Contacts of the strand formed by residues 47 - 55 (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 VAL 47 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C PRO* 3.7 4.0 - - - -
26D VAL* 3.8 30.3 - - + -
38D LEU* 3.8 13.9 - - + -
40D SER 3.6 1.8 - - - -
41D ILE* 3.9 0.7 - - + -
45D MSE 3.6 10.1 - - - +
46D ASN* 1.3 80.7 - - - +
48D ALA* 1.3 60.6 + - - +
49D LEU* 3.8 20.5 + - + -
71D VAL 3.7 0.9 - - - +
72D PHE* 3.7 2.3 - - - -
73D LEU* 3.0 41.9 + - + +
78D VAL* 4.5 6.5 - - + -
81D ILE* 3.6 29.8 - - + -
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Residues in contact with ALA 48 (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* 3.4 11.5 - - + +
7C LEU* 2.7 39.7 - - + -
38D LEU* 3.6 4.2 - - - +
39D GLU* 3.1 21.6 + - + -
40D SER* 2.6 29.1 + - - +
47D VAL* 1.3 73.3 - - - +
49D LEU* 1.3 66.3 + - - +
71D VAL 3.5 6.1 - - - +
72D PHE* 5.5 0.4 - - - -
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Residues in contact with LEU 49 (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* 5.5 0.2 - - - +
24D VAL* 4.1 15.7 - - + -
26D VAL* 4.5 4.9 - - + -
34D TYR* 4.2 13.7 - - + +
36D GLY* 3.9 17.5 - - - +
37D ARG 3.4 13.9 - - - +
38D LEU* 3.9 8.5 - - - -
39D GLU* 4.7 2.9 - - - +
47D VAL* 3.8 17.9 - - + +
48D ALA* 1.3 84.8 - - - +
50D SER* 1.3 67.5 + - - +
52D ALA* 3.7 29.6 - - + -
70D ASP* 3.2 12.1 - - - +
71D VAL* 3.1 27.4 + - + -
73D LEU* 4.3 20.2 - - + -
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Residues in contact with SER 50 (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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37D ARG* 3.0 37.1 + - - +
39D GLU* 4.2 15.4 + - - +
49D LEU* 1.3 74.1 + - - +
51D SER* 1.3 80.3 + - - +
52D ALA 3.4 0.2 - - - -
70D ASP* 2.7 24.7 + - - +
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Residues in contact with SER 51 (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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35D SER 3.6 6.8 - - - +
36D GLY* 4.2 1.7 - - - -
37D ARG* 4.1 25.5 + - - -
50D SER* 1.3 86.0 + - - +
52D ALA* 1.3 64.1 + - - +
53D THR* 3.8 1.4 + - - +
66D LYS* 3.8 19.8 + - - -
67D PHE 3.0 19.8 + - - -
68D ASN* 4.7 7.7 + - - -
69D SER 3.8 11.9 + - - +
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Residues in contact with ALA 52 (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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34D TYR* 5.0 4.7 - - + -
35D SER 3.2 8.1 - - - +
36D GLY* 4.3 0.7 - - - -
49D LEU* 3.7 28.5 - - + -
51D SER* 1.3 75.4 - - - +
53D THR* 1.3 57.1 + - - +
67D PHE* 2.6 49.6 + - + -
71D VAL* 3.5 29.4 - - + +
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Residues in contact with THR 53 (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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33D LEU 3.8 0.2 - - - +
34D TYR* 3.3 4.0 - - - -
35D SER* 2.8 39.1 + - - +
51D SER 4.3 2.5 - - - +
52D ALA* 1.3 73.5 - - - +
54D GLU* 1.3 60.4 + - - +
55D HIS* 3.3 21.5 + - - -
63D LEU* 4.2 9.9 - - + -
65D ASN 3.4 9.9 - - - -
66D LYS* 3.0 43.5 - - + +
67D PHE* 4.8 0.2 - - - -
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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
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161A GLY* 5.0 1.7 - - - -
19C LYS* 2.9 26.5 + - - -
32D LEU* 3.5 10.6 - - + +
33D LEU 3.0 5.4 - - - +
34D TYR* 3.0 34.3 + - + -
53D THR* 1.3 73.9 - - - +
55D HIS* 1.3 64.9 + - - +
63D LEU* 3.4 4.5 - - - +
64D LEU* 3.1 32.8 + - + +
65D ASN* 2.3 62.0 + - + +
67D PHE* 4.6 6.1 - - + -
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Residues in contact with HIS 55 (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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32D LEU* 3.5 5.9 - - - +
33D LEU* 2.5 52.0 + - + +
35D SER* 4.9 3.7 - - - -
53D THR* 3.3 27.6 + - - -
54D GLU* 1.3 80.1 + - - +
56D TYR* 1.3 54.7 + - - +
57D GLU 3.5 0.2 - - - -
58D SER 3.1 23.6 - - - +
59D ASN* 3.2 40.4 + - + +
62D LYS 2.2 33.8 + - - +
63D LEU* 4.1 15.7 - - + -
64D LEU* 4.4 4.7 - - - -
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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
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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