Contacts of the helix formed by residues 52 - 67 (chain D) in PDB entry 4M3P
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 HIS 52 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ARG* 3.3 30.2 + - - -
327C LYS* 5.8 0.2 - - - -
38D TYR* 3.6 38.8 + + + -
48D ALA* 2.7 19.9 + - + +
51D GLU* 1.3 103.5 + - + +
53D PRO* 1.3 65.9 - - - +
54D GLU* 3.1 26.8 + - - +
55D ALA* 3.0 12.4 + - + +
56D VAL* 3.4 8.3 + - - +
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Residues in contact with PRO 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ALA 3.8 5.8 - - - +
49D ALA 3.6 15.9 - - - +
50D VAL* 3.4 17.7 - - - +
51D GLU 3.5 2.5 - - - +
52D HIS* 1.3 90.1 - - - +
54D GLU* 1.3 64.4 + - - +
56D VAL* 3.2 2.4 + - + +
57D ARG* 2.8 49.5 + - - +
106D ILE* 4.0 15.5 - - + +
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Residues in contact with GLU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 3.8 18.3 - - - +
61C ARG* 4.6 21.7 - - - +
38D TYR* 5.1 2.6 + - - -
51D GLU 4.7 0.3 - - - +
52D HIS* 3.2 33.3 + - - +
53D PRO* 1.3 98.5 - - - +
55D ALA* 1.3 58.0 + - - +
57D ARG* 3.7 13.8 - - - +
58D GLN* 3.1 28.2 + - - +
501D SRT 4.0 15.8 - - - +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 3.6 28.9 - - - +
62C GLU* 5.1 0.6 - - - +
33D LEU* 4.2 9.1 - - + +
36D ARG* 5.6 1.2 + - - -
38D TYR* 3.6 34.1 - - + -
52D HIS* 3.0 12.5 + - + +
54D GLU* 1.3 77.2 - - + +
56D VAL* 1.3 67.9 + - + +
58D GLN* 3.5 2.4 + - - +
59D LEU* 3.2 23.2 + - - +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PHE* 4.1 7.1 - - + -
33D LEU* 4.3 10.8 - - + -
48D ALA* 3.7 22.0 - - + +
49D ALA* 3.7 28.5 - - + +
52D HIS 3.4 0.6 + - - +
53D PRO 3.2 6.4 + - - +
55D ALA* 1.3 76.3 - - + +
57D ARG* 1.3 62.5 + - - +
59D LEU* 3.2 4.7 + - - +
60D HIS* 3.1 41.0 + - + +
74D PHE* 4.0 26.9 - - + -
103D ALA* 5.7 0.9 - - - -
106D ILE* 4.0 17.0 - - + -
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Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PRO* 2.8 37.3 + - - +
54D GLU* 3.7 18.7 - - - +
56D VAL* 1.3 74.6 - - - +
58D GLN* 1.3 61.6 + - - +
59D LEU 3.4 0.2 + - - -
60D HIS* 3.4 4.0 + - - +
61D ARG* 3.0 56.7 + - - +
106D ILE* 3.6 25.7 - - + +
109D GLN* 2.7 32.3 + - - +
110D VAL* 4.1 6.7 - - + -
501D SRT 3.0 40.8 + - - +
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Residues in contact with GLN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 6.1 0.2 - - - +
38C TYR* 3.0 32.4 + - - -
54C GLU* 3.6 23.4 - - - +
55C ALA* 3.8 14.4 - - - +
58C GLN* 4.1 28.9 - - + -
36D ARG* 5.2 2.2 - - - +
54D GLU 3.1 19.4 + - - +
55D ALA 4.0 3.6 - - - +
56D VAL 3.3 0.2 - - - -
57D ARG* 1.3 76.0 - - - +
59D LEU* 1.3 58.0 + - - +
61D ARG* 3.1 14.4 + - - +
62D GLU* 2.8 54.8 + - - +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PHE* 3.8 25.4 - - + +
32D ALA* 3.8 20.6 - - + -
33D LEU* 3.6 31.4 - - + -
36D ARG* 3.8 20.4 - - - +
55D ALA 3.2 14.9 + - - +
56D VAL 3.2 6.2 + - - +
58D GLN* 1.3 71.9 - - - +
60D HIS* 1.3 66.1 + - - +
62D GLU* 3.1 23.1 + - - +
63D PHE* 3.0 51.9 + - + -
304D PRO* 4.4 4.0 - - + -
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Residues in contact with HIS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASP* 4.6 0.8 + - - -
29D PHE* 3.2 30.4 - + - -
56D VAL* 3.1 28.1 + - + +
57D ARG 3.6 7.2 - - - +
59D LEU* 1.3 74.3 - - - +
61D ARG* 1.3 57.5 + - - +
63D PHE* 3.2 4.9 + - - +
64D LEU* 2.9 28.2 + - - +
71D MET* 3.7 23.1 - - + +
72D GLN 3.3 27.5 + - - -
74D PHE* 4.7 6.8 + - - +
103D ALA 4.9 1.6 + - - -
106D ILE* 3.9 21.5 - - + -
107D ALA* 4.0 22.5 + - + +
110D VAL* 3.8 20.2 - - + -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C TYR* 4.5 4.4 + - - +
54C GLU* 4.7 11.6 - - - +
57D ARG* 3.0 35.7 + - - +
58D GLN* 3.1 22.4 + - - +
60D HIS* 1.3 76.7 - - - +
62D GLU* 1.3 57.7 + - - +
64D LEU* 3.6 5.8 - - + +
65D ARG* 2.9 30.5 + - - +
109D GLN* 3.7 16.2 - - - +
110D VAL* 3.8 14.3 - - + +
113D GLU* 2.7 43.9 + - - +
501D SRT 2.5 37.0 + - - -
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 5.9 0.2 - - - +
36C ARG* 3.5 34.1 + - - +
38C TYR* 3.5 11.3 - - + +
55C ALA* 5.1 1.0 - - - +
36D ARG* 2.8 40.7 + - - -
58D GLN* 2.8 48.0 + - - +
59D LEU* 3.1 9.3 + - - +
61D ARG* 1.3 74.0 - - - +
63D PHE* 1.3 58.6 + - - +
65D ARG* 3.4 5.7 + - - +
66D ALA* 3.0 28.1 + - - +
304D PRO* 3.5 23.8 - - + +
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Residues in contact with PHE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASP* 3.9 7.9 - - + -
27D GLY* 3.4 36.1 - - - -
28D GLY 3.9 2.7 - - - -
29D PHE* 3.6 31.2 - + - -
32D ALA* 5.3 1.1 - - + -
59D LEU* 3.0 43.9 + - + -
60D HIS* 3.7 6.3 - - - +
62D GLU* 1.3 73.4 - - - +
64D LEU* 1.3 65.2 + - - +
66D ALA* 3.0 10.4 + - - +
67D GLY 3.2 0.7 + - - -
68D SER* 3.0 32.9 + - - +
71D MET* 4.6 2.0 - - + -
302D PHE 3.6 11.4 - - - -
303D GLU* 3.7 25.8 - - - -
304D PRO* 3.7 9.0 - - + -
307D ILE* 3.6 19.3 - - + -
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D HIS 2.9 17.0 + - - +
61D ARG* 3.6 9.0 - - + +
63D PHE* 1.3 73.4 - - - +
65D ARG* 1.3 63.2 + - - +
67D GLY* 3.1 15.6 + - - -
68D SER 3.7 11.0 + - - +
71D MET* 3.8 12.0 - - + +
110D VAL* 3.6 29.4 - - + +
113D GLU* 4.1 10.8 - - + +
114D GLY* 3.9 26.0 - - - +
115D ASP 4.5 2.9 - - - +
116D ALA* 3.6 31.6 - - + -
323D PRO* 4.5 5.2 - - - +
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Residues in contact with ARG 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG 4.9 2.7 - - - +
37C GLY 2.9 30.9 + - - -
38C TYR* 3.4 32.4 - - - -
52C HIS* 3.5 27.4 + - - -
61D ARG 2.9 17.6 + - - +
62D GLU 3.6 4.7 - - - +
63D PHE 3.3 0.2 - - - -
64D LEU* 1.3 75.6 - - - +
66D ALA* 1.3 60.1 + - - +
67D GLY 3.2 0.7 - - - -
323D PRO* 3.2 36.5 + - + +
324D ALA* 2.9 35.0 + - + +
326D GLU* 3.0 30.3 + - - +
327D LYS* 3.6 14.8 - - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D GLU 3.0 17.1 + - - +
63D PHE* 3.0 8.0 + - - +
65D ARG* 1.3 76.4 - - - +
67D GLY* 1.3 56.6 + - - +
68D SER 3.7 0.2 - - - -
304D PRO* 3.2 31.0 - - + +
307D ILE* 3.7 9.6 - - + +
308D ARG* 3.3 28.1 + - + +
311D ALA* 3.7 4.7 - - - +
322D PRO* 3.4 10.6 - - - +
324D ALA* 3.9 11.9 - - + -
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Residues in contact with GLY 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.5 18.5 - - - +
64D LEU 3.1 9.4 + - - -
65D ARG 3.2 1.0 - - - -
66D ALA* 1.3 80.2 - - - +
68D SER* 1.3 67.2 + - - +
69D ASN* 3.4 9.8 + - - +
311D ALA* 4.5 5.2 - - - -
318D ARG* 3.9 11.3 + - - -
322D PRO* 3.6 15.3 - - - -
323D PRO* 5.1 1.8 - - - -
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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