Contacts of the strand formed by residues 6 - 14 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ARG* 3.8 32.9 - - - +
17C GLY 5.7 0.6 - - - +
277C LYS* 5.3 8.5 - - - +
4H GLU 4.3 0.2 - - - -
5H CYS* 1.3 74.3 - - - +
7H VAL* 1.3 64.0 + - - +
34H GLU* 3.1 36.1 + - + +
36H ASP* 2.9 27.1 + - - +
74H VAL 5.0 1.3 - - - -
76H GLN 3.1 26.7 + - - +
77H TYR* 3.5 23.3 - - + -
78H ASP* 2.9 40.3 + - - +
79H TYR 3.1 6.1 + - - -
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Residues in contact with VAL 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ARG* 1.3 80.2 - - - +
8H LEU* 1.3 58.3 + - - +
9H SER* 3.4 5.4 + - - +
28H LEU* 4.4 14.4 - - + -
33H PHE* 3.8 37.5 - - + -
34H GLU 2.8 9.9 + - - +
35H VAL* 3.5 4.8 - - + +
36H ASP 2.8 30.9 + - - -
77H TYR* 4.0 3.4 - - - -
79H TYR* 3.7 22.0 - - + -
81H LEU* 4.2 14.6 - - + -
242H LEU* 3.6 29.2 - - + -
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Residues in contact with LEU 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 4.4 2.7 - - + -
7H VAL* 1.3 69.2 - - - +
9H SER* 1.3 58.4 + - - +
10H ILE* 3.6 20.8 + - + +
36H ASP* 3.4 14.6 - - + +
38H VAL* 4.0 24.5 - - + -
66H TYR* 5.1 6.3 - - + -
69H LEU* 5.0 2.9 - - + -
77H TYR* 3.4 46.7 - - + +
79H TYR 3.2 12.3 + - - +
80H VAL* 3.6 12.7 - - + +
81H LEU 3.1 20.2 + - - +
97H ILE* 4.7 9.2 - - + -
101H LEU* 4.2 18.2 - - + -
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Residues in contact with SER 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 3.4 4.7 + - - -
8H LEU* 1.3 72.1 - - - +
10H ILE* 1.3 59.5 + - - +
11H GLN* 2.7 23.1 + - - -
21H ASN* 2.7 31.6 + - - +
24H ALA* 4.5 1.6 - - - +
25H THR* 6.5 0.2 - - - -
28H LEU* 5.3 2.7 - - - -
35H VAL* 4.4 13.0 - - - -
36H ASP 2.8 13.4 + - - +
37H ALA* 3.5 0.5 - - - -
38H VAL* 3.0 24.3 + - - +
81H LEU* 3.1 20.4 + - - +
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Residues in contact with ILE 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 3.9 33.0 - - + +
9H SER* 1.3 74.5 + - - +
11H GLN* 1.3 62.1 + - - +
38H VAL* 3.4 21.5 - - + +
40H SER* 4.9 1.1 - - - -
62H LEU* 4.9 9.2 - - + -
80H VAL* 5.3 1.1 - - + -
81H LEU 2.6 12.4 + - - +
82H THR* 3.3 10.7 - - + -
83H GLY 2.9 25.3 + - - +
84H TYR 4.9 0.3 - - - +
85H THR* 5.5 1.1 + - - +
90H PHE* 3.5 36.6 - - + -
94H VAL* 4.3 28.0 - - + -
97H ILE* 5.2 7.9 - - + -
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Residues in contact with GLN 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H SER* 2.7 24.7 + - - +
10H ILE* 1.3 82.5 - - - +
12H SER* 1.3 60.5 + - - +
20H GLY* 3.6 14.1 - - - +
21H ASN* 3.1 16.3 + - - +
24H ALA* 3.4 22.4 - - - +
38H VAL 3.1 5.3 + - - -
39H ASN* 3.0 11.3 - - - -
40H SER* 2.8 29.9 + - - -
81H LEU* 4.0 14.0 - - - +
82H THR 4.1 2.2 - - - -
83H GLY* 3.5 17.2 - - - +
84H TYR 4.0 8.5 - - - +
113H ASP* 6.0 0.8 - - - +
235H ASP* 3.2 28.0 + - - +
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Residues in contact with SER 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H GLN* 1.3 76.3 - - - +
13H HIS* 1.3 59.6 + - - +
19H VAL* 4.1 0.7 - - - +
20H GLY* 3.1 12.7 - - - -
21H ASN* 2.6 33.6 + - - +
40H SER* 3.1 4.3 + - - -
41H VAL* 3.1 28.0 - - - -
84H TYR* 3.4 22.1 + - - +
7401H PLP 2.8 30.6 + - - +
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Residues in contact with HIS 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ALA* 2.6 44.4 + - + -
39C ASN* 3.2 27.2 + - - -
12H SER* 1.3 73.8 - - - +
14H VAL* 1.3 74.4 + - - +
19H VAL 4.9 0.2 - - - -
21H ASN* 4.9 1.4 - - + +
22H ARG* 3.9 24.1 + - - +
39H ASN* 3.4 25.7 + - + +
41H VAL* 2.8 18.2 + - - +
42H GLN* 3.2 23.0 - - + -
43H PHE 2.9 23.6 + - - -
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Residues in contact with VAL 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H HIS* 1.3 87.2 + - - +
15H VAL* 1.3 65.9 + - - +
16H ARG 3.0 22.2 - - - +
17H GLY 3.5 20.2 - - - +
19H VAL* 3.4 33.9 - - + +
22H ARG* 3.3 21.7 - - + +
43H PHE* 3.3 4.7 - - + +
45H ASN* 3.6 28.9 - - - +
46H HIS 4.1 0.9 - - - +
7401H PLP 4.4 8.3 - - + -
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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