Contacts of the helix formed by residues 32 - 55 (chain L) in PDB entry 5PRC
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 GLY 32 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L THR* 5.2 2.0 - - - -
22L PHE* 2.7 35.2 + - - +
23L ASP 4.6 0.2 - - - -
30L PHE* 3.7 19.5 - - - -
31L VAL* 1.3 82.0 - - - +
33L PHE* 1.3 67.1 + - - -
34L PHE 3.1 3.3 + - - -
35L GLY 3.2 3.8 + - - -
36L VAL* 3.2 8.5 + - - +
106L GLU* 3.8 4.9 - - - -
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Residues in contact with PHE 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L THR* 5.6 0.6 - - - +
17L ILE* 3.4 58.0 + - + +
18L GLY* 5.2 3.6 - - - -
22L PHE* 3.5 35.6 - + + +
32L GLY* 1.3 72.1 - - - -
34L PHE* 1.3 80.3 + + + +
36L VAL* 3.2 10.8 + - + +
37L SER* 3.0 33.4 + - - -
106L GLU* 4.0 3.8 + - - -
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Residues in contact with PHE 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258H LEU* 6.2 1.3 - - + -
16L LEU* 3.8 15.9 - - + -
17L ILE* 3.4 33.9 - - + -
32L GLY 3.1 0.8 - - - -
33L PHE* 1.3 89.5 - + - +
35L GLY* 1.3 57.9 + - - +
36L VAL 3.1 1.3 - - - -
37L SER* 3.4 11.5 + - - +
38L ALA* 2.7 36.1 + - - +
99L SER* 3.4 23.8 - - - +
102L LEU* 3.3 47.3 - - + -
103L ARG* 3.6 9.9 - - + +
106L GLU* 3.5 24.9 - - - +
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Residues in contact with GLY 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L VAL* 3.2 24.2 + - - -
32L GLY 3.2 4.0 + - - -
34L PHE* 1.3 76.3 - - - +
36L VAL* 1.3 56.8 + - - +
38L ALA* 3.6 1.6 - - - +
39L ILE* 3.0 36.8 + - - +
103L ARG* 3.7 16.5 - - - +
501M MQ7 3.7 13.5 - - - -
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Residues in contact with VAL 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L PHE* 3.6 36.6 - - + -
31L VAL* 3.8 12.6 - - + -
32L GLY 3.2 12.5 + - - +
33L PHE* 3.2 15.1 + - + +
34L PHE 3.1 0.4 - - - -
35L GLY* 1.3 77.6 - - - +
37L SER* 1.3 61.7 + - - +
39L ILE* 3.5 5.0 + - - +
40L PHE* 3.1 22.4 + - + +
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Residues in contact with SER 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L PHE* 3.0 20.8 + - - -
34L PHE* 3.4 23.1 + - - -
36L VAL* 1.3 76.0 - - - +
38L ALA* 1.3 64.6 + - - +
40L PHE* 3.1 9.0 + - - +
41L PHE* 3.0 40.1 + - - -
99L SER* 2.9 22.1 + - - -
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Residues in contact with ALA 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L PHE 2.7 24.3 + - - +
35L GLY* 3.6 7.2 - - - +
37L SER* 1.3 72.6 + - - +
39L ILE* 1.3 63.7 + - + +
41L PHE* 3.2 2.1 + - - +
42L ILE* 3.0 34.0 + - + +
96L ALA* 4.5 9.3 - - - +
99L SER* 3.3 19.6 + - - -
100L TRP* 4.4 24.5 - - + +
103L ARG* 5.5 1.1 - - - -
501M MQ7 5.3 0.4 - - + -
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Residues in contact with ILE 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L GLY 3.0 19.1 + - - +
36L VAL* 3.8 5.6 - - - +
38L ALA* 1.3 76.3 - - + +
40L PHE* 1.3 64.9 + - - +
42L ILE* 3.7 18.1 - - + +
43L PHE* 3.1 26.9 + - + +
501M MQ7 3.7 68.2 - - + -
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Residues in contact with PHE 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L VAL* 3.1 15.6 + - + +
37L SER* 3.1 14.7 + - - +
39L ILE* 1.3 79.9 - - - +
41L PHE* 1.3 78.3 + + - +
43L PHE* 3.4 12.6 + + - -
44L LEU* 3.0 63.7 + - + +
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Residues in contact with PHE 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L SER* 3.0 40.8 + - - +
38L ALA 3.8 3.1 - - - +
40L PHE* 1.3 94.9 - + - +
42L ILE* 1.3 58.2 + - - +
44L LEU* 3.3 7.2 - - + +
45L GLY* 2.7 31.4 + - - -
91L VAL* 4.6 13.2 - - + -
92L CYS* 3.7 40.0 - - - +
95L GLY* 3.6 32.5 - - - -
96L ALA* 3.8 5.8 - - - +
99L SER* 4.4 1.3 - - - -
402L BPB 4.2 1.8 - - - +
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Residues in contact with ILE 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ALA* 3.0 32.9 + - + +
39L ILE* 3.7 13.7 - - + +
41L PHE* 1.3 73.3 - - - +
43L PHE* 1.3 58.7 + - + +
45L GLY* 3.0 2.3 + - - -
46L VAL* 2.7 50.9 + - + +
96L ALA* 4.3 3.8 - - + -
100L TRP* 5.3 0.4 - - + -
402L BPB 4.1 50.4 - - + +
501M MQ7 4.0 26.9 - - + -
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Residues in contact with PHE 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L ILE* 3.1 16.6 + - + +
40L PHE* 3.4 15.3 - + - -
42L ILE* 1.3 81.8 - - - +
44L LEU* 1.3 95.2 + - + +
46L VAL* 3.8 4.1 - - - +
47L SER* 2.8 44.5 + - - -
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Residues in contact with LEU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L PHE* 3.0 49.4 + - + +
41L PHE* 3.3 11.9 - - + +
43L PHE* 1.3 97.1 - - + +
45L GLY* 1.3 63.8 + - - +
47L SER* 3.0 5.5 + - - -
48L LEU* 3.0 37.7 + - + +
92L CYS* 3.5 19.7 - - - -
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Residues in contact with GLY 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L PHE 2.7 19.2 + - - -
42L ILE 3.6 0.4 - - - -
44L LEU* 1.3 72.1 - - - +
46L VAL* 1.3 56.9 + - - +
48L LEU* 3.2 9.3 + - - +
49L ILE* 2.9 37.0 + - - +
89L ILE* 4.2 4.7 - - - +
92L CYS* 3.6 20.6 - - - -
402L BPB 4.5 9.0 - - - -
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Residues in contact with VAL 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L ILE* 2.7 32.4 + - + +
43L PHE* 4.0 4.5 - - - +
45L GLY* 1.3 76.3 - - - +
47L SER* 1.3 63.8 + - - +
49L ILE* 3.3 10.5 + - + +
50L GLY* 3.0 18.7 + - - -
304L BCB 4.4 33.0 - - + -
402L BPB 4.8 5.8 - - + -
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Residues in contact with SER 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L PHE* 2.8 42.4 + - - -
44L LEU* 3.0 6.5 + - - -
46L VAL* 1.3 78.6 - - - +
48L LEU* 1.3 64.1 + - - +
50L GLY* 3.1 3.2 + - - +
51L TYR* 3.0 22.6 + - - +
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Residues in contact with LEU 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L LEU* 3.0 32.1 + - + +
45L GLY* 3.5 7.0 - - - +
47L SER* 1.3 73.3 - - - +
49L ILE* 1.3 60.7 + - - +
50L GLY 3.1 0.2 + - - -
51L TYR* 3.2 4.5 + - + -
52L ALA* 2.8 35.6 + - - +
85L PHE* 4.3 23.3 - - + +
88L ALA* 4.1 24.9 - - + -
89L ILE* 3.7 14.6 - - + +
92L CYS* 4.0 18.4 - - - -
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Residues in contact with ILE 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L GLY 2.9 21.9 + - - +
46L VAL* 3.5 9.9 - - + +
48L LEU* 1.3 74.6 - - - +
50L GLY* 1.3 56.4 + - - +
52L ALA* 3.8 0.5 - - - +
53L ALA* 2.8 36.3 + - + +
64L ILE* 5.9 2.5 - - + -
66L ILE* 3.8 21.4 - - + +
89L ILE* 3.9 20.4 - - + -
148L TYR* 6.1 2.2 - - + -
304L BCB 3.9 21.8 - - + -
402L BPB 3.7 37.7 - - + -
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Residues in contact with GLY 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L VAL 3.0 13.8 + - - -
47L SER* 3.1 4.4 + - - -
49L ILE* 1.3 75.0 - - - +
51L TYR* 1.3 59.8 + - - +
53L ALA* 3.3 3.6 + - - -
54L SER* 2.9 31.3 + - - -
59L TRP* 3.7 11.9 - - - -
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Residues in contact with TYR 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L SER 3.0 15.3 + - - +
48L LEU* 3.9 4.9 - - + +
50L GLY* 1.3 71.5 - - - +
52L ALA* 1.3 69.9 + - - +
54L SER* 2.7 25.4 + - - -
55L GLN* 3.0 30.6 + - + +
80L LEU* 4.9 7.7 - - + +
85L PHE* 3.1 37.9 - + + -
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Residues in contact with ALA 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L LEU 2.8 22.2 + - - +
49L ILE 3.8 2.0 - - - +
51L TYR* 1.3 73.1 - - - +
53L ALA* 1.3 64.1 + - - +
55L GLN* 2.9 19.1 + - - +
56L GLY* 3.5 4.3 + - - -
66L ILE* 4.0 21.1 - - + -
81L LEU* 4.7 2.8 - - + +
85L PHE* 3.5 43.2 - - + -
89L ILE* 4.7 0.2 - - + -
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Residues in contact with ALA 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L ILE* 2.8 25.6 + - + +
52L ALA* 1.3 74.9 - - - +
54L SER* 1.3 61.2 + - - +
56L GLY* 3.2 12.5 + - - +
58L THR* 3.7 17.7 - - - +
59L TRP* 3.7 26.7 - - + -
64L ILE* 3.8 29.1 - - + +
66L ILE* 4.6 4.7 - - + +
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Residues in contact with SER 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L GLY 2.9 15.7 + - - -
51L TYR* 2.7 24.5 + - - -
53L ALA* 1.3 73.3 - - - +
55L GLN* 1.3 72.8 + - - +
56L GLY 3.1 11.9 + - - +
59L TRP* 3.4 26.2 + - - +
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Residues in contact with GLN 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L TYR* 3.2 41.1 - - + +
52L ALA 2.9 9.7 + - - +
54L SER* 1.3 91.0 + - - +
56L GLY* 1.3 56.7 + - - +
81L LEU* 3.6 42.5 - - + +
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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