Contacts of the helix formed by residues 60 - 69 (chain D) in PDB entry 4WLU
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 HIS 60 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LYS* 5.0 3.0 + - - -
244C ALA* 3.9 28.8 - - + +
33D SER* 3.5 17.9 - - - +
38D GLN* 5.6 2.5 - - - +
59D ALA* 1.3 91.0 - - + +
61D THR* 1.3 62.1 + - - +
62D PRO* 3.4 6.8 - - - +
63D GLY* 3.2 13.1 + - - -
64D VAL* 3.2 16.5 + - + +
81D LEU* 4.0 4.8 - - - +
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ALA* 4.2 6.3 - - + -
33D SER* 3.6 14.1 - - - +
55D LEU* 3.7 32.3 - - + +
56D TYR 3.7 18.6 - - - +
57D ASP* 3.7 4.5 + - + +
59D ALA 3.1 2.8 + - - -
60D HIS* 1.3 74.6 - - - +
62D PRO* 1.3 59.8 - - - +
64D VAL* 3.1 4.4 + - + +
65D ALA* 2.8 32.7 + - - +
79D GLY* 4.5 1.3 - - - -
80D TYR 2.7 27.1 + - - -
81D LEU* 3.4 16.1 - - - +
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Residues in contact with PRO 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ALA* 4.3 12.0 - - + +
60D HIS* 3.4 6.1 - - - -
61D THR* 1.3 96.3 - - - +
63D GLY* 1.3 56.2 + - - +
65D ALA* 3.5 5.1 + - + +
66D ALA* 3.0 30.0 + - - +
79D GLY* 4.9 8.7 - - - +
81D LEU* 4.2 29.2 - - + -
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Residues in contact with GLY 63 (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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237C VAL* 4.5 0.5 - - - +
240C ALA* 3.6 25.5 + - - -
241C LYS* 3.7 27.2 - - - +
60D HIS 3.2 7.1 + - - -
61D THR 3.2 0.6 - - - -
62D PRO* 1.3 76.7 - - - +
64D VAL* 1.3 61.0 + - - +
66D ALA* 3.5 1.7 + - - +
67D ASP* 3.0 29.5 + - - +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LYS* 4.8 6.5 - - - +
249C LEU* 4.1 13.2 - - + -
32D ALA* 4.3 14.4 - - + +
33D SER* 4.1 12.6 - - - +
38D GLN* 3.7 29.8 - - + +
41D SER* 5.3 0.4 - - - -
55D LEU* 4.0 17.9 - - + -
60D HIS* 3.2 16.1 + - + +
61D THR* 3.1 9.3 + - - +
63D GLY* 1.3 76.1 - - - +
65D ALA* 1.3 58.9 + - - +
67D ASP* 3.4 7.4 - - - +
68D LEU* 3.0 38.0 + - + +
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LEU* 4.0 4.9 - - + +
61D THR 2.8 16.6 + - - +
62D PRO* 3.9 4.0 - - + +
64D VAL* 1.3 74.2 - - - +
66D ALA* 1.3 60.1 + - - +
68D LEU 3.3 0.7 + - - -
69D SER* 2.8 34.7 + - - -
77D VAL* 3.9 18.2 - - + +
78D LYS* 3.9 7.0 - - - -
79D GLY* 3.5 30.1 - - - +
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Residues in contact with ALA 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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236C GLU* 5.1 8.5 - - + +
237C VAL* 4.3 13.2 - - + -
240C ALA* 3.8 20.9 - - + -
62D PRO 3.0 18.7 + - - +
63D GLY 3.6 5.6 - - - +
65D ALA* 1.3 74.2 - - - +
67D ASP* 1.3 64.5 + - - +
69D SER* 2.7 23.8 + - - -
70D HIS* 3.6 12.9 + - - -
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Residues in contact with ASP 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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237C VAL* 4.2 13.6 - - + +
241C LYS* 3.3 11.2 + - - -
247C ALA* 4.1 4.7 - - - -
248C THR* 3.0 31.4 + - - -
249C LEU* 3.0 19.4 + - + +
250C SER* 2.7 53.7 + - - -
63D GLY 3.0 15.9 + - - +
64D VAL* 3.4 6.7 - - - +
66D ALA* 1.3 80.9 - - - +
68D LEU* 1.3 63.1 + - - +
69D SER 3.3 0.2 + - - -
70D HIS* 3.4 7.6 + - - +
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Residues in contact with LEU 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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249C LEU* 3.7 31.0 - - + -
41D SER* 3.6 34.1 - - - +
42D LEU* 3.7 22.9 - - - -
45D LYS* 3.3 19.9 - - + -
53D LEU* 4.5 4.5 - - + -
55D LEU* 3.7 20.4 - - + -
64D VAL* 3.0 22.8 + - + +
65D ALA 4.0 2.5 - - - +
67D ASP* 1.3 76.9 - - - +
69D SER* 1.3 61.3 + - - +
70D HIS 3.1 2.2 + - - -
71D ILE* 3.1 30.1 + - + +
77D VAL* 4.2 11.9 - - + -
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Residues in contact with SER 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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179C THR* 3.4 19.6 - - - +
180C PHE* 5.2 0.9 - - - -
183C GLU* 4.5 8.0 - - - +
229C ARG* 5.9 0.9 + - - -
236C GLU* 5.3 0.5 + - - -
45D LYS* 4.7 3.8 + - - +
65D ALA 2.8 18.8 + - - -
66D ALA* 2.7 24.1 + - - -
68D LEU* 1.3 72.2 - - - +
70D HIS* 1.3 66.8 + - - +
71D ILE 3.3 3.1 + - - +
77D VAL* 4.3 25.8 - - - +
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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