Contacts of the helix formed by residues 63 - 77 (chain D) in PDB entry 4I6U
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 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D MET* 4.3 0.4 - - - -
61D GLU 4.1 1.4 + - - -
62D VAL* 1.3 76.5 - - - +
64D ASP* 1.3 65.5 + - - +
65D VAL* 3.6 5.7 + - - +
66D VAL* 3.0 31.8 + - - +
67D PHE* 2.9 20.4 + - - +
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Residues in contact with ASP 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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4A PHE* 3.6 29.3 - - - -
5A LEU* 4.9 9.4 - - - +
75A ILE* 4.2 22.2 - - + +
104A PEG 5.3 4.2 - - - +
54D GLU* 4.9 9.8 - - - +
57D MET* 3.2 30.7 - - + +
58D LYS* 6.2 0.2 - - - +
62D VAL 4.5 1.9 - - - +
63D SER* 1.3 71.5 - - - +
65D VAL* 1.3 65.2 + - - +
67D PHE* 3.1 3.1 + - - +
68D PHE* 3.1 31.9 + - + -
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Residues in contact with VAL 65 (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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72A ILE* 4.0 26.8 - - + +
75A ILE* 3.8 30.7 - - + -
76A LEU* 3.9 30.5 - - + -
104A PEG 6.0 1.1 - - - -
63D SER* 3.3 5.6 + - - +
64D ASP* 1.3 75.1 - - - +
66D VAL* 1.3 60.3 + - + +
68D PHE* 3.2 4.1 + - - +
69D GLU* 2.9 49.0 + - - +
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Residues in contact with VAL 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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62D VAL* 3.9 17.3 - - + -
63D SER* 3.0 26.0 + - - +
65D VAL* 1.3 78.6 - - + +
67D PHE* 1.3 64.3 + - - +
69D GLU* 3.2 15.8 + - - +
70D MET* 3.0 38.5 + - + +
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Residues in contact with PHE 67 (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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9D VAL* 4.2 15.3 - - + -
12D VAL* 3.6 26.0 - - + +
13D ILE* 4.0 18.2 - - + -
16D ILE* 3.8 18.2 - - + -
53D LEU* 3.9 25.6 - - + -
57D MET* 3.4 39.7 - - + -
60D LEU* 5.3 2.5 - - + -
62D VAL* 4.1 10.9 - - + +
63D SER 2.9 9.3 + - - +
64D ASP 3.6 0.2 - - - +
66D VAL* 1.3 78.3 - - - +
68D PHE* 1.3 83.3 + + - +
70D MET* 3.3 7.9 + - - +
71D LEU* 2.9 36.9 + - + +
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Residues in contact with PHE 68 (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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5A LEU* 3.7 40.6 - - + -
68A PHE* 3.6 39.3 - + + -
71A LEU* 3.9 13.0 - - + -
72A ILE* 3.8 23.6 - - + -
75A ILE* 4.5 7.0 - - + -
50D ILE* 6.5 0.7 - - + -
53D LEU* 4.5 11.0 - - + -
57D MET* 4.4 8.3 - - + -
64D ASP* 3.1 31.7 + - + +
65D VAL* 4.9 0.4 - - - -
67D PHE* 1.3 94.5 - + - +
69D GLU* 1.3 58.6 + - - +
71D LEU* 3.5 10.1 - - + +
72D ILE* 2.9 33.4 + - - +
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Residues in contact with GLU 69 (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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72A ILE* 3.8 19.6 - - + +
65D VAL* 2.9 37.8 + - - +
66D VAL* 3.2 17.5 + - + +
68D PHE* 1.3 72.8 - - - +
70D MET* 1.3 64.2 + - + +
72D ILE* 3.4 7.3 + - + +
73D LYS* 3.1 33.7 + - + +
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Residues in contact with MET 70 (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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12D VAL* 3.9 14.3 - - + +
15D LYS* 3.8 37.5 - - + +
16D ILE* 3.8 37.2 - - + -
19D GLU* 4.5 7.9 - - - +
62D VAL* 5.2 0.7 - - - -
66D VAL* 3.0 33.9 + - + +
67D PHE 3.4 7.4 - - - +
69D GLU* 1.3 74.8 - - + +
71D LEU* 1.3 62.6 + - - +
73D LYS* 3.3 14.4 + - + +
74D GLU* 3.0 25.6 + - - +
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Residues in contact with LEU 71 (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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68A PHE* 3.7 38.4 - - + -
5D LEU* 4.1 1.8 - - + -
8D LYS* 3.8 18.4 - - + +
9D VAL* 3.8 45.3 - - + +
12D VAL* 4.0 9.8 - - + +
67D PHE* 2.9 21.1 + - + +
68D PHE* 3.5 24.2 - - + +
69D GLU 3.3 0.2 - - - -
70D MET* 1.3 72.4 - - - +
72D ILE* 1.3 67.0 + - - +
74D GLU* 3.2 3.3 + - - +
75D ILE* 2.9 36.9 + - + +
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Residues in contact with ILE 72 (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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65A VAL* 4.2 22.0 - - + +
68A PHE* 3.8 30.7 - - + -
69A GLU* 4.0 22.2 - - + +
72A ILE* 3.8 19.5 - - + -
68D PHE 2.9 21.0 + - - +
69D GLU* 3.6 7.4 - - + +
71D LEU* 1.3 73.9 - - - +
73D LYS* 1.3 60.6 + - + +
75D ILE* 3.1 9.7 + - + +
76D LEU* 2.9 50.4 + - + +
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Residues in contact with LYS 73 (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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69D GLU* 3.1 24.2 + - + +
70D MET* 3.5 13.2 - - + +
71D LEU 3.3 0.2 - - - -
72D ILE* 1.3 77.6 - - + +
74D GLU* 1.3 65.0 + - - +
76D LEU* 3.3 10.3 + - + +
77D LYS* 3.2 31.3 + - - +
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Residues in contact with GLU 74 (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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8D LYS* 4.0 32.9 + - + +
11D PHE* 3.3 41.2 - - + -
12D VAL* 4.3 12.8 - - + +
15D LYS* 4.4 14.7 + - - +
70D MET 3.0 17.3 + - - +
71D LEU* 3.6 5.6 - - - +
72D ILE 3.2 0.2 - - - -
73D LYS* 1.3 79.3 - - - +
75D ILE* 1.3 62.6 + - - +
77D LYS* 3.1 50.2 + - - +
78D HIS 4.0 0.9 + - - -
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Residues in contact with ILE 75 (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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64A ASP* 4.0 26.5 - - + +
65A VAL* 3.6 23.6 - - + -
68A PHE* 4.6 4.9 - - + -
102A ACT 5.7 1.8 - - + -
4D PHE* 4.1 22.6 - - + -
5D LEU* 4.2 10.1 - - + -
8D LYS* 4.1 20.0 - - + -
71D LEU* 2.9 37.8 + - + +
72D ILE* 3.5 10.5 - - - +
74D GLU* 1.3 75.9 - - - +
76D LEU* 1.3 59.0 + - + +
78D HIS* 3.0 29.8 + - - +
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Residues in contact with LEU 76 (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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65A VAL* 3.9 12.6 - - + -
102A ACT 3.4 34.1 - - + +
72D ILE* 2.9 39.5 + - + +
73D LYS* 3.7 9.4 - - + +
75D ILE* 1.3 71.4 - - + +
77D LYS* 1.3 65.1 + - - +
78D HIS* 3.1 9.7 + - - -
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Residues in contact with LYS 77 (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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8D LYS* 5.5 0.4 - - - +
15D LYS* 5.7 2.8 - - - +
73D LYS* 3.2 26.8 + - - +
74D GLU* 3.1 43.7 + - - +
76D LEU* 1.3 76.5 - - - +
78D HIS* 1.3 67.8 + - + +
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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