Contacts of the strand formed by residues 6 - 14 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 3.5 36.6 - - - +
277D LYS* 5.2 9.3 - - - +
5G CYS* 1.3 72.5 - - - +
7G VAL* 1.3 63.8 + - - +
8G LEU 4.3 0.2 - - - -
34G GLU* 3.2 35.7 - - + +
36G ASP* 2.9 26.8 + - - +
74G VAL 4.9 2.9 + - - -
76G GLN 3.1 26.7 + - - +
77G TYR* 3.4 25.8 - - + -
78G ASP* 3.0 39.3 + - - +
79G TYR 3.1 6.4 + - - +
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Residues in contact with VAL 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ARG* 1.3 79.1 - - - +
8G LEU* 1.3 61.9 + - - +
9G SER* 3.4 5.1 + - - +
28G LEU* 4.2 14.4 - - + -
33G PHE* 3.7 38.4 - - + -
34G GLU 2.8 10.6 + - - +
35G VAL* 3.6 4.0 - - + +
36G ASP 2.8 26.7 + - - -
77G TYR* 4.1 3.1 - - - -
79G TYR* 3.8 21.1 - - + -
81G LEU* 4.2 14.8 - - + -
242G LEU* 3.6 29.2 - - + -
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Residues in contact with LEU 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 4.9 1.6 - - + -
7G VAL* 1.3 68.7 - - - +
9G SER* 1.3 57.4 + - - +
10G ILE* 3.6 19.9 + - + +
36G ASP* 3.4 16.2 - - + +
38G VAL* 4.1 23.8 - - + -
66G TYR* 5.3 4.9 - - + -
69G LEU* 5.0 3.6 - - + -
77G TYR* 3.5 48.3 - - + +
79G TYR 3.2 13.1 + - - +
80G VAL* 3.6 11.9 - - + +
81G LEU 3.1 21.8 + - - +
97G ILE* 4.6 10.5 - - + -
101G LEU* 4.2 17.0 - - + -
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Residues in contact with SER 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 3.4 4.8 + - - -
8G LEU* 1.3 72.9 - - - +
10G ILE* 1.3 60.0 + - - +
11G GLN* 2.8 21.9 + - - -
21G ASN* 2.6 29.0 + - - +
24G ALA* 4.5 2.0 - - - +
25G THR* 6.5 0.2 - - - -
28G LEU* 5.3 2.2 - - - -
35G VAL* 4.3 14.6 - - - -
36G ASP 2.9 11.7 + - - +
37G ALA* 3.5 1.6 - - - -
38G VAL* 3.0 26.3 + - - +
81G LEU* 3.1 19.5 + - - +
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Residues in contact with ILE 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LEU* 4.1 30.7 - - + +
9G SER* 1.3 74.8 - - - +
11G GLN* 1.3 61.1 + - - +
38G VAL* 3.4 20.4 - - + +
40G SER* 4.8 0.9 - - - -
62G LEU* 4.9 10.8 - - + -
80G VAL* 5.4 1.1 - - + -
81G LEU 2.7 12.0 + - - +
82G THR* 3.3 9.4 - - + -
83G GLY 2.9 24.6 + - - +
84G TYR 4.9 0.3 - - - +
85G THR* 5.5 1.1 + - - +
90G PHE* 3.5 37.0 - - + -
94G VAL* 4.1 31.4 - - + -
97G ILE* 5.2 6.5 - - + -
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Residues in contact with GLN 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G SER* 2.8 24.4 + - - +
10G ILE* 1.3 82.4 - - - +
12G SER* 1.3 62.7 + - - +
20G GLY* 3.8 8.7 - - - +
21G ASN* 2.9 31.2 + - - +
24G ALA* 3.3 23.4 - - - +
38G VAL 3.1 1.8 + - - -
39G ASN* 3.1 5.5 - - - -
40G SER* 2.8 28.0 + - - -
81G LEU* 3.8 14.2 - - - +
82G THR 4.2 2.7 - - - -
83G GLY* 3.6 19.5 - - - +
84G TYR 4.1 5.8 - - - +
113G ASP* 5.9 0.7 - - - +
235G ASP* 3.2 27.6 + - - +
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Residues in contact with SER 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLN* 1.3 77.0 - - - +
13G HIS* 1.3 58.4 + - - +
19G VAL* 4.2 0.7 - - - +
20G GLY* 3.0 14.7 - - - -
21G ASN* 2.6 34.0 + - - +
40G SER* 3.0 10.0 + - - -
41G VAL* 3.2 21.5 - - - -
84G TYR* 3.4 23.4 + - - +
6401G PLP 2.7 30.3 + - - +
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Residues in contact with HIS 13 (chain G).
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* 5.3 2.3 + - - -
37D ALA* 3.4 26.8 + - + -
39D ASN* 3.4 25.2 + - - -
12G SER* 1.3 75.5 - - - +
14G VAL* 1.3 83.1 + - - +
15G VAL 4.0 0.2 - - - -
19G VAL 4.9 0.4 - - - -
21G ASN* 5.2 1.0 - - + +
22G ARG* 4.0 25.5 + - - +
39G ASN* 3.5 28.6 + - + +
41G VAL* 2.8 19.7 + - - +
42G GLN* 3.2 21.3 + - + -
43G PHE* 2.9 23.9 + - - +
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Residues in contact with VAL 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G HIS* 1.3 90.0 + - - +
15G VAL* 1.3 67.8 + - - +
16G ARG 3.2 22.7 - - - +
17G GLY 3.4 21.1 - - - +
19G VAL* 3.5 30.3 + - + +
22G ARG* 3.4 19.8 - - + +
43G PHE* 3.2 4.9 - - + +
45G ASN* 3.6 30.5 - - - +
46G HIS 3.9 0.9 - - - +
290G GLU* 5.8 0.2 - - - +
6401G PLP 4.3 8.7 - - + -
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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