Contacts of the strand formed by residues 13 - 20 (chain B) in PDB entry 3QS1
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 MET 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A PHE* 4.8 12.3 - - + -
8B ASP* 3.6 0.7 - - - +
9B VAL* 3.1 55.1 + - + +
11B ASN 3.8 0.6 - - - -
12B VAL* 1.3 84.2 + - + +
14B TYR* 1.3 75.4 + - - +
15B TYR* 4.2 10.8 - - + -
30B ILE* 3.3 34.1 - - + -
115B GLY* 4.8 3.1 - - - -
116B GLN* 3.7 34.5 - - + +
117B PHE* 4.4 8.5 - - + -
217B GLY 5.7 4.5 - - - +
303B ASP* 4.5 2.2 - - - -
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Residues in contact with TYR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.5 22.7 - - + -
7B ASN 3.3 7.6 - - - +
8B ASP* 3.2 38.3 + - + -
11B ASN 4.4 2.5 - - - -
13B MET* 1.3 82.5 - - - +
15B TYR* 1.3 63.6 + - - +
29B PHE 4.0 0.2 - - - +
30B ILE* 3.7 28.9 - - + +
31B PHE* 4.5 2.1 + - - -
153B PHE* 6.2 1.3 - - + -
155B LEU* 3.7 36.3 - - + +
156B PRO* 2.9 42.2 + - + -
216B SER 5.1 4.7 - - - +
303B ASP* 3.3 27.6 - - - -
307B ARG* 3.2 16.8 + - - +
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Residues in contact with TYR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.1 5.6 - - - -
7B ASN* 2.7 75.3 + - + +
8B ASP 4.8 1.1 - - - -
9B VAL* 5.0 6.5 - - + -
13B MET* 4.2 12.8 - - + -
14B TYR* 1.3 76.8 - - - +
16B GLY* 1.3 60.2 + - - +
28B ALA* 3.7 17.9 - - + -
29B PHE 3.3 16.4 - - - +
31B PHE* 5.3 0.2 - - - -
116B GLN* 3.0 51.1 + - - -
117B PHE* 4.4 12.3 - - + -
160B LYS* 5.9 0.7 + - - -
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Residues in contact with GLY 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 5.5 1.3 - - - -
5B THR 3.7 16.6 - - - -
6B LEU* 4.4 2.7 - - - +
7B ASN* 5.2 1.8 - - - -
15B TYR* 1.3 77.6 - - - +
17B GLU* 1.3 66.4 + - - +
28B ALA* 4.2 3.8 - - - -
29B PHE* 3.0 28.1 + - - +
31B PHE* 3.6 17.7 - - - -
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 3.6 23.3 - - - +
5B THR 4.7 2.6 + - - -
16B GLY* 1.3 76.2 - - - +
18B ALA* 1.3 61.6 + - - +
19B GLN* 4.3 11.2 + - - +
26B LYS* 3.2 39.4 + - - +
27B PHE 3.1 15.5 - - - +
28B ALA* 5.2 2.9 - - + -
31B PHE* 4.2 1.7 - - - -
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 5.6 0.2 - - - -
16B GLY 3.9 0.2 + - - -
17B GLU* 1.3 76.0 - - - +
19B GLN* 1.3 76.1 + - - +
26B LYS 3.9 0.3 - - - -
27B PHE* 2.9 33.7 + - - +
29B PHE* 3.3 24.2 - - + -
31B PHE* 4.8 2.5 - - + -
89B VAL* 5.5 1.3 - - + -
90B THR 3.6 11.4 - - - +
91B ILE* 4.0 23.1 - - + +
92B ALA 5.8 0.2 - - - +
121B VAL* 5.5 0.2 - - + -
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Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 4.3 20.0 + - - +
18B ALA* 1.3 95.0 + - - +
20B ILE* 1.3 69.9 + - - +
21B GLY 5.5 0.2 - - - +
24B LYS* 3.5 44.5 + - + +
25B GLN 3.3 7.9 - - - +
26B LYS* 4.3 18.5 - - + +
89B VAL* 3.5 4.3 - - - +
90B THR* 2.8 54.6 + - - +
92B ALA 3.8 11.9 + - - +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 1.3 81.5 - - - +
21B GLY* 1.3 66.1 + - - +
25B GLN* 3.0 33.2 + - - +
27B PHE* 3.7 18.2 - - + -
29B PHE* 4.7 7.4 - - + -
38B LEU* 4.3 5.6 - - + -
40B VAL* 4.1 17.0 - - + -
56B TYR* 3.3 37.5 - - + +
87B ASP* 4.7 0.4 - - + +
88B ILE 3.8 4.0 - - - -
89B VAL* 4.0 18.6 - - + -
101B PHE* 3.8 38.6 - - + -
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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