Contacts of the helix formed by residues 31 - 51 (chain C) in PDB entry 3P4P
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 THR 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU 3.2 7.7 + - - +
28C ARG* 2.7 21.6 + - - +
30C GLY* 1.3 77.0 - - - +
32C ALA* 1.3 62.0 + - - +
34C PRO* 3.1 8.5 - - - +
35C ALA* 3.1 23.0 + - - +
78C ALA* 3.4 35.7 - - + +
81C LEU* 3.9 16.8 - - + -
82C HIS* 3.7 30.1 + - + +
81D ARG* 3.1 12.8 + - - -
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Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLU 3.5 12.0 + - - +
30C GLY 2.9 0.2 + - - -
31C THR* 1.3 82.1 + - - +
33C VAL* 1.3 56.6 + - + +
35C ALA* 3.2 8.0 + - - +
36C VAL* 2.9 27.9 + - - +
77D CYS* 6.3 1.1 - - - -
78D GLY* 3.3 27.8 - - - +
81D ARG* 3.4 26.4 - - + +
82D MET* 3.4 13.5 - - + +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLU 5.9 0.2 - - - +
30C GLY* 2.9 13.0 + - - +
32C ALA* 1.3 75.0 - - + +
34C PRO* 1.4 76.8 - - + +
35C ALA 3.2 0.3 + - - -
36C VAL* 3.2 6.1 + - - +
37C TRP* 2.9 22.1 + - + +
82D MET* 3.3 27.0 - - + +
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Residues in contact with PRO 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLY 3.2 11.2 - - - +
31C THR* 3.1 17.0 - - - +
33C VAL* 1.4 89.6 - - + +
35C ALA* 1.3 63.6 + - - +
37C TRP* 3.5 13.1 - - + +
38C PHE* 2.9 25.5 + - - +
71C ILE* 6.4 0.2 - - + -
74C ILE* 5.2 9.2 - - + -
75C THR* 3.9 32.4 - - + +
78C ALA* 4.0 18.4 - - + -
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C THR* 3.1 16.4 + - - +
32C ALA* 3.2 14.1 - - - +
33C VAL 3.0 0.8 - - - -
34C PRO* 1.3 80.5 - - - +
36C VAL* 1.3 62.5 + - - +
38C PHE* 3.3 7.5 + - - +
39C SER* 3.2 18.8 + - - -
75C THR* 5.7 0.4 - - - -
24D SER* 5.5 9.2 - - - +
32D ILE* 6.5 0.9 - - - -
74D PRO* 4.6 22.5 - - + +
77D CYS* 6.5 0.9 - - - -
78D GLY* 5.0 2.0 - - - -
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA 2.9 5.1 + - - -
33C VAL 3.6 0.7 - - - +
35C ALA* 1.3 77.3 - - - +
37C TRP* 1.3 56.6 + - - +
39C SER* 3.2 5.9 + - - -
40C ILE* 2.9 34.5 + - + +
74D PRO 4.9 0.9 - - - -
75D LEU* 3.8 30.7 - - + +
78D GLY* 3.6 26.9 - - - -
79D LEU* 3.9 15.7 - - + +
82D MET* 3.4 33.9 - - + -
103D LEU* 6.3 0.7 - - + -
107D LEU* 5.9 0.9 - - + -
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Residues in contact with TRP 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 2.9 16.4 + - + +
34C PRO* 3.2 12.8 + - + +
36C VAL* 1.3 75.1 - - - +
38C PHE* 1.3 69.8 + - - +
40C ILE* 3.1 21.5 + - + +
41C GLU* 2.9 54.7 + - + +
44C PHE* 6.2 2.7 - + - -
62C PHE* 4.1 18.2 - + - -
68C ILE* 4.4 10.8 - - + -
71C ILE* 3.5 30.7 - - + +
72C ASN* 3.2 21.2 - - - +
75C THR* 3.4 20.5 + - + -
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Residues in contact with PHE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C PRO 2.9 19.3 + - - +
35C ALA* 3.6 5.8 - - - +
37C TRP* 1.3 73.8 - - - +
39C SER* 1.3 58.2 + - - +
41C GLU* 3.3 22.5 + - + +
42C LEU* 3.0 67.1 + - + +
72C ASN* 4.9 0.9 - - - -
75C THR* 3.9 13.0 - - + -
28D ALA* 5.1 2.2 - - + -
31D MET* 3.7 21.1 - - + -
32D ILE* 3.5 53.8 - - + -
35D VAL* 4.2 20.4 - - + -
36D GLY* 4.8 2.5 - - - -
70D MET* 4.3 12.8 - - + -
74D PRO* 6.5 0.9 - - + -
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Residues in contact with SER 39 (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 ALA 3.2 10.3 + - - -
36C VAL* 3.2 10.6 + - - -
38C PHE* 1.3 72.9 - - - +
40C ILE* 1.3 68.3 + - - +
42C LEU* 3.4 9.7 + - - +
43C ILE* 3.2 26.4 + - - +
70D MET 3.9 1.4 + - - -
71D ILE* 2.3 38.4 + - - +
74D PRO* 3.8 11.1 - - - +
75D LEU* 3.6 21.0 - - - +
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 2.9 26.7 + - + +
37C TRP* 3.2 24.9 - - + +
39C SER* 1.3 75.8 - - - +
41C GLU* 1.3 56.3 + - + +
43C ILE* 2.8 33.8 + - + +
44C PHE* 3.2 37.1 + - + -
75D LEU* 4.7 2.7 - - + -
107D LEU* 4.1 29.2 - - + -
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Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C TRP* 2.9 57.5 + - + +
38C PHE* 3.6 24.2 - - + +
40C ILE* 1.3 76.0 - - + +
42C LEU* 1.3 64.8 + - + +
44C PHE* 3.2 12.9 + - + +
45C GLY 3.1 16.8 + - - -
59C PHE* 3.4 17.9 - - + -
62C PHE* 3.8 12.4 - - + -
63C LEU* 4.0 7.6 - - + +
68C ILE* 3.6 12.6 - - - +
72C ASN* 3.0 32.1 + - - +
35D VAL* 5.9 2.0 - - + +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 3.0 58.9 + - + +
39C SER* 3.6 3.1 - - - +
40C ILE 3.2 0.2 - - - -
41C GLU* 1.3 77.5 - - + +
43C ILE* 1.3 56.2 + - - +
45C GLY* 3.2 3.0 + - - +
46C LEU* 2.9 24.4 + - - +
59C PHE* 5.3 1.6 - - + -
31D MET* 5.0 3.8 - - + -
35D VAL* 4.1 22.7 - - + -
67D LEU* 5.8 6.5 - - + -
70D MET* 3.7 29.4 - - + +
71D ILE* 3.4 34.3 - - + +
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Residues in contact with ILE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER 3.2 18.3 + - - +
40C ILE* 2.8 17.9 + - + +
42C LEU* 1.3 73.6 - - - +
44C PHE* 1.3 71.6 + - + +
45C GLY 3.1 0.9 + - - -
46C LEU* 3.1 11.9 + - + +
47C PHE* 3.1 42.3 + - + -
71D ILE* 3.6 22.9 - - + -
75D LEU* 4.6 1.8 - - + -
107D LEU* 4.0 31.9 - - + +
110D VAL* 4.2 12.3 - - + -
111D THR* 3.8 17.3 - - - +
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Residues in contact with PHE 44 (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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37C TRP* 6.2 2.7 - + - -
40C ILE* 3.2 27.7 + - + -
41C GLU* 3.2 13.4 + - + +
43C ILE* 1.3 80.4 - - + +
45C GLY* 1.3 51.5 + - - +
47C PHE* 3.2 4.8 + - - +
48C ALA* 2.7 38.3 + - - +
59C PHE* 3.3 19.5 - + + -
62C PHE* 5.1 18.4 - + - -
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Residues in contact with GLY 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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41C GLU 3.1 4.6 + - - -
42C LEU* 3.5 4.0 - - - -
43C ILE 3.1 0.4 - - - -
44C PHE* 1.3 70.0 - - - +
46C LEU* 1.3 56.1 + - - +
47C PHE 2.9 0.9 - - - -
49C LEU* 2.8 39.3 + - - +
56C TRP* 4.1 12.0 - - - -
59C PHE* 2.8 31.6 - - - -
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Residues in contact with LEU 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 LEU 2.9 15.4 + - - +
43C ILE* 3.5 11.0 - - - +
45C GLY* 1.3 71.1 - - - +
47C PHE* 1.3 62.3 + - + +
49C LEU* 3.7 15.0 - - + +
50C LYS* 3.1 29.3 + - + +
58D ALA* 5.3 7.0 - - + +
64D ARG* 6.1 0.7 - - - +
67D LEU* 5.1 13.0 - - + -
71D ILE* 4.5 8.7 - - + -
111D THR* 3.6 19.5 - - + +
114D GLY* 3.5 37.0 - - - +
115D VAL* 3.5 32.8 - - + -
117D THR* 6.2 0.9 - - + -
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Residues in contact with PHE 47 (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 ILE* 3.1 44.7 + - + +
44C PHE* 3.9 4.5 - - - +
45C GLY 2.9 0.8 - - - -
46C LEU* 1.3 82.8 - - + +
48C ALA* 1.3 61.2 + - - +
49C LEU 3.0 1.1 - - - -
50C LYS* 2.9 5.7 + - + +
51C ASN* 2.8 37.9 + - - +
110D VAL* 4.0 21.8 - - + -
113D ILE* 4.5 7.4 - - + -
114D GLY* 3.6 32.5 - - - -
118D ILE* 4.2 35.0 - - + -
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Residues in contact with ALA 48 (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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44C PHE 2.7 20.9 + - - +
45C GLY 4.2 0.4 - - - +
47C PHE* 1.3 73.1 - - - +
49C LEU* 1.3 61.3 + - - +
51C ASN* 3.2 6.2 + - - -
52C GLY 3.2 22.7 - - - +
55C ALA* 3.6 36.5 - - + +
56C TRP* 3.3 9.5 + - + +
59C PHE* 3.9 16.6 - - + -
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Residues in contact with LEU 49 (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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45C GLY 2.8 20.2 + - - +
46C LEU* 3.7 13.7 - - + +
48C ALA* 1.3 79.6 - - - +
50C LYS* 1.3 62.2 + - - +
51C ASN 3.6 0.2 + - - -
52C GLY* 3.6 6.1 + - - -
56C TRP* 3.3 36.7 - - + -
51D TYR* 3.9 9.1 + - + +
54D VAL* 3.4 32.8 - - + -
55D LEU* 3.6 35.7 - - + +
58D ALA* 3.4 33.2 - - + -
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Residues in contact with LYS 50 (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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46C LEU* 3.1 21.2 + - + +
47C PHE* 2.9 16.0 + - + +
49C LEU* 1.3 85.1 - - - +
51C ASN* 1.3 60.7 + - - +
52C GLY* 3.1 4.7 + - - -
55D LEU* 5.7 4.0 - - - -
59D GLN* 4.3 12.5 + - - -
114D GLY* 4.5 8.1 - - - +
117D THR* 3.6 31.3 - - + +
118D ILE* 3.1 58.5 + - + +
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Residues in contact with ASN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 2.8 22.4 + - - +
48C ALA* 3.2 1.6 + - - -
50C LYS* 1.3 81.1 + - - +
52C GLY* 1.3 62.3 + - - +
54C GLU* 4.8 4.7 + - - +
55C ALA* 4.0 20.7 + - + +
118D ILE* 4.3 22.0 - - - +
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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