Contacts of the helix formed by residues 7 - 24 (chain F) in PDB entry 6RI7
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 THR 7 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F VAL* 1.3 80.4 - - - +
8F ARG* 1.3 67.9 + - - +
9F GLU* 3.1 25.4 - - + +
10F GLY* 3.1 9.7 + - - +
11F TYR 2.9 18.4 + - - -
74F ILE* 4.7 0.9 - - - -
75F VAL 4.9 4.3 - - - +
76F ASP* 4.5 4.5 - - - +
87F PHE* 3.6 22.4 - - + -
88F GLY* 5.7 0.2 - - - -
104F ARG* 3.8 25.4 + - - +
106F VAL* 3.8 21.9 - - + +
107F GLY 5.2 2.2 - - - +
110F GLU* 6.1 3.6 - - - +
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Residues in contact with ARG 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F VAL 4.1 0.8 + - - -
7F THR* 1.3 75.7 - - - +
9F GLU* 1.3 69.3 + - - +
11F TYR* 3.1 11.3 + - - +
12F GLU* 2.9 45.9 + - - +
74F ILE* 3.3 48.4 - - - +
76F ASP* 3.2 45.1 + - - +
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Residues in contact with GLU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F THR* 3.1 22.3 - - + +
8F ARG* 1.3 80.6 + - - +
10F GLY* 1.3 58.2 + - - +
12F GLU* 3.3 20.0 + - - +
13F LYS* 2.9 27.9 + - - +
76F ASP* 4.0 7.2 - - - +
104F ARG* 4.8 9.2 + - - -
114F ARG* 5.3 4.0 + - - +
115F LYS* 3.3 32.1 - - + +
156F VAL* 5.9 2.6 - - - +
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Residues in contact with GLY 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F VAL* 4.7 1.8 - - - -
7F THR* 3.1 13.3 + - - +
9F GLU* 1.3 80.0 - - - +
11F TYR* 1.3 55.7 + - - +
13F LYS* 3.2 7.2 + - - +
14F LEU* 2.8 35.5 + - - +
110F GLU* 3.7 29.6 - - - +
114F ARG* 6.1 0.9 - - - -
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Residues in contact with TYR 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948D SER* 4.6 5.9 - - - -
1022D PRO* 3.8 27.4 - - + +
6F VAL* 3.9 17.3 - - + +
7F THR 2.9 12.9 + - - +
8F ARG* 3.1 13.2 + - - +
10F GLY* 1.3 71.7 - - - +
12F GLU* 1.3 69.4 + - + +
14F LEU* 3.1 12.3 + - + +
15F LYS* 3.0 44.6 + - + +
69F MET* 3.1 49.4 + - + +
72F LEU* 5.1 10.1 - - + -
74F ILE* 3.4 35.4 - - + -
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Residues in contact with GLU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ARG* 2.9 36.3 + - + +
9F GLU* 3.3 21.9 - - - +
11F TYR* 1.3 78.1 - - + +
13F LYS* 1.3 58.0 + - - +
15F LYS* 3.3 12.9 + - + +
16F GLN* 2.9 28.3 + - - +
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Residues in contact with LYS 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F GLU 2.9 14.7 + - - +
10F GLY* 3.2 9.6 + - - +
12F GLU* 1.3 76.7 - - - +
14F LEU* 1.3 59.0 - - + +
16F GLN* 3.1 19.9 + - + +
17F GLU* 2.9 54.3 + - + +
110F GLU* 4.2 19.3 - - - +
112F PHE* 4.9 12.8 - - - -
114F ARG* 3.5 51.2 - - - +
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Residues in contact with LEU 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F VAL* 5.1 4.5 - - + -
10F GLY 2.8 19.4 + - - +
11F TYR* 3.1 20.8 + - + +
13F LYS* 1.3 75.0 - - + +
15F LYS* 1.3 66.5 + - - +
17F GLU* 3.3 9.2 + - - +
18F LEU* 2.9 24.5 + - - +
61F ARG* 5.2 3.1 - - - +
65F LEU* 3.9 32.5 - - + +
68F CYS* 5.3 5.8 - - + -
69F MET* 4.4 15.5 - - + -
72F LEU* 4.3 23.3 - - + -
109F ASP* 4.4 17.3 - - + +
110F GLU* 3.9 17.0 - - + +
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Residues in contact with LYS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944D ALA 4.9 1.8 + - - -
945D ALA* 4.5 7.1 + - - +
948D SER* 2.4 36.2 + - - -
949D SER* 5.5 4.3 - - - -
11F TYR* 3.0 38.2 + - + +
12F GLU* 3.5 10.3 - - + +
14F LEU* 1.3 74.3 - - - +
16F GLN* 1.3 57.0 + - - +
18F LEU* 3.2 9.8 + - + +
19F ASN* 2.9 44.8 + - - +
69F MET* 3.5 24.8 - - + +
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Residues in contact with GLN 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F GLU 2.9 13.3 + - - +
13F LYS* 3.2 26.0 + - + +
14F LEU 3.1 0.2 - - - -
15F LYS* 1.3 79.0 - - - +
17F GLU* 1.3 59.9 + - + +
19F ASN* 3.3 5.4 + - - +
20F TYR* 2.9 30.8 + - + +
114F ARG* 5.2 5.7 + - - -
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Residues in contact with GLU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LYS* 2.9 47.8 + - + +
14F LEU* 3.9 6.4 - - - +
16F GLN* 1.3 73.9 - - + +
18F LEU* 1.3 64.1 + - - +
20F TYR* 4.1 8.1 - - + -
21F LEU* 2.9 40.5 + - + +
61F ARG* 2.8 36.0 + - - +
65F LEU* 4.1 8.0 - - + +
112F PHE* 5.1 6.6 - - - -
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Residues in contact with LEU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941D ALA* 4.9 15.0 - - + +
944D ALA* 5.2 9.2 - - + -
945D ALA* 5.5 7.4 - - + +
14F LEU 2.9 13.9 + - - +
15F LYS* 3.4 13.0 - - + +
16F GLN 3.2 0.2 - - - -
17F GLU* 1.3 77.7 - - - +
19F ASN* 1.3 64.0 + - - +
21F LEU* 3.9 2.5 - - + +
22F TRP* 2.9 34.5 + - + +
62F VAL* 3.6 37.9 - - + +
65F LEU* 5.0 14.1 - - + +
66F THR* 4.7 7.0 - - + +
69F MET* 5.0 18.8 - - + -
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Residues in contact with ASN 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827D GLU* 5.1 6.8 - - - +
945D ALA* 5.4 8.0 - - - +
15F LYS* 2.9 31.0 + - - +
16F GLN* 3.8 5.1 - - - +
18F LEU* 1.3 80.7 - - - +
20F TYR* 1.3 66.2 + - - +
22F TRP* 5.1 1.3 - - - -
23F ARG* 2.9 59.9 + - + +
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Residues in contact with TYR 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLN* 2.9 19.4 + - + +
17F GLU* 3.2 8.9 + - + +
19F ASN* 1.3 75.5 - - - +
21F LEU* 1.3 74.0 + - + +
23F ARG* 5.3 2.7 - - - +
24F GLU* 3.0 66.0 + - + +
25F GLU* 3.2 27.8 + - + +
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F GLU* 2.9 39.5 + - + +
18F LEU* 4.0 3.6 - - + +
20F TYR* 1.3 98.2 - - + +
22F TRP* 1.3 58.2 + - + +
23F ARG 2.9 10.1 + - - -
25F GLU* 3.3 13.3 + - - +
26F ARG* 3.0 29.5 + - - +
58F ILE* 3.5 39.5 - - + +
61F ARG* 4.8 22.0 - - + +
62F VAL* 5.7 7.6 - - + +
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Residues in contact with TRP 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827D GLU* 4.3 25.8 + - - +
832D LYS* 5.5 10.1 - - - +
937D ILE* 4.8 15.5 - - + -
938D GLY* 4.5 16.1 + - - -
941D ALA* 3.2 34.4 - - + +
942D SER* 5.0 1.5 - - - +
1243D LEU* 3.9 28.7 - - + -
18F LEU* 2.9 30.0 + - + +
19F ASN* 4.7 1.1 - - - +
21F LEU* 1.3 73.3 - - - +
23F ARG* 1.3 56.3 + - - +
26F ARG* 4.2 26.5 - - + +
27F PRO* 4.4 8.9 - - - +
58F ILE* 6.5 0.7 - - + -
59F ASP* 4.8 6.7 - - - -
62F VAL* 4.7 17.7 - - + -
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Residues in contact with ARG 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827D GLU* 3.6 40.8 + - + +
829D GLY* 5.5 6.1 - - - +
951D GLN* 6.0 3.8 - - - +
19F ASN* 2.9 46.0 + - + +
20F TYR* 5.3 1.4 - - - +
22F TRP* 1.3 80.5 - - - +
24F GLU* 1.3 80.6 + - + +
27F PRO* 3.2 19.3 - - - +
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Residues in contact with GLU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F TYR* 3.0 46.8 + - + +
23F ARG* 1.3 103.7 + - + +
25F GLU* 1.3 66.1 + - - +
27F PRO* 3.1 12.4 - - - +
28F GLU* 3.2 29.0 + - - +
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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
------------------------------------------------------------
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