Contacts of the helix formed by residues 11 - 22 (chain P) in PDB entry 3K9Q
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 GLY 11 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0P NAD 3.1 31.8 + - - -
9P GLY 3.1 9.1 + - - -
10P PHE* 1.4 74.3 - - - +
12P ARG* 1.3 61.2 + - - -
13P ILE 3.4 2.2 - - - -
14P GLY 4.1 0.6 - - - +
15P ARG* 2.8 43.6 + - - +
96P CYS 5.3 0.2 - - - -
190Q PRO* 5.1 0.9 - - - -
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Residues in contact with ARG 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0P NAD 3.1 32.1 + - - +
11P GLY* 1.3 70.4 - - - +
13P ILE* 1.3 68.9 + - + +
15P ARG* 3.1 23.5 - - - +
16P LEU* 3.0 37.2 + - - +
48P ASP* 2.7 44.5 + - - -
50P MET* 5.1 2.8 - - - +
51P GLN* 3.4 7.3 - - - +
182P GLY 6.1 0.2 - - - +
317P GLU* 2.8 50.6 + - + +
187Q GLN* 4.0 24.6 + - + -
188Q ASP* 3.3 29.7 - - - +
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Residues in contact with ILE 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0P NAD 2.9 79.5 + - + +
12P ARG* 1.3 74.5 - - - +
14P GLY* 1.3 58.4 + - - +
16P LEU* 3.7 1.1 - - + +
17P ALA* 2.8 28.6 + - + +
96P CYS* 4.3 4.7 - - + -
120P SER* 3.9 13.0 - - - +
317P GLU* 4.1 16.8 - - + +
320P TYR* 4.3 5.8 - - + -
321P THR* 3.9 20.9 - - - +
324P LEU* 3.9 27.8 - - + -
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Residues in contact with GLY 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0P NAD 4.6 0.2 + - - -
7P ILE* 3.4 27.0 - - - +
9P GLY 3.4 24.0 + - - -
10P PHE* 4.2 2.9 - - - -
11P GLY* 3.4 5.3 + - - +
12P ARG 3.3 0.4 - - - -
13P ILE* 1.3 77.8 - - - +
15P ARG* 1.3 57.7 + - - +
17P ALA* 3.2 2.9 + - - +
18P PHE* 2.9 23.0 + - - +
96P CYS* 4.0 9.9 - - - +
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Residues in contact with ARG 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P PHE* 2.8 70.0 + - + +
11P GLY* 2.8 37.3 + - - +
12P ARG* 3.1 28.2 - - - +
14P GLY* 1.3 68.6 - - - -
16P LEU* 1.3 67.1 + - + +
18P PHE* 3.0 4.9 + - - +
19P ARG* 2.9 31.7 + - - +
44P LEU* 3.1 55.6 + - - +
45P LEU* 3.9 6.8 - - + +
48P ASP* 5.2 1.3 + - - +
188Q ASP* 2.9 36.4 + - - +
190Q PRO* 4.3 4.2 - - - +
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Residues in contact with LEU 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P ARG* 3.0 30.9 + - - +
15P ARG* 1.3 80.7 - - + +
17P ALA* 1.3 56.6 + - - +
19P ARG* 3.4 24.4 + - - +
20P ARG* 3.0 29.5 + - - +
48P ASP* 3.6 22.9 - - - +
51P GLN* 3.8 26.2 - - + -
317P GLU* 3.6 37.7 - - + -
318P MET* 4.3 13.6 - - + +
321P THR* 3.5 17.5 - - + +
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Residues in contact with ALA 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P ILE* 4.6 0.4 - - + -
13P ILE 2.8 19.4 + - - +
14P GLY* 3.6 4.3 - - - +
15P ARG 3.2 0.2 - - - -
16P LEU* 1.3 75.8 - - - +
18P PHE* 1.3 58.4 + - - +
20P ARG* 3.8 1.0 - - - +
21P ILE* 2.9 37.2 + - - +
94P LEU* 3.5 31.9 - - + -
321P THR* 3.4 16.3 - - + +
324P LEU* 4.9 5.8 - - + -
325P VAL* 4.2 8.3 - - + -
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Residues in contact with PHE 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P ILE* 3.8 6.9 - - + +
10P PHE* 3.8 22.2 - + + -
14P GLY 2.9 13.5 + - - +
15P ARG 3.0 8.5 + - - +
17P ALA* 1.3 79.1 - - - +
19P ARG* 1.3 65.7 + - - +
21P ILE* 3.3 1.9 + - - +
22P GLN* 3.3 48.6 + - + +
29P VAL* 3.6 42.4 - - + -
32P VAL* 4.7 0.2 - - + -
45P LEU* 3.7 32.5 - - + -
54P PHE* 4.7 1.1 - + - -
65P PHE* 4.7 3.1 - + - -
67P VAL* 3.9 26.7 - - + -
72P VAL* 3.9 18.8 - - + -
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Residues in contact with ARG 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P ARG* 2.9 16.9 + - - +
16P LEU* 3.7 24.3 - - + +
18P PHE* 1.3 78.1 - - - +
20P ARG* 1.3 62.4 + - - +
22P GLN* 3.1 25.0 + - - +
23P GLU* 3.9 8.7 + - - +
44P LEU 4.8 0.4 + - - -
45P LEU* 3.0 34.0 + - + +
46P LYS 4.0 1.6 + - - -
48P ASP* 3.3 21.0 + - - +
51P GLN* 3.7 20.0 + - - +
52P GLY 2.9 30.5 + - - -
53P ARG 4.0 5.1 + - - -
54P PHE* 3.5 34.4 - - + +
318P MET* 5.3 8.5 - - + +
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Residues in contact with ARG 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LEU 3.0 17.5 + - - +
17P ALA 3.8 3.6 - - - +
18P PHE 3.3 0.2 - - - -
19P ARG* 1.3 77.2 - - - +
21P ILE* 1.3 63.6 + - - +
23P GLU* 3.2 45.4 + - - +
24P VAL* 3.4 23.6 - - - +
287P THR* 3.6 24.0 + - - +
318P MET* 4.5 15.3 - - - -
321P THR* 4.2 7.6 - - + -
322P ALA* 3.9 24.1 + - - +
325P VAL* 4.0 21.9 - - + +
326P ARG* 4.2 24.2 - - - +
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Residues in contact with ILE 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P VAL* 4.3 9.4 - - + -
7P ILE* 4.8 1.1 - - + -
17P ALA 2.9 24.6 + - - +
18P PHE 3.7 4.0 - - - +
19P ARG 3.2 0.2 - - - -
20P ARG* 1.3 71.8 - - - +
22P GLN* 1.3 66.2 + - - +
23P GLU 3.0 6.0 + - - -
24P VAL* 3.2 23.5 + - - +
27P LEU* 3.7 36.7 - - + +
28P GLU* 4.4 0.7 - - - -
29P VAL* 3.7 33.9 - - + +
94P LEU* 4.6 7.9 - - + -
325P VAL* 4.1 19.1 - - + -
328P LEU* 3.9 22.0 - - + -
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Residues in contact with GLN 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P PHE* 3.3 50.6 + - + +
19P ARG 3.1 14.8 + - - +
21P ILE* 1.3 83.9 - - - +
23P GLU* 1.3 57.0 + - + +
24P VAL 3.6 1.1 + - - -
29P VAL* 5.0 2.4 + - - +
54P PHE* 4.2 19.3 - - + -
67P VAL* 4.1 18.2 + - - +
68P ASN* 4.6 9.3 + - - +
70P LYS* 4.8 19.0 - - - +
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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
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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