Contacts of the strand formed by residues 20 - 27 (chain K) in PDB entry 3Q3G
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 20 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12K GLU* 3.6 45.5 - - + +
14K VAL* 4.0 9.4 - - + -
19K SER* 1.3 75.1 - - - +
21K LYS* 1.3 61.8 + - - +
22K LEU* 3.9 10.1 - - + -
83K LEU 3.7 0.9 - - - +
84K GLN* 3.3 5.7 - - - +
85K LEU* 2.9 59.6 + - + -
88K LEU* 3.8 20.9 - - + -
120K VAL* 4.2 8.7 - - + -
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Residues in contact with LYS 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K SER* 4.8 1.7 + - - -
12K GLU* 4.2 10.9 + - - +
20K VAL* 1.3 74.7 - - - +
22K LEU* 1.3 65.3 + - - +
23K SER* 4.2 1.2 + - - -
71K THR 5.9 0.4 - - - -
73K THR* 4.0 13.2 + - - +
82K TYR* 3.7 40.9 - - + -
83K LEU 3.4 9.6 - - - +
84K GLN* 3.9 29.9 + - + +
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Residues in contact with LEU 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K SER* 3.7 7.6 - - - +
12K GLU* 3.9 8.3 - - + +
20K VAL* 3.9 24.7 - - + -
21K LYS* 1.3 75.2 - - - +
23K SER* 1.3 60.0 + - - +
38K TRP* 4.1 13.6 - - + -
82K TYR* 3.2 8.2 - - - +
83K LEU* 2.8 51.5 + - + +
85K LEU* 4.5 3.6 - - + -
96K TYR* 3.7 32.1 - - + -
118K THR* 3.9 26.7 - - + -
120K VAL* 3.8 24.7 - - + -
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Residues in contact with SER 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K GLN* 3.5 6.9 + - - +
9K SER* 3.0 38.0 + - - -
21K LYS 4.2 0.8 + - - -
22K LEU* 1.3 75.0 - - - +
24K CYS* 1.3 61.5 + - - +
38K TRP* 4.1 3.4 - - - -
80K THR* 3.7 19.1 - - - -
81K ALA 3.5 4.5 - - - -
82K TYR* 3.7 15.0 - - - -
118K THR* 4.9 0.2 + - - -
707K GOL 3.1 23.8 + - - -
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Residues in contact with CYS 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU* 4.0 14.6 - - - -
7K GLN 3.4 5.6 - - - -
8K GLN* 4.1 1.6 - - + -
23K SER* 1.3 77.0 - - - +
25K THR* 1.3 61.5 + - - +
26K PRO* 4.0 3.6 - - - +
36K MET* 4.0 17.3 - - - -
38K TRP* 3.8 10.8 - - + -
80K THR* 3.4 1.0 - - - -
81K ALA* 2.8 39.0 + - + +
98K CYS* 2.0 52.9 - - + -
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Residues in contact with THR 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU* 4.6 0.7 - - - -
7K GLN* 2.7 38.6 + - - +
24K CYS* 1.3 70.5 - - - +
26K PRO* 1.4 70.3 - - + +
27K SER* 3.6 0.9 + - - -
78K SER 3.7 8.5 - - - +
79K ASN* 3.2 19.3 - - + +
80K THR* 2.7 23.6 + - - +
707K GOL 2.7 32.7 + - - +
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Residues in contact with PRO 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K GLN 3.5 6.3 - - - +
6K LEU* 3.5 28.2 - - + -
24K CYS 4.0 3.6 - - - +
25K THR* 1.4 85.5 - - - +
27K SER* 1.3 59.9 + - - +
28K GLY 4.0 0.3 + - - -
29K PHE* 3.6 32.9 - - + +
31K ILE* 3.5 24.7 - - + -
36K MET* 3.8 4.3 - - + -
79K ASN* 3.0 44.6 + - - +
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Residues in contact with SER 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLN* 3.6 19.0 + - - -
4K VAL* 3.4 6.5 - - - +
5K GLN* 2.9 37.7 + - - +
7K GLN* 5.5 4.8 + - - +
25K THR 3.6 2.7 + - - -
26K PRO* 1.3 72.1 - - - +
28K GLY* 1.3 59.0 + - - +
29K PHE* 3.6 1.3 + - - -
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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