Contacts of the helix formed by residues 65 - 75 (chain D) in PDB entry 4K71
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 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D GLU* 5.6 4.0 - - - -
63D ASP 3.9 1.6 + - - -
64D LYS* 1.3 78.0 - - - +
66D LEU* 1.3 65.8 + - - +
67D HIS* 3.7 11.8 + - - +
68D THR* 2.8 34.0 + - - -
69D LEU* 3.1 20.8 + - - +
95D GLU* 5.7 0.2 - - - +
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Residues in contact with LEU 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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6D GLU* 4.0 21.4 - - + +
7D VAL* 3.7 43.1 - - + +
10D ARG* 4.2 7.2 - - + -
64D LYS 5.3 0.7 - - - +
65D SER* 1.3 73.1 - - - +
67D HIS* 1.3 60.8 + - + +
69D LEU* 3.2 6.3 + - + -
70D PHE* 2.9 56.6 + - + -
251D LEU* 3.8 27.1 - - + -
252D GLU* 3.4 32.5 - - - +
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Residues in contact with HIS 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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30D TYR* 4.5 7.2 - - - -
65D SER* 3.2 11.2 + - - +
66D LEU* 1.3 80.0 - - + +
68D THR* 1.3 58.7 + - - +
70D PHE* 4.0 5.8 - + - +
71D GLY* 2.9 24.9 + - - -
95D GLU* 3.2 20.1 + - + +
96D PRO* 6.0 4.6 - - - +
99D ASN* 3.1 45.2 + - - +
100D GLU* 5.7 0.4 - - - -
247D HIS* 4.4 11.0 + + - -
248D GLY 5.7 0.2 - - - -
249D ASP* 2.6 33.3 + - - -
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Residues in contact with THR 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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64D LYS* 4.3 23.6 - - + -
65D SER* 2.8 27.8 + - - -
67D HIS* 1.3 76.3 - - - +
69D LEU* 1.3 60.0 + - - +
72D ASP* 2.9 52.0 + - - +
95D GLU* 3.6 26.9 + - + +
98D ARG* 3.3 3.5 + - - +
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Residues in contact with LEU 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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7D VAL* 4.1 18.4 - - + -
46D VAL* 4.1 31.2 - - + -
49D PHE* 3.6 39.7 - - + -
64D LYS* 5.4 7.6 - - + +
65D SER 3.1 12.8 + - - +
66D LEU* 3.6 10.3 - - + +
68D THR* 1.3 77.9 - - - +
70D PHE* 1.3 76.2 + - + +
72D ASP* 3.3 7.6 + - + +
73D LYS* 3.2 28.3 + - + +
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Residues in contact with PHE 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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7D VAL* 5.7 0.4 - - + -
19D PHE* 5.7 0.2 - + - -
23D VAL* 4.0 13.5 - - + -
26D ALA* 4.7 15.0 - - + -
27D PHE* 3.7 27.9 - + + -
30D TYR* 4.6 26.2 - + + -
46D VAL* 3.8 24.0 - - + -
66D LEU* 2.9 37.2 + - + +
67D HIS* 4.1 5.4 - + - +
69D LEU* 1.3 89.2 - - + +
71D GLY* 1.3 52.9 + - - +
73D LYS* 3.1 5.1 + - - +
74D LEU* 2.8 38.5 + - - +
248D GLY 5.8 3.4 - - - -
250D LEU 6.3 0.7 - - - -
251D LEU* 3.8 31.2 - - + -
252D GLU* 6.1 0.7 - - - -
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Residues in contact with GLY 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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67D HIS 2.9 15.8 + - - -
70D PHE* 1.3 73.1 - - - +
72D ASP* 1.3 64.5 + - - +
74D LEU* 3.3 8.8 + - - +
75D CYS* 3.0 30.5 + - - +
95D GLU* 4.1 1.3 - - - -
98D ARG* 3.2 26.5 - - - -
102D PHE* 5.0 5.2 - - - -
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Residues in contact with ASP 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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64D LYS* 5.4 4.5 + - - +
68D THR* 2.9 33.9 + - - +
69D LEU* 3.3 8.0 + - + +
71D GLY* 1.3 75.4 - - - +
73D LYS* 1.3 67.4 + - + +
75D CYS* 3.6 6.2 + - - +
76D THR* 3.6 16.8 + - - +
98D ARG* 2.9 27.5 + - - +
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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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27D PHE* 4.1 13.7 - - + -
42D LEU* 3.4 21.1 - - + +
45D GLU* 2.5 52.1 + - - +
46D VAL* 3.7 23.3 - - + +
69D LEU* 3.2 20.4 + - + +
70D PHE 3.1 8.6 + - - +
72D ASP* 1.3 79.3 - - + +
74D LEU* 1.3 62.7 + - - +
76D THR* 2.7 33.5 + - + +
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Residues in contact with LEU 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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27D PHE* 3.9 28.7 - - + +
30D TYR* 3.3 41.1 - - + -
31D LEU* 3.4 35.1 - - + +
39D HIS* 4.8 1.8 - - - +
42D LEU* 4.3 7.6 - - + -
70D PHE 2.8 23.4 + - - +
71D GLY* 3.3 5.8 + - - +
73D LYS* 1.3 71.9 - - - +
75D CYS* 1.3 58.2 + - - +
76D THR 3.2 0.2 - - - -
77D VAL* 3.2 10.2 + - - +
78D ALA* 2.8 26.7 + - - +
102D PHE* 4.1 28.5 - - + -
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Residues in contact with CYS 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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71D GLY 3.0 19.7 + - - +
72D ASP* 3.6 4.0 + - - +
73D LYS 3.2 0.4 - - - -
74D LEU* 1.3 72.4 - - - +
76D THR* 1.3 62.4 + - - +
77D VAL 3.2 1.7 + - - -
78D ALA 4.0 0.9 - - - +
79D THR* 3.6 20.9 + - + +
91D CYS* 2.1 59.0 - - + +
98D ARG* 3.9 22.0 - - - +
102D PHE* 4.0 9.9 - - - -
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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