Contacts of the strand formed by residues 37 - 46 (chain D) in PDB entry 6NQN
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 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D GLY* 3.1 1.4 - - - -
32D LYS* 2.7 46.4 + - + +
35D GLU* 3.9 15.0 + - + +
36D GLY* 1.3 82.9 - - - +
38D GLN* 1.3 60.7 + - - +
68D PHE* 3.9 3.2 - - - +
211D GLU 3.4 5.4 - - - +
212D HIS* 3.8 39.4 - - + -
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Residues in contact with GLN 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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10D ILE* 3.4 22.9 - - + +
30D LEU* 3.3 13.7 - - - +
31D GLY* 3.7 5.6 - - - -
37D LYS* 1.3 77.2 - - - +
39D SER* 1.3 63.6 + - - +
40D MET* 3.6 17.6 - - - +
61D PHE 4.7 0.2 + - - -
63D KZ4 3.7 18.6 - - - +
65D ASN* 4.4 4.2 + - - +
68D PHE* 3.6 30.7 - - + +
116D TYR* 4.3 4.0 + - - -
210D HIS* 3.4 5.8 - - - +
211D GLU* 2.9 63.2 + - + +
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Residues in contact with SER 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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10D ILE* 4.6 1.4 - - - +
29D GLY* 3.2 1.7 - - - -
30D LEU* 2.9 46.8 + - - +
38D GLN* 1.3 77.9 - - - +
40D MET* 1.3 64.7 + - - +
208D ASN* 4.9 3.8 + - - -
209D LEU 3.1 7.2 - - - -
210D HIS* 3.4 37.3 + - - -
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Residues in contact with MET 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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10D ILE* 4.1 14.6 - - + -
12D LEU* 3.7 27.1 - - + -
27D GLY* 5.6 0.2 - - - -
28D VAL 3.3 16.4 - - - +
29D GLY* 3.7 5.2 - - - +
38D GLN* 3.6 22.9 - - - +
39D SER* 1.3 78.5 - - - +
41D ASP* 1.3 65.0 + - - +
42D LEU* 3.8 22.9 - - + -
61D PHE* 3.6 31.9 - - - +
63D KZ4 3.8 7.6 - - - -
116D TYR* 4.7 0.2 - - + -
207D VAL 3.6 1.2 - - - +
208D ASN* 3.5 6.0 + - - +
209D LEU* 3.0 42.9 + - + +
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Residues in contact with ASP 41 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D GLU 4.1 0.2 - - - +
27D GLY* 3.2 1.7 - - - -
28D VAL* 2.8 45.4 + - + +
40D MET* 1.3 75.9 - - - +
42D LEU* 1.3 61.2 + - - +
43D LYS* 5.4 5.3 - - + +
207D VAL 3.4 4.2 - - - +
208D ASN* 3.2 28.6 + - - +
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Residues in contact with LEU 42 (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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12D LEU* 4.0 3.4 - - + -
25D ILE* 4.1 2.9 - - + -
26D GLU 3.3 6.1 - - - +
27D GLY* 3.8 16.6 - - - -
40D MET* 3.8 23.3 - - + -
41D ASP* 1.3 76.1 - - - +
43D LYS* 1.3 62.4 + - - +
54D TYR* 3.4 21.0 + - + +
61D PHE* 3.6 44.9 - - + -
205D SER 3.5 0.7 - - - +
206D ASN* 3.4 6.9 - - - +
207D VAL* 2.9 40.1 + - + +
209D LEU* 3.9 28.9 - - + -
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Residues in contact with LYS 43 (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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25D ILE* 3.4 3.9 - - - -
26D GLU* 2.8 38.4 + - - +
27D GLY* 6.2 0.7 - - - -
28D VAL* 6.3 6.4 - - - +
41D ASP* 5.4 4.5 - - + +
42D LEU* 1.3 76.4 - - - +
44D VAL* 1.3 65.7 + - - +
45D LYS* 2.9 42.0 + - - +
205D SER 3.2 6.1 - - - +
206D ASN* 3.5 21.5 - - - +
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Residues in contact with VAL 44 (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 ALA 3.7 5.4 - - - +
25D ILE* 3.9 11.4 - - + -
43D LYS* 1.3 72.7 - - - +
45D LYS* 1.3 63.7 + - - +
46D GLU 3.4 22.7 - - - +
48D GLY* 3.8 23.6 - - - +
50D LEU* 3.8 34.1 - - + -
54D TYR* 4.4 2.5 - - + +
203D ASP 5.5 0.2 - - - +
204D TYR 3.8 18.6 - - - +
205D SER* 3.0 24.1 + - - +
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Residues in contact with LYS 45 (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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13D ARG* 4.5 10.1 - - - +
24D ALA 2.7 15.9 + - - +
26D GLU* 3.5 41.7 - - + +
43D LYS* 2.9 53.2 - - + +
44D VAL* 1.3 79.5 - - - +
46D GLU* 1.3 67.0 + - + +
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Residues in contact with GLU 46 (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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13D ARG* 3.2 20.7 + - - -
15D GLU* 5.5 1.2 - - - +
23D PHE* 3.2 10.6 - - - +
24D ALA* 3.0 46.1 + - + +
44D VAL* 3.4 8.1 - - - +
45D LYS* 1.3 84.4 - - + +
47D GLY* 1.3 63.4 + - - +
48D GLY 3.3 4.2 + - - +
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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