Contacts of the helix formed by residues 53 - 65 (chain C) in PDB entry 4D10
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 GLU 53 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 3.8 29.2 - - + +
28C ILE* 3.7 21.7 - - + +
50C ASP* 5.5 1.6 - - - +
52C GLN* 1.3 78.0 - - - +
54C HIS* 1.3 64.0 + - - +
55C SER 3.3 0.9 - - - -
56C LEU* 3.3 33.2 + - + +
57C GLY 3.4 4.5 + - - -
84C PHE* 5.2 2.4 - - - -
89C ASN 5.3 0.2 - - - +
90C GLY* 4.4 4.0 - - - -
91C GLU 4.4 4.7 + - - -
92C HIS* 4.1 32.8 + - + +
93C ILE* 3.4 30.3 - - - +
96C ALA* 4.5 5.9 - - + +
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Residues in contact with HIS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU 5.5 0.8 + - - -
8C PHE* 4.0 28.7 - + + -
9C VAL* 4.0 16.5 - - + +
12C VAL* 3.4 36.3 - - + +
24C LEU* 5.5 1.7 - - - +
28C ILE* 5.4 4.3 - - - -
39C LEU* 5.3 4.8 - - + +
42C LEU* 5.5 5.9 - - + +
46C LEU* 3.7 30.1 - - + -
52C GLN* 3.2 5.3 - - + +
53C GLU* 1.3 78.6 - - - +
55C SER* 1.3 57.6 + - - +
57C GLY* 3.2 4.1 + - - -
58C VAL* 2.9 47.2 + - + +
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASP* 4.2 6.3 - - - -
46C LEU* 3.8 14.1 - - - +
51C VAL* 3.5 27.9 + - - +
52C GLN 2.8 22.7 + - - -
54C HIS* 1.3 77.2 - - - +
56C LEU* 1.3 58.6 + - - +
58C VAL* 3.6 5.6 - - - +
59C LEU* 2.8 41.3 + - - +
84C PHE* 3.3 19.7 - - - -
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 5.4 2.2 - - + -
53C GLU* 3.3 23.1 + - + +
54C HIS 3.2 0.4 - - - -
55C SER* 1.3 82.7 + - - +
57C GLY* 1.3 53.1 + - - +
59C LEU* 4.1 1.5 - - - +
60C ALA* 2.8 37.1 + - - +
84C PHE* 3.7 31.9 - - + -
93C ILE* 5.6 0.2 - - + -
96C ALA* 3.6 29.2 - - + +
99C THR* 3.5 30.3 - - - +
100C PHE* 3.7 33.9 - - + +
103C LEU* 3.9 10.1 - - + -
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Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 4.1 26.2 - - - +
31C SER* 5.1 6.3 - - - -
53C GLU 3.4 5.0 + - - -
54C HIS 3.2 6.7 + - - -
56C LEU* 1.3 75.2 - - - +
58C VAL* 1.3 59.3 + - - +
60C ALA* 3.8 4.3 - - - +
61C VAL* 3.0 37.8 + - - +
99C THR* 5.6 0.2 - - - -
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.8 55.1 - - + +
40C SER* 5.7 0.2 - - - -
42C LEU* 6.1 1.3 - - + -
43C ASP* 4.6 12.1 - - + +
46C LEU* 5.2 3.1 - - + -
54C HIS* 2.9 38.1 + - + +
55C SER* 3.6 11.0 - - - +
57C GLY* 1.3 76.7 - - - +
59C LEU* 1.3 59.3 + - + +
61C VAL* 3.4 5.2 + - - +
62C LEU* 2.9 41.3 + - + +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ASP* 5.6 3.1 - - - +
55C SER* 2.8 28.8 + - - +
56C LEU 4.1 1.3 - - - +
58C VAL* 1.3 73.7 - - + +
60C ALA* 1.3 60.6 + - - +
62C LEU* 3.2 10.7 + - + +
63C PHE* 3.0 33.3 + - + -
77C LEU* 3.9 22.7 - - + -
80C GLN* 4.5 14.8 - - + +
81C VAL* 3.8 31.4 - - + +
84C PHE* 3.9 39.0 - - + -
103C LEU* 3.7 15.7 - - + -
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU 2.8 23.9 + - - +
57C GLY* 3.8 5.6 - - - +
59C LEU* 1.3 71.2 - - - +
61C VAL* 1.3 59.3 + - + +
63C PHE* 3.3 4.2 + - - +
64C VAL* 2.8 34.3 + - + +
99C THR* 4.3 31.2 - - + +
102C GLY 6.1 0.2 - - - -
103C LEU* 3.7 14.4 - - + +
106C GLN* 5.8 0.2 - - - +
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C SER* 3.7 24.7 - - - +
33C GLU 5.7 0.2 - - - +
35C LEU* 3.8 37.0 - - + -
39C LEU* 4.5 6.1 - - + -
57C GLY* 3.0 22.2 + - - +
58C VAL* 3.7 4.9 - - - +
60C ALA* 1.3 74.4 - - + +
62C LEU* 1.3 64.7 + - - +
64C VAL* 3.1 23.7 + - + +
65C LYS* 3.2 23.2 + - + +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 5.5 7.9 - - + -
40C SER* 5.7 9.4 - - - +
58C VAL* 2.9 40.9 + - + +
59C LEU* 3.2 16.6 + - + +
61C VAL* 1.3 76.8 - - - +
63C PHE* 1.3 58.3 + - + +
65C LYS* 3.4 24.7 - - - +
69C PRO* 3.4 42.8 - - - +
70C SER* 4.7 5.6 - - - +
77C LEU* 3.7 33.7 - - + -
80C GLN* 5.3 3.4 - - - +
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Residues in contact with PHE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LEU* 3.0 24.0 + - + +
60C ALA* 3.9 4.0 - - - +
62C LEU* 1.3 76.2 - - + +
64C VAL* 1.3 63.9 + - - +
65C LYS* 3.2 3.0 + - - -
66C PHE* 4.2 5.5 + - - -
69C PRO* 4.8 14.7 - - + +
77C LEU* 3.9 21.8 - - + -
78C PHE* 6.1 1.8 - - - -
81C VAL* 3.8 25.1 - - + -
103C LEU* 3.8 16.8 - - + -
106C GLN* 3.1 52.2 - - + +
107C LEU* 3.7 39.5 - - + -
110C ALA* 4.2 13.0 - - + -
114C ARG* 5.6 1.8 - - - -
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ALA* 2.8 22.9 + - + +
61C VAL* 3.1 17.0 + - + +
63C PHE* 1.3 75.3 - - - +
65C LYS* 1.3 62.9 + - - +
66C PHE* 3.0 39.5 + - + -
106C GLN* 4.8 10.3 - - + -
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.4 24.9 + - - -
36C ALA* 4.8 9.5 - - - +
37C LYS* 5.1 2.4 - - - +
39C LEU* 6.0 2.2 - - - -
61C VAL* 3.2 27.4 + - + +
62C LEU* 3.4 26.5 - - - +
63C PHE 3.2 1.0 - - - -
64C VAL* 1.3 75.2 - - - +
66C PHE* 1.3 66.6 + - - +
67C SER* 3.1 29.8 + - - +
68C MET* 4.6 18.2 - - + +
69C PRO* 4.8 5.2 - - + +
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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