Contacts of the strand formed by residues 4 - 13 (chain D) in PDB entry 3QN3
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 ILE 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D VAL* 1.3 78.4 - - - +
5D GLU* 1.3 61.7 + - - +
6D ASP 4.1 2.9 - - - +
7D VAL* 3.6 31.2 - - + -
25D VAL* 4.1 17.3 - - + -
27D LEU* 3.9 17.7 - - + -
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Residues in contact with GLU 5 (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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3D VAL* 3.4 2.3 + - + -
4D ILE* 1.3 75.4 - - - +
6D ASP* 1.3 64.2 + - + +
26D THR* 2.8 15.9 + - + +
27D LEU 3.7 15.7 - - - +
28D SER* 3.1 31.5 - - - +
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Residues in contact with ASP 6 (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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4D ILE* 3.7 1.0 - - - +
5D GLU* 1.3 84.5 - - + +
7D VAL* 1.3 81.9 + - - +
8D ARG* 4.2 14.4 - - - +
24D GLU* 4.5 2.1 - - - +
25D VAL* 3.4 2.8 - - - +
26D THR* 2.9 48.0 + - + +
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Residues in contact with VAL 7 (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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4D ILE* 3.6 23.6 - - + -
6D ASP* 1.3 87.3 + - - +
8D ARG* 1.3 70.2 + - - +
23D ALA* 6.1 2.5 - - + -
24D GLU 3.5 7.2 - - - +
25D VAL* 4.3 14.8 - - + -
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Residues in contact with ARG 8 (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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404C PHE* 3.7 41.8 - - - +
6D ASP* 4.2 15.5 - - - +
7D VAL* 1.3 82.2 - - - +
9D ALA* 1.3 62.9 + - - +
10D TYR* 3.6 28.3 - - - +
23D ALA* 3.3 4.5 - - - +
24D GLU* 2.7 78.0 + - - +
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Residues in contact with ALA 9 (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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8D ARG* 1.3 81.1 + - - +
10D TYR* 1.3 69.9 + - - +
21D VAL* 3.9 19.1 - - + -
22D LYS 3.1 13.0 - - - +
23D ALA* 4.2 5.4 - - + -
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Residues in contact with TYR 10 (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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400C LEU* 5.4 1.6 - - + -
401C GLU* 2.5 47.4 + - + +
404C PHE* 3.6 34.8 - + + -
8D ARG* 3.6 37.9 + - - +
9D ALA* 1.3 81.3 - - - +
11D GLU* 1.3 65.1 + - - +
12D VAL* 3.7 24.6 + - + -
21D VAL* 3.8 5.2 - - - +
22D LYS* 3.0 55.2 + - + +
24D GLU* 4.7 16.2 + - + +
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Residues in contact with GLU 11 (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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175C LYS* 2.6 45.7 + - - +
400C LEU* 3.6 15.9 - - + +
404C PHE* 5.6 0.7 - - - -
10D TYR* 1.3 77.5 - - - +
12D VAL* 1.3 68.4 + - - +
19D PRO* 3.9 26.2 - - + +
20D THR 3.5 9.2 - - - +
21D VAL* 5.2 0.7 - - + +
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Residues in contact with VAL 12 (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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397C ASN* 3.5 36.6 - - + +
400C LEU* 4.1 7.6 - - + -
10D TYR* 3.7 28.7 + - + -
11D GLU* 1.3 80.5 - - - +
13D LEU* 1.3 66.6 + - - +
19D PRO* 3.2 8.3 - - - +
20D THR* 2.9 47.9 + - + +
21D VAL 4.7 0.4 - - - -
22D LYS* 3.8 26.0 - - + +
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Residues in contact with LEU 13 (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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178C LEU* 4.2 24.5 - - + -
182C CYS* 3.7 27.6 - - - -
387C LEU* 4.8 3.6 - - + +
393C THR* 4.2 18.5 + - + -
396C TYR* 4.3 18.6 - - + -
397C ASN* 2.9 33.1 + - - +
400C LEU* 5.0 2.5 - - + -
12D VAL* 1.3 80.7 - - - +
14D ASP* 1.3 69.5 + - - +
17D GLY* 3.9 22.2 - - - +
18D ASN 3.5 7.0 - - - +
19D PRO* 4.5 6.7 - - + -
20D THR* 4.2 3.4 - - - +
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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