Contacts of the strand formed by residues 14 - 19 (chain Q) in PDB entry 6D84
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 LEU 14 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58K MET* 3.3 29.0 - - + +
59K LEU* 3.4 28.1 - - + +
6Q LEU* 4.6 8.7 - - + -
7Q LEU 3.4 14.4 - - - +
8Q PHE* 4.4 7.4 - - + +
12Q GLY 3.4 5.6 + - - +
13Q LYS* 1.3 68.3 - - - +
15Q ARG* 1.3 62.6 + - - +
16Q LEU 3.4 30.1 - - - +
17Q GLN* 3.5 31.6 - - + +
29Q LYS* 4.7 9.6 - - - +
32Q THR* 4.4 19.1 - - + -
36Q VAL* 6.3 0.4 - - + -
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Residues in contact with ARG 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K ARG* 5.1 9.7 - - - +
55K TYR* 5.2 7.7 + - - -
58K MET* 3.2 28.1 - - - +
59K LEU* 5.8 4.6 - - - +
220O GLU* 4.7 9.5 + - - -
7Q LEU* 2.8 15.7 + - + +
9Q SER* 4.4 8.6 - - - +
13Q LYS* 3.6 31.7 + - - +
14Q LEU* 1.3 78.5 + - - +
16Q LEU* 1.3 59.5 + - + +
65Q LEU* 3.7 27.8 - - + -
100Q GLU* 3.8 13.9 + - - +
103Q ILE* 4.9 13.3 - - + +
104Q ILE* 3.5 45.1 - - - +
107Q PHE* 4.9 6.2 - - - +
111Q TYR* 4.2 1.4 + - - -
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Residues in contact with LEU 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K MET* 4.7 0.4 - - - -
5Q ILE* 4.5 2.0 - - + -
6Q LEU* 3.4 1.2 - - - -
7Q LEU* 2.6 73.1 + - + -
14Q LEU* 3.4 8.1 - - - +
15Q ARG* 1.3 79.9 - - - +
17Q GLN* 1.3 74.7 + - - +
18Q LYS* 4.4 2.2 - - + -
87Q TYR* 4.6 8.3 - - + +
103Q ILE* 5.9 2.7 - - + -
107Q PHE* 5.0 1.3 - - + +
110Q ALA* 4.4 23.3 - - + -
111Q TYR* 3.6 39.3 - - + +
114Q LEU* 4.1 21.5 - - + -
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Residues in contact with GLN 17 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K HIS* 3.6 37.0 + - - -
58K MET* 4.1 9.5 - - + +
91K LEU* 4.4 12.8 - - + +
5Q ILE 3.3 4.9 - - - -
6Q LEU* 3.8 13.2 - - + -
14Q LEU* 3.5 28.0 - - + +
16Q LEU* 1.3 76.0 - - - +
18Q LYS* 1.3 65.5 + - - +
19Q TRP* 3.7 23.7 + - + +
25Q ASP* 5.6 1.4 + - - -
28Q ARG* 5.1 7.9 - - - +
29Q LYS* 4.9 7.4 + - - +
32Q THR* 4.7 5.9 + - - -
111Q TYR* 3.6 26.5 + - - +
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Residues in contact with LYS 18 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K LEU* 6.3 1.0 - - - +
90K MET* 3.7 43.8 + - - +
91K LEU* 5.1 11.5 - - + +
128K CYS* 4.2 11.5 - - - +
4Q PHE* 3.3 8.8 - - - +
5Q ILE* 2.6 46.9 + - + +
6Q LEU* 4.3 0.7 - - - +
16Q LEU* 4.4 1.1 - - + -
17Q GLN* 1.3 78.9 - - - +
19Q TRP* 1.3 76.6 + - - +
20Q TYR* 3.6 44.2 - - + +
111Q TYR* 5.5 5.0 - - + -
114Q LEU* 4.1 18.2 - - + -
115Q ASP* 4.2 9.2 + - - -
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Residues in contact with TRP 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K MET 5.5 2.3 - - - +
128K CYS* 4.6 6.6 - - - +
129K MET* 5.8 2.1 - - - +
3Q HIS 4.1 0.2 - - - -
4Q PHE* 3.9 25.6 - + + -
6Q LEU* 4.8 9.4 - - + -
17Q GLN* 3.7 23.5 + - + +
18Q LYS* 1.3 92.0 - - - +
20Q TYR* 1.3 62.8 + - - +
21Q ILE* 3.3 21.6 + - + +
22Q THR* 5.5 3.0 - - - +
23Q LEU* 3.7 37.0 - - + -
28Q ARG* 3.5 57.8 - - + +
31Q ILE* 3.9 26.7 - - + -
32Q THR* 3.4 23.1 - - - -
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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