Contacts of the strand formed by residues 21 - 29 (chain D) in PDB entry 3M4D
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 LYS 21 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LYS 5.4 1.1 - - - +
47C ASN* 3.3 37.7 - - + +
19D THR* 3.8 17.2 + - - +
20D VAL* 1.3 74.2 - - - +
22D THR* 1.3 61.1 + - - +
40D TYR* 4.8 1.3 - - + -
41D SER* 3.4 1.0 - - - -
42D PHE* 2.8 41.1 + - + +
288D LYS 5.4 4.4 + - - +
289D GLU* 3.6 46.9 + - + +
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Residues in contact with THR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C THR 3.8 17.3 - - - +
13C ASP 5.2 2.5 - - - +
14C ILE* 3.8 7.1 - - + +
45C ASP* 5.0 1.2 + - - -
47C ASN* 2.9 10.8 + - - +
48C HIS* 2.7 35.2 + - - +
49C ASN* 2.9 21.5 + - - +
20D VAL* 3.9 16.6 - - + +
21D LYS* 1.3 78.8 - - - +
23D GLY* 1.3 60.1 + - - +
39D PHE* 4.1 6.1 - - + -
40D TYR* 3.2 15.8 + - - -
41D SER* 3.6 19.3 - - - +
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Residues in contact with GLY 23 (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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48C HIS* 3.4 10.0 + - - -
49C ASN* 3.1 17.9 - - - -
22D THR* 1.3 79.7 - - - +
24D ASP* 1.3 58.5 + - - -
39D PHE* 3.3 8.5 - - - -
40D TYR* 2.9 46.4 + - - -
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 4.3 1.2 - - - +
48C HIS* 2.8 27.7 + - - +
49C ASN* 2.7 17.0 + - - +
50C LYS* 3.2 15.2 + - + +
52C LEU* 4.2 5.5 - - - +
99C SER* 3.4 11.9 + - - +
231C VAL* 5.7 0.2 - - - +
233C THR* 4.0 22.7 - - + +
23D GLY* 1.3 71.0 - - - -
25D LEU* 1.3 74.7 + - - +
26D VAL* 4.3 1.1 - - + -
37D LYS* 2.7 35.7 + - - +
38D VAL 3.4 1.8 - - - -
39D PHE* 3.6 14.7 - - - -
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Residues in contact with LEU 25 (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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49C ASN* 3.6 15.0 - - - +
50C LYS* 4.3 7.2 - - - +
24D ASP* 1.3 93.4 + - - +
26D VAL* 1.3 61.3 + - - +
27D THR* 5.2 1.1 - - - -
36D LYS 3.7 1.2 - - - +
37D LYS* 3.3 3.1 - - - -
38D VAL* 2.9 43.6 + - + +
40D TYR* 4.1 13.7 - - + -
282D TYR* 3.8 35.2 + - + -
291D MET* 3.4 34.1 - - + +
292D THR* 4.1 4.7 - - + -
293D ASN* 3.4 22.9 - - - +
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Residues in contact with VAL 26 (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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50C LYS* 4.4 7.0 - - - +
97C GLN* 3.1 29.0 + - - +
98C ILE 3.6 6.7 - - - +
99C SER* 3.8 24.9 - - - +
162C ASP* 3.8 18.6 - - + -
233C THR* 4.7 5.4 - - - +
24D ASP* 4.3 1.5 - - + -
25D LEU* 1.3 73.4 - - - +
27D THR* 1.3 69.4 + - - +
35D HIS* 3.5 26.5 - - + +
36D LYS 3.4 3.6 - - - +
37D LYS* 3.5 27.1 - - + -
293D ASN* 5.0 2.2 + - - +
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Residues in contact with THR 27 (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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97C GLN* 4.8 1.6 - - - +
25D LEU 5.2 0.3 - - - -
26D VAL* 1.3 78.2 + - - +
28D TYR* 1.3 69.2 + - - +
29D ASP* 4.1 1.6 - - + -
34D MET 3.7 0.9 - - - +
35D HIS* 3.9 0.2 - - - -
36D LYS* 2.8 56.0 + - - +
280D GLU* 4.0 21.6 + - - +
282D TYR* 4.6 4.1 + - - -
293D ASN* 3.1 27.9 + - - -
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Residues in contact with TYR 28 (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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160C PRO 3.7 8.4 + - - -
161C THR* 3.4 49.4 - - + +
162C ASP* 3.4 33.8 + - + +
27D THR* 1.3 81.5 - - - +
29D ASP* 1.3 62.1 + - - +
30D LYS* 3.3 52.6 + - + +
33D GLY* 3.7 16.1 - - - -
34D MET 3.3 28.9 - - - -
35D HIS* 3.6 5.4 - - + +
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Residues in contact with ASP 29 (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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27D THR* 4.0 2.6 + - + -
28D TYR* 1.3 71.7 - - - +
30D LYS* 1.3 57.1 + - - +
31D GLU* 3.2 10.9 + - - +
32D ASN* 2.8 44.2 + - + -
33D GLY* 2.8 24.8 + - - -
34D MET* 2.8 24.4 + - + +
36D LYS* 4.8 4.9 - - - +
278D SER* 2.7 29.8 + - - +
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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
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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