU* 1.3 60.7 + - - +
76A GLN* 3.1 12.3 + - - +
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Residues in contact with LEU 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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41A LEU* 3.7 21.3 - - + +
44A ALA* 4.6 7.0 - - + -
45A LYS* 4.1 19.7 - - + +
49A GLU 5.1 3.6 - - - +
51A LEU* 4.1 26.9 - - + +
71A ILE* 2.9 38.6 + - + +
72A ALA 3.8 0.4 - - - +
74A GLU* 1.3 74.3 - - - +
76A GLN* 1.3 69.5 + - - +
77A THR* 3.5 22.0 + - + +
103A GLY 4.6 5.8 - - - +
105A VAL* 4.2 14.4 - - + -
152A THR* 4.6 4.0 - - - +
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Residues in contact with GLN 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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45A LYS* 5.1 8.5 - - - +
72A ALA 2.9 5.9 + - - -
73A SER* 3.3 13.9 + - - +
74A GLU 3.1 11.2 + - - +
75A LEU* 1.3 83.0 - - - +
77A THR* 1.3 61.5 + - - +
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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
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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