Contacts of the helix formed by residues 22 - 43 (chain T) in PDB entry 3P71
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 ASN 22 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T ASP 2.8 1.6 + - - +
21T GLU* 1.3 77.2 - - + +
23T ASP* 1.3 64.0 + - - +
24T GLU 3.4 1.8 - - - -
25T GLY 3.2 4.2 + - - -
26T VAL* 3.0 37.5 + - + +
173T ARG* 6.2 0.2 - - - +
203T TYR 4.8 4.8 + - - -
249T GLN 3.2 16.4 - - - +
250T CYS* 3.5 0.3 - - - -
251T ASP* 2.9 59.4 + - - +
253T ALA* 5.1 4.2 - - - +
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Residues in contact with ASP 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T ASP* 2.9 34.3 + - - +
22T ASN* 1.3 80.9 + - - +
24T GLU* 1.3 61.1 + - - +
26T VAL* 3.4 7.0 + - - +
27T ARG* 2.9 53.4 + - - +
123T PHE* 4.0 12.9 - - + -
173T ARG* 2.8 42.1 + - - -
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Residues in contact with GLU 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T ASP 4.5 1.6 + - - -
21T GLU 4.7 5.3 + - - +
22T ASN 3.4 0.2 - - - -
23T ASP* 1.3 75.8 - - - +
25T GLY* 1.3 58.3 + - - +
27T ARG* 3.3 28.1 + - - +
28T GLY* 3.0 24.8 + - - -
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Residues in contact with GLY 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21T GLU 5.2 0.6 + - - -
22T ASN 3.2 5.0 + - - -
24T GLU* 1.3 79.2 - - - +
26T VAL* 1.3 61.0 + - - +
28T GLY* 3.2 11.1 + - - -
29T THR* 3.6 13.9 + - - +
248T ARG* 4.1 12.3 + - - +
249T GLN* 3.4 27.7 + - - +
250T CYS* 3.9 10.8 - - - +
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Residues in contact with VAL 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C AN6 3.5 39.2 - - + +
22T ASN* 3.0 40.1 + - - +
23T ASP* 3.8 7.4 - - - +
25T GLY* 1.3 74.6 - - - +
27T ARG* 1.3 60.6 + - - +
29T THR* 2.5 28.0 + - - -
123T PHE* 4.4 6.3 - - + -
203T TYR* 3.7 39.0 - - + +
250T CYS* 4.2 9.0 - - - -
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Residues in contact with ARG 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C AN6 4.0 9.4 - - - +
23T ASP* 2.9 38.1 + - - +
24T GLU* 3.3 36.9 + - - +
26T VAL* 1.3 75.6 - - - +
28T GLY* 1.3 62.1 + - - +
29T THR 3.2 0.7 + - - -
30T CYS* 3.4 19.6 + - - +
31T GLU* 4.3 1.4 + - - +
123T PHE* 3.5 42.6 - - + +
125T MET* 3.6 39.2 - - + +
126T ILE* 3.8 15.2 - - + +
129T ARG* 5.9 0.2 + - - -
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Residues in contact with GLY 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24T GLU 3.0 14.1 + - - -
25T GLY* 3.2 7.4 + - - -
26T VAL 3.2 0.6 - - - -
27T ARG* 1.3 76.8 - - - +
29T THR* 1.3 61.1 + - - +
30T CYS 3.2 0.2 - - - -
31T GLU* 3.3 19.9 + - - +
32T ASP 3.6 0.2 + - - -
248T ARG* 3.2 20.0 + - - -
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Residues in contact with THR 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C LEU* 3.8 14.7 - - + +
310C AN6 3.4 27.2 - - - +
25T GLY 3.7 11.4 - - - +
26T VAL 2.5 21.9 + - - +
27T ARG 3.1 0.2 - - - -
28T GLY* 1.3 74.8 - - - +
30T CYS* 1.3 64.2 + - - +
31T GLU 3.2 0.2 - - - -
32T ASP* 3.1 4.6 + - - +
33T ALA 3.0 20.3 + - - -
203T TYR* 3.6 25.8 + - + +
248T ARG* 4.1 15.5 - - - +
250T CYS* 3.8 17.5 - - - -
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Residues in contact with CYS 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C AN6 3.3 32.1 - - - +
27T ARG 3.4 12.5 + - - +
28T GLY 3.2 0.2 - - - -
29T THR* 1.3 81.4 + - - +
31T GLU* 1.3 59.5 + - - +
33T ALA* 4.1 0.9 - - - +
34T SER* 2.7 40.9 + - - -
100T GLY* 3.9 24.9 - - - -
101T MET* 4.0 22.9 - - - -
126T ILE* 4.1 12.3 - - + -
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Residues in contact with GLU 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T ARG 4.3 1.2 + - - +
28T GLY* 3.3 14.1 + - - +
29T THR 3.2 0.6 - - - -
30T CYS* 1.3 79.9 - - - +
32T ASP* 1.3 63.7 + - - +
34T SER* 3.8 4.7 - - - -
35T LEU* 3.1 39.1 + - + +
55T VAL* 5.2 6.1 - - + -
56T ARG* 3.7 36.2 + - - +
129T ARG* 5.1 11.8 + - - +
248T ARG* 5.5 0.8 + - - +
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Residues in contact with ASP 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ASP* 4.7 11.1 - - - +
307C TYR 4.7 4.9 + - - +
309C LEU* 3.4 20.9 - - + +
28T GLY 3.6 2.4 + - - -
29T THR* 3.1 10.8 + - - +
31T GLU* 1.3 79.3 - - - +
33T ALA* 1.3 63.2 + - - +
35T LEU* 3.3 12.0 + - - +
36T CYS* 3.0 38.9 + - - -
62T LYS* 5.4 4.8 + - - -
70T TYR* 4.7 1.9 + - - -
248T ARG* 3.0 42.1 + - - +
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Residues in contact with ALA 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C LEU* 3.4 30.7 - - - +
310C AN6 4.0 22.7 - - - +
29T THR 3.0 10.9 + - - +
30T CYS 4.2 2.0 - - - +
32T ASP* 1.3 76.0 - - - +
34T SER* 1.3 57.2 - - - +
36T CYS* 3.3 1.2 + - - +
37T LYS* 2.8 38.1 + - + +
70T TYR* 3.6 17.9 + - + +
73T ARG* 4.4 1.1 - - - +
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Residues in contact with SER 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C AN6 5.2 3.1 + - - -
30T CYS* 2.7 24.4 + - - -
31T GLU* 3.8 5.6 - - - -
33T ALA* 1.3 77.9 - - - +
35T LEU* 1.3 57.7 + - - +
37T LYS* 3.8 6.4 - - - +
38T ARG* 2.9 25.8 + - - +
51T ILE* 4.0 5.6 - - - +
55T VAL* 3.6 32.5 - - - +
101T MET* 3.4 32.8 + - - +
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Residues in contact with LEU 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31T GLU* 3.1 34.9 + - + +
32T ASP* 3.6 10.1 - - - +
34T SER* 1.3 74.9 - - - +
36T CYS* 1.3 63.2 + - - +
38T ARG* 4.0 2.2 - - - +
39T PHE* 3.1 24.8 + - - +
55T VAL* 3.9 11.2 - - + +
56T ARG* 3.5 65.6 - - + +
58T SER* 4.4 20.1 + - - -
62T LYS* 4.7 20.6 - - - +
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Residues in contact with CYS 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ASP* 5.2 4.7 - - - -
307C TYR 5.2 1.1 - - - -
32T ASP* 3.0 30.1 + - - +
33T ALA 3.7 2.7 - - - +
35T LEU* 1.3 74.7 - - - +
37T LYS* 1.3 65.5 + - - +
39T PHE* 3.3 2.9 + - - +
40T ALA* 3.2 23.6 + - - +
62T LYS* 3.8 36.1 - - - -
66T ILE* 4.2 8.1 - - + -
67T ASN* 4.5 3.7 - - - +
70T TYR* 3.4 40.1 - - + +
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Residues in contact with LYS 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C AN6 3.0 38.9 + - - +
33T ALA* 2.8 24.1 + - - +
34T SER* 3.9 4.0 - - - +
36T CYS* 1.3 73.2 - - - +
38T ARG* 1.3 61.8 + - - +
40T ALA* 3.5 0.9 + - - +
41T VAL* 3.1 28.8 + - - +
46T TRP* 3.9 24.3 - - + -
51T ILE* 3.9 16.8 - - + -
70T TYR* 3.8 17.9 - - + -
73T ARG* 4.1 11.9 - - - +
74T VAL* 4.3 12.8 - - + +
102T ASP* 5.3 7.1 + - - +
198T GLU* 3.0 24.4 + - - -
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Residues in contact with ARG 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T SER 2.9 17.5 + - - +
35T LEU 4.0 2.9 - - - +
37T LYS* 1.3 75.8 - - - +
39T PHE* 1.3 58.8 + - - +
41T VAL* 3.2 4.4 + - + +
42T SER* 2.8 28.4 + - - -
51T ILE* 4.0 19.8 - - + +
52T GLN* 3.6 44.7 + - - +
55T VAL* 2.7 47.3 + - + -
56T ARG* 3.3 11.8 - - - +
57T LEU* 3.1 47.9 - - + +
58T SER 5.6 0.2 - - - +
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Residues in contact with PHE 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T LEU 3.1 18.4 + - - +
36T CYS 3.3 4.4 + - - +
38T ARG* 1.3 76.7 - - - +
40T ALA* 1.3 61.8 + - - +
42T SER* 2.7 31.2 + - - -
43T ILE* 3.2 30.6 + - + +
57T LEU* 4.3 7.0 - - + -
58T SER* 3.7 33.6 - - - +
59T LYS 5.5 1.3 - - - -
60T GLU 4.6 0.9 - - - -
61T ARG* 3.5 46.9 - - + -
62T LYS* 3.5 29.6 - - + -
67T ASN* 3.7 20.2 - - - -
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Residues in contact with ALA 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T CYS 3.2 15.6 + - - +
37T LYS 3.9 0.9 - - - +
39T PHE* 1.3 75.3 - - - +
41T VAL* 1.3 63.6 + - - +
43T ILE* 3.2 13.7 + - - +
44T GLY 3.0 6.6 + - - -
45T TYR* 3.0 35.7 + - + -
46T TRP* 3.7 26.5 - - + -
67T ASN* 4.0 19.9 + - + +
70T TYR* 5.2 1.6 - - + -
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Residues in contact with VAL 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T LYS* 3.1 18.1 + - + +
38T ARG* 3.4 11.4 - - + +
40T ALA* 1.3 77.0 - - - +
42T SER* 1.3 62.1 + - - +
44T GLY* 3.0 14.6 + - - -
45T TYR 4.5 0.2 - - - +
46T TRP* 3.5 54.9 - - + +
47T HIS* 4.8 0.2 - - - -
48T ASP* 3.6 37.0 - - + +
51T ILE* 4.7 5.2 - - + -
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Residues in contact with SER 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T ARG* 2.8 18.7 + - - -
39T PHE* 2.7 24.6 + - - -
41T VAL* 1.3 74.5 - - - +
43T ILE* 1.3 66.0 + - - +
44T GLY 3.3 0.4 + - - -
57T LEU* 3.6 31.4 - - - +
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Residues in contact with ILE 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T PHE* 3.3 26.9 - - + +
40T ALA* 3.4 8.3 - - - +
42T SER* 1.3 88.1 + - - +
44T GLY* 1.3 58.6 + - - +
45T TYR* 3.4 25.1 + - + -
61T ARG* 3.5 21.5 - - - +
67T ASN* 3.8 11.2 - - - +
299T LEU* 3.7 20.8 - - + +
300T GLU* 3.6 26.7 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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