Contacts of the strand formed by residues 33 - 41 (chain D) in PDB entry 4M75
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 LEU 33 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ASN* 3.2 47.1 - - + +
26D VAL 4.1 11.9 - - - +
27D LYS* 4.6 14.4 - - + +
31D GLY 3.2 3.2 + - - -
32D LEU* 1.3 71.2 - - - +
34D TYR* 1.3 68.1 + - - +
35D SER* 4.2 0.9 - - - +
54D GLU* 3.0 8.0 - - - +
55D HIS* 2.5 52.4 + - + +
57D GLU 4.0 12.1 - - - +
58D SER* 3.7 17.9 - - - -
59D ASN* 3.5 23.8 - - - +
80D TYR* 5.2 4.3 - - - +
65E MSE 3.8 6.3 - - + -
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Residues in contact with TYR 34 (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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19C LYS* 3.5 11.8 + - - -
74C THR* 4.3 7.1 - - - +
75C LEU* 4.0 28.4 - - + +
24D VAL 4.1 0.3 - - - +
25D ASN* 3.9 1.0 - - - -
26D VAL* 3.2 35.6 + - - +
28D LEU* 3.5 26.5 - - + -
32D LEU* 3.1 41.6 - - + +
33D LEU* 1.3 78.4 - - - +
35D SER* 1.3 61.8 + - - +
36D GLY 4.1 0.7 + - - -
49D LEU* 4.2 8.9 - - + +
52D ALA* 5.0 3.6 - - + -
53D THR 3.3 6.1 - - - +
54D GLU* 3.0 42.0 + - + -
67D PHE* 4.1 13.9 - + - -
71D VAL* 5.5 0.4 - - + -
73D LEU* 4.2 17.3 - - + -
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Residues in contact with SER 35 (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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23D THR* 4.4 1.0 - - - +
24D VAL 3.7 0.2 - - - -
25D ASN* 3.2 7.6 - - - -
33D LEU* 4.2 1.4 - - - +
34D TYR* 1.3 73.0 - - - +
36D GLY* 1.3 57.6 + - - +
49D LEU* 4.3 0.7 - - - -
51D SER 3.6 2.8 - - - +
52D ALA* 3.2 4.7 - - - -
53D THR* 2.8 44.1 + - - +
55D HIS* 4.9 4.0 - - - -
59D ASN* 4.5 10.1 + - - -
84D GLN* 2.8 41.7 + - - -
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Residues in contact with GLY 36 (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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23D THR* 3.2 8.9 - - - -
24D VAL* 2.9 36.0 + - - +
35D SER* 1.3 76.4 + - - +
37D ARG* 1.3 61.2 + - - -
49D LEU* 3.9 19.1 - - - +
50D SER 4.1 9.4 - - - -
51D SER* 4.2 3.6 - - - -
52D ALA* 4.3 0.7 - - - -
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Residues in contact with ARG 37 (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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21D GLY 4.8 8.3 - - - +
22D LYS 3.4 6.3 - - - +
23D THR* 3.6 19.4 + - - +
36D GLY* 1.3 71.2 - - - -
38D LEU* 1.3 60.5 + - - +
39D GLU 3.1 6.3 + - - -
49D LEU* 3.4 2.2 - - - -
50D SER* 3.0 41.2 + - - +
51D SER* 4.1 20.7 + - - -
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Residues in contact with LEU 38 (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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19D ILE* 3.4 46.0 - - + +
20D ILE* 3.5 14.5 - - + +
21D GLY* 2.9 25.5 + - - +
22D LYS 2.7 14.5 + - - +
24D VAL* 3.3 20.9 - - + -
36D GLY 3.8 0.4 + - - -
37D ARG* 1.3 68.5 - - - +
39D GLU* 1.3 59.7 + - - +
40D SER* 3.5 19.7 - - - +
41D ILE* 4.5 10.5 - - + -
47D VAL* 3.8 17.0 - - + -
48D ALA 3.6 17.0 - - - +
49D LEU* 3.9 2.5 - - + -
81D ILE* 5.3 6.7 - - + -
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Residues in contact with GLU 39 (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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7C LEU* 4.4 16.6 - - + -
20D ILE* 5.2 6.6 - - - +
21D GLY* 5.2 1.5 + - - -
37D ARG 3.1 5.7 + - - -
38D LEU* 1.3 74.5 - - - +
40D SER* 1.3 69.0 + - - +
48D ALA* 3.1 15.2 + - + +
49D LEU 4.8 1.3 - - - +
50D SER* 4.2 20.8 + - - +
70D ASP* 4.7 5.7 - - - +
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Residues in contact with SER 40 (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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4C PRO* 3.6 18.2 - - - -
7C LEU* 4.7 5.6 - - - -
20D ILE* 5.9 4.0 - - - -
38D LEU* 3.5 8.1 - - - +
39D GLU* 1.3 86.2 - - - +
41D ILE* 1.3 72.2 + - - +
47D VAL* 3.5 0.9 - - - -
48D ALA* 2.6 44.5 + - - +
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Residues in contact with ILE 41 (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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4C PRO* 3.5 5.9 - - - +
16D LEU* 4.0 42.0 - - + +
19D ILE* 5.3 0.2 - - + -
20D ILE* 5.1 6.1 - - + +
38D LEU* 4.5 14.6 - - + -
40D SER* 1.3 82.2 + - - +
42D ASP* 1.3 76.5 + - - +
45D MSE 4.1 15.9 - - + -
46D ASN 2.5 26.7 - - - +
47D VAL* 3.9 4.3 - - + -
81D ILE* 3.3 34.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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