Contacts of the helix formed by residues 38 - 58 (chain C) in PDB entry 1AYP
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 ASP 38 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 2.8 33.3 + - - -
36C PRO 3.3 2.6 + - - -
37C LYS* 1.4 78.8 - - - +
39C ALA* 1.3 59.6 + - - +
40C THR* 3.8 6.3 + - - -
41C ASP* 2.9 28.1 + - - +
42C ARG* 3.0 34.9 + - - +
104C THR* 3.9 20.8 - - + +
106C ASN* 4.4 0.2 - - - +
109C TYR* 3.6 14.4 - - + -
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 1.3 72.1 - - - +
40C THR* 1.3 69.2 + - - +
42C ARG* 3.1 28.2 + - - +
43C CYS* 3.2 13.2 + - - -
101C ASN* 3.0 28.3 - - - +
104C THR* 4.1 13.5 - - + +
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Residues in contact with THR 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 3.7 33.0 - - + +
24C TYR* 4.0 18.4 - - + -
28C CYS* 4.2 0.3 - - - -
38C ASP* 3.4 3.7 + - - -
39C ALA* 1.3 75.0 - - - +
41C ASP* 1.4 55.9 + - - +
43C CYS* 3.0 31.2 + - - +
44C CYS 3.8 0.5 + - - -
98C PHE* 3.6 25.5 - - + +
101C ASN* 3.6 28.1 + - + +
102C LYS 4.9 0.4 - - - +
104C THR* 3.8 11.1 - - - +
105C TYR* 4.0 15.2 - - + -
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Residues in contact with ASP 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 3.9 7.2 - - + -
25C GLY* 4.3 2.5 - - - -
26C CYS* 3.0 23.5 + - - +
27C HIS* 2.9 27.0 + - - +
28C CYS* 3.6 14.5 + - - -
36C PRO* 3.1 10.9 - - + +
37C LYS* 2.8 27.4 + - + +
38C ASP* 2.9 23.1 + - - +
40C THR* 1.4 71.7 - - - +
42C ARG* 1.3 62.7 + - - +
44C CYS* 3.1 11.1 + - - +
45C VAL* 3.2 12.5 + - - +
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PRO* 3.7 20.8 - - + +
38C ASP 3.0 23.2 + - - +
39C ALA* 3.1 19.0 + - - +
41C ASP* 1.3 69.9 - - - +
43C CYS* 1.3 67.1 + - - +
44C CYS 2.9 2.4 + - - -
45C VAL* 3.0 21.5 + - + +
46C THR* 3.3 15.1 + - - -
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Residues in contact with CYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ALA 3.2 13.9 + - - -
40C THR* 3.0 13.8 + - - +
42C ARG* 1.3 76.1 - - - +
44C CYS* 1.3 57.3 + - - +
46C THR* 3.7 7.2 - - - +
47C HIS* 3.2 24.8 + - - +
94C ALA* 4.6 7.6 - - - +
97C CYS* 2.0 64.8 - - + -
98C PHE* 3.5 19.1 - - + -
101C ASN* 3.7 8.7 - - - -
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Residues in contact with CYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C HIS* 3.8 4.0 - - - -
28C CYS* 2.0 68.0 - - - +
41C ASP 3.1 6.5 + - - +
42C ARG 3.0 0.6 - - - -
43C CYS* 1.3 77.7 - - - +
45C VAL* 1.4 65.7 + - - +
46C THR 3.1 1.3 - - - -
47C HIS* 3.8 0.5 - - - +
48C ASP* 2.9 28.2 + - - +
98C PHE* 3.4 22.2 - - - -
203C INB 3.5 15.9 - - + +
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Residues in contact with VAL 45 (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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27C HIS* 4.1 25.1 - - + +
36C PRO* 4.1 19.5 - - + -
41C ASP 3.2 15.5 + - - +
42C ARG* 3.0 15.2 + - + +
44C CYS* 1.4 74.4 - - - +
46C THR* 1.3 73.5 + - - +
48C ASP* 3.1 7.1 + - - +
49C CYS* 3.0 30.6 + - - -
122C PRO* 4.1 26.5 - - + -
123C ARG* 4.9 2.9 - - - +
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Residues in contact with THR 46 (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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42C ARG 3.3 9.1 + - - -
43C CYS* 3.7 11.1 - - - +
45C VAL* 1.3 85.0 - - - +
47C HIS* 1.3 62.8 + - - +
49C CYS* 3.0 18.0 + - + +
50C CYS* 3.0 14.2 + - + +
93C ALA* 6.2 3.8 - - + -
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Residues in contact with HIS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.4 26.9 - + - -
43C CYS 3.2 13.8 + - - +
44C CYS 3.2 2.2 + - - -
46C THR* 1.3 76.6 - - - +
48C ASP* 1.4 63.7 + - - +
50C CYS* 2.8 18.7 + - - +
51C TYR* 2.9 37.5 + + - +
90C CYS* 3.3 33.0 - - - -
91C ASP* 3.2 22.8 + - - -
94C ALA* 3.7 15.7 - - + -
203C INB 2.8 38.4 + - + +
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Residues in contact with ASP 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C HIS* 3.4 16.3 + - - +
31C GLY 3.0 11.3 - - - +
32C GLY* 4.6 0.2 - - - -
44C CYS 2.9 13.8 + - - +
45C VAL* 3.2 9.9 - - - +
47C HIS* 1.4 74.6 - - - +
49C CYS* 1.4 55.6 + - - +
51C TYR* 3.3 2.4 + - - -
52C LYS* 2.9 28.2 + - - +
203C INB 2.7 55.6 + - + +
305C CA 2.4 31.2 - - - -
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Residues in contact with CYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 3.0 22.8 + - - -
46C THR* 3.0 13.6 + - + +
48C ASP* 1.4 75.1 - - - +
50C CYS* 1.3 63.6 + - - +
51C TYR 3.2 0.5 + - - -
52C LYS* 4.1 4.7 - - - +
53C ARG* 3.4 26.2 + - - +
56C LYS* 5.4 0.2 + - - -
123C ARG* 4.4 6.3 - - - -
124C CYS* 2.0 61.4 - - + +
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Residues in contact with CYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 3.0 12.0 + - + +
47C HIS* 2.8 11.3 + - - +
49C CYS* 1.3 72.0 - - - +
51C TYR* 1.3 58.3 + - - +
53C ARG* 3.6 22.6 - - - +
54C LEU* 3.2 30.0 + - - +
86C GLN* 4.2 5.6 - - - -
90C CYS* 2.0 54.1 - - - -
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Residues in contact with TYR 51 (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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1C ASN 4.9 3.8 + - - -
2C LEU* 5.0 3.2 - - + +
5C PHE* 4.7 5.2 - - - +
47C HIS* 2.9 36.1 + + - +
48C ASP* 3.6 7.2 - - - +
49C CYS 3.2 0.2 - - - -
50C CYS* 1.3 72.5 - - - +
52C LYS* 1.3 57.9 + - - +
54C LEU* 2.7 26.9 + - + +
55C GLU* 3.0 19.2 + - - +
61C THR* 3.8 25.7 + - + +
62C LYS* 4.0 23.2 + - + -
87C LEU* 3.5 29.5 - - + +
90C CYS* 3.6 15.9 - - - -
91C ASP* 2.7 22.7 + - - -
203C INB 3.7 39.0 - - + +
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Residues in contact with LYS 52 (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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48C ASP 2.9 20.2 + - - +
49C CYS* 4.1 5.4 - - - +
51C TYR* 1.3 69.7 - - - +
53C ARG* 1.3 62.4 + - - +
55C GLU* 3.3 16.7 + - - +
56C LYS* 2.9 51.0 + - + +
123C ARG* 3.7 20.0 - - - +
124C CYS* 3.3 32.1 - - - -
203C INB 3.6 29.6 - - - +
115E LYS* 5.6 0.7 - - + -
118E ARG* 3.9 29.5 - - - +
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Residues in contact with ARG 53 (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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49C CYS 3.4 14.1 + - - +
50C CYS* 3.6 22.4 + - - +
51C TYR 3.2 0.2 - - - -
52C LYS* 1.3 78.3 - - - +
54C LEU* 1.3 83.0 + - - +
56C LYS* 3.5 28.9 + - - +
57C ARG* 3.3 23.0 + - - +
86C GLN* 3.4 32.1 + - - +
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Residues in contact with LEU 54 (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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50C CYS* 3.2 15.4 + - - +
51C TYR* 2.7 15.3 + - - +
53C ARG* 1.3 98.3 - - - +
55C GLU* 1.3 58.8 + - - +
57C ARG* 3.4 4.7 + - + +
58C GLY 3.4 2.8 + - - -
59C CYS* 2.9 48.7 + - + +
60C GLY 5.3 0.4 - - - +
61C THR* 3.6 11.2 - - + -
83C CYS 4.9 1.6 - - - +
86C GLN* 3.9 28.7 - - + +
87C LEU* 3.9 42.4 - - + +
90C CYS* 4.4 7.6 - - - -
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Residues in contact with GLU 55 (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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51C TYR* 3.0 22.9 + - - +
52C LYS* 3.3 18.7 + - - +
54C LEU* 1.3 73.6 - - - +
56C LYS* 1.4 57.5 + - - +
58C GLY* 2.7 26.5 + - - -
59C CYS 3.5 10.3 + - - +
61C THR* 4.1 19.9 + - + +
62C LYS* 5.1 4.1 + - - -
203C INB 4.0 15.9 - - - +
63D PHE 5.8 0.3 - - - +
64D LEU* 3.9 10.4 - - + +
84D ARG* 3.1 13.1 + - - +
115E LYS* 4.9 15.1 - - - +
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Residues in contact with LYS 56 (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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52C LYS* 2.9 50.2 + - + +
53C ARG* 3.5 34.0 - - + +
55C GLU* 1.4 72.4 - - - +
57C ARG* 1.3 58.1 + - - +
124C CYS* 6.1 2.8 - - - +
81D ASP* 4.2 2.1 - - - +
84D ARG* 2.9 29.3 + - - +
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ARG 3.3 12.2 + - - +
54C LEU* 3.8 6.7 - - + +
55C GLU 3.1 1.4 + - - -
56C LYS* 1.3 79.3 - - - +
58C GLY* 1.3 56.0 + - - +
59C CYS* 3.4 9.9 - - - +
81D ASP* 3.2 17.9 - - - +
83D CYS* 5.2 1.4 - - - -
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Residues in contact with GLY 58 (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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55C GLU 2.7 14.5 + - - -
56C LYS 3.2 1.0 + - - -
57C ARG* 1.3 72.5 - - - +
59C CYS* 1.3 61.6 + - - +
60D GLY 3.1 20.8 + - - -
64D LEU* 3.6 10.0 - - - +
81D ASP* 3.4 8.3 - - - -
83D CYS* 3.5 22.3 - - - -
84D ARG* 3.4 16.8 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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