Contacts of the strand formed by residues 6 - 14 (chain D) in PDB entry 1RFU
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 ARG 6 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D GLU 4.2 0.4 - - - -
5D CYS* 1.3 73.6 - - - +
7D VAL* 1.3 64.1 + - - +
8D LEU 4.4 0.2 - - - -
34D GLU* 3.1 35.9 + - + +
36D ASP* 2.9 27.0 + - - +
74D VAL 5.0 1.1 - - - -
76D GLN 3.1 26.7 + - - +
77D TYR* 3.6 22.4 - - + -
78D ASP* 2.9 40.3 + - - +
79D TYR 3.2 5.9 + - - -
16G ARG* 3.1 39.6 - - - +
17G GLY 5.6 0.2 - - - +
277G LYS* 5.0 10.7 - - - +
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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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6D ARG* 1.3 79.1 - - - +
8D LEU* 1.3 57.7 + - - +
9D SER* 3.4 3.8 + - - +
28D LEU* 4.2 17.0 - - + -
33D PHE* 3.7 37.9 - - + -
34D GLU 2.8 10.5 + - - +
35D VAL* 3.5 4.7 - - + +
36D ASP 2.8 32.7 + - - +
77D TYR* 3.9 3.8 - - - -
79D TYR* 3.7 21.3 - - + -
81D LEU* 4.2 12.3 - - + -
242D LEU* 3.7 28.9 - - + -
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Residues in contact with LEU 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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7D VAL* 1.3 69.6 - - - +
9D SER* 1.3 57.7 + - - +
10D ILE* 3.7 22.4 + - + +
36D ASP* 3.4 14.8 - - + +
38D VAL* 4.1 23.6 - - + -
66D TYR* 5.2 5.8 - - + -
69D LEU* 5.0 3.1 - - + -
77D TYR* 3.4 49.4 - - + +
79D TYR 3.2 11.7 + - - +
80D VAL* 3.5 12.3 - - + +
81D LEU 3.1 21.5 + - - +
97D ILE* 4.7 9.2 - - + -
101D LEU* 4.2 17.5 - - + -
15G VAL* 4.6 1.8 - - + -
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Residues in contact with SER 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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7D VAL* 3.4 5.2 + - - -
8D LEU* 1.3 71.9 - - - +
10D ILE* 1.3 60.4 + - - +
11D GLN* 2.6 34.1 + - - -
21D ASN* 2.7 21.2 + - - +
24D ALA* 4.6 1.8 - - - +
25D THR* 6.5 0.2 - - - -
28D LEU* 5.3 2.7 - - - -
35D VAL* 4.3 13.0 - - - -
36D ASP 2.9 12.4 + - - +
37D ALA* 3.5 0.3 - - - -
38D VAL 3.0 26.3 + - - +
81D LEU* 3.0 18.1 + - - -
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Residues in contact with ILE 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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8D LEU* 4.0 32.3 - - + +
9D SER* 1.3 75.0 + - - +
11D GLN* 1.3 63.0 + - - +
38D VAL* 3.4 20.2 - - + +
40D SER* 5.2 0.2 - - - -
62D LEU* 4.9 10.8 - - + -
80D VAL* 5.4 1.3 - - + -
81D LEU 2.6 8.5 + - - -
82D THR* 3.2 13.8 - - + -
83D GLY 2.8 25.1 + - - +
84D TYR 4.9 0.5 - - - +
85D THR* 5.4 1.1 + - - +
90D PHE* 3.6 36.8 - - + -
94D VAL* 4.2 29.4 - - + -
97D ILE* 5.3 6.7 - - + -
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Residues in contact with GLN 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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9D SER* 2.6 25.8 + - - +
10D ILE* 1.3 81.9 - - - +
12D SER* 1.3 62.8 + - - +
20D GLY* 3.7 14.3 - - - +
21D ASN* 3.3 14.3 + - - +
24D ALA* 3.4 21.8 - - - +
38D VAL 3.1 5.4 + - - +
39D ASN* 3.1 11.1 - - - -
40D SER* 2.8 29.4 + - - -
81D LEU* 3.8 15.4 - - - +
82D THR 4.2 2.0 - - - -
83D GLY* 3.5 16.9 - - - +
84D TYR 3.9 9.0 - - - +
113D ASP* 6.0 0.6 - - - +
235D ASP* 3.4 26.1 + - - +
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Residues in contact with SER 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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11D GLN* 1.3 77.7 - - - +
13D HIS* 1.3 59.8 + - - +
19D VAL* 4.2 0.7 - - - +
20D GLY* 3.0 15.9 - - - -
21D ASN* 2.6 32.6 + - - +
40D SER* 3.0 10.0 + - - -
41D VAL* 3.2 21.3 - - - -
84D TYR* 3.3 23.8 + - - +
3401D PLP 2.7 29.7 + - - +
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Residues in contact with HIS 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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12D SER* 1.3 72.5 - - - +
14D VAL* 1.3 84.5 + - - +
15D VAL 3.9 0.2 - - - -
21D ASN* 5.3 1.4 - - + +
22D ARG* 4.0 23.3 + - - +
39D ASN* 3.4 32.0 + - + +
41D VAL* 2.7 24.0 + - - +
42D GLN* 3.2 21.2 + - + -
43D PHE* 2.9 23.7 + - - +
13G HIS* 5.3 2.8 + + - -
37G ALA* 3.4 24.3 + - + -
39G ASN* 3.1 26.9 + - - -
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Residues in contact with VAL 14 (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 HIS* 1.3 87.4 + - - +
15D VAL* 1.3 66.4 + - - +
16D ARG 3.1 22.0 - - - +
17D GLY* 3.3 21.5 - - - +
19D VAL* 3.5 33.4 + - + +
22D ARG* 3.3 21.4 - - + +
43D PHE* 3.3 5.2 - - + -
45D ASN* 3.7 29.2 - - - +
46D HIS* 3.9 2.5 - - + +
3401D PLP 4.4 7.9 - - + -
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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