Contacts of the helix formed by residues 9 - 27 (chain A) in PDB entry 4KPF
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 LEU 9 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 1.3 72.3 + - - +
10A GLU* 1.3 64.4 + - - +
12A ILE* 3.0 1.5 + - - -
13A MET* 3.0 51.7 + - + +
519C LEU* 4.1 22.4 - - + +
523C TYR* 3.3 47.6 - - + -
530C VAL* 5.9 4.9 - - + -
606C VAL* 4.2 15.3 - - + -
607C THR 2.7 20.0 + - - +
608C ILE* 4.7 6.3 - - + -
614C ALA* 4.4 11.4 - - + -
617C ARG* 5.3 0.2 - - - -
618C VAL* 4.1 12.1 - - + -
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 3.1 11.5 + - - +
9A LEU* 1.3 79.8 - - - +
11A ASP* 1.3 61.9 + - - +
14A GLY 3.5 7.1 + - - -
610C ASP 6.0 1.3 - - - +
613C ARG* 4.4 23.6 - - + +
614C ALA* 4.6 9.1 - - + +
617C ARG* 2.9 44.2 + - + +
618C VAL* 6.5 0.2 - - - -
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Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 5.2 5.2 - - + -
8A SER* 3.4 27.8 + - - +
9A LEU 3.2 0.6 - - - -
10A GLU* 1.3 81.5 - - - +
12A ILE* 1.3 59.9 + - - +
14A GLY* 3.9 1.7 - - - -
15A GLU* 3.5 21.8 + - - +
617C ARG* 5.1 2.1 + - - +
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 4.9 11.2 - - + +
8A SER 2.8 18.5 + - - +
9A LEU* 3.0 3.6 + - - +
11A ASP* 1.3 74.5 - - - +
13A MET* 1.3 66.5 - - - +
14A GLY 3.1 1.1 - - - -
15A GLU* 5.4 1.1 - - - -
16A ARG* 3.2 40.3 + - + +
519C LEU* 4.3 20.2 - - + -
537C ILE* 5.2 7.6 - - + -
604C ILE* 6.0 2.7 - - + -
606C VAL* 5.6 4.7 - - + -
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Residues in contact with MET 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.0 33.0 + - + +
12A ILE* 1.3 72.8 - - - +
14A GLY* 1.3 60.2 + - - +
16A ARG* 4.0 0.7 - - - -
17A PHE* 3.0 32.9 + - - +
516C THR* 3.5 26.9 - - - +
519C LEU* 3.8 22.2 - - - -
520C THR* 3.3 30.5 - - + -
617C ARG* 4.2 8.7 - - + -
618C VAL* 4.1 21.5 - - + -
621C LEU* 3.4 15.6 - - + +
622C MET* 3.7 20.0 - - + -
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Residues in contact with GLY 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU 3.5 13.8 + - - -
11A ASP* 3.7 4.9 + - - -
12A ILE 3.1 1.0 - - - -
13A MET* 1.3 78.7 - - - +
15A GLU* 1.3 63.1 + - - +
18A GLY* 3.0 25.5 + - - -
617C ARG* 4.2 12.1 - - - +
632C TRP* 4.3 16.2 - - - -
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP 3.5 15.3 + - - +
14A GLY* 1.3 72.5 - - - +
16A ARG* 1.3 79.6 + - - +
18A GLY* 5.5 0.2 - - - -
19A ARG* 3.0 27.5 + - - +
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.2 26.9 + - + +
13A MET* 4.2 0.4 - - - +
14A GLY 3.1 1.0 - - - -
15A GLU* 1.3 97.1 + - - +
17A PHE* 1.3 61.4 + - - +
19A ARG* 3.3 3.9 + - - +
20A TYR* 3.0 28.8 + - - +
512C ALA* 3.6 34.3 - - - +
515C GLN* 3.1 36.0 + - + +
516C THR* 3.7 17.3 - - - +
519C LEU* 6.4 1.3 - - + -
537C ILE* 5.0 6.7 - - + +
539C LEU* 5.7 2.2 - - - +
604C ILE* 4.2 22.4 - - - +
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Residues in contact with PHE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET 3.0 18.3 + - - +
14A GLY 4.4 0.2 - - - +
16A ARG* 1.3 73.9 - - - +
18A GLY* 1.3 62.2 + - - +
20A TYR* 4.6 9.6 - + - -
21A SER* 2.8 48.6 + - - -
172A ALA* 4.7 11.7 - - + -
513C HIS* 4.7 13.2 - + - -
516C THR* 4.1 15.9 - - + +
621C LEU* 3.6 47.8 - - + -
622C MET* 3.9 24.7 - - + -
629C ARG* 4.1 26.2 - - + -
632C TRP* 4.8 5.2 - + + -
633C ILE* 4.5 5.6 - - + -
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLY 3.0 14.7 + - - -
15A GLU* 5.5 0.4 - - - -
17A PHE* 1.3 74.5 - - - +
19A ARG* 1.3 66.7 + - - +
21A SER* 4.4 0.4 - - - -
22A LYS* 3.1 26.9 + - - +
632C TRP* 4.3 13.4 - - - -
637C VAL* 3.9 20.5 - - - +
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Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.0 24.6 + - - +
16A ARG* 3.3 7.6 + - - +
17A PHE 3.3 0.2 - - - -
18A GLY* 1.3 76.6 - - - +
20A TYR* 1.3 62.9 + - - +
22A LYS* 3.7 4.6 + - - +
23A TYR* 3.3 19.8 + - - +
509C THR* 3.8 8.1 - - + +
512C ALA* 4.5 9.0 - - + -
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG 3.0 13.0 + - - +
17A PHE* 3.9 14.6 - + - +
19A ARG* 1.3 77.0 - - - +
21A SER* 1.3 70.4 + - - +
23A TYR* 3.0 4.3 + - - +
24A ILE* 2.9 59.9 + - + +
28A ARG* 3.9 8.2 + - - -
172A ALA* 5.2 5.2 - - + -
458C LYS* 3.6 9.7 + - - -
509C THR* 3.7 31.0 - - - +
510C ASP* 3.7 19.3 - - - -
512C ALA* 4.9 0.4 - - - +
513C HIS* 3.2 63.3 + + + +
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 2.8 34.9 + - - -
18A GLY* 3.9 5.2 - - - -
20A TYR* 1.3 76.8 - - - +
22A LYS* 1.3 65.5 + - - +
24A ILE* 3.1 11.0 + - - +
25A ILE* 2.9 28.3 + - - +
172A ALA* 4.6 4.5 - - - -
633C ILE* 3.9 28.5 - - - -
637C VAL* 4.8 4.5 - - - -
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLY 3.1 16.9 + - - +
19A ARG* 3.8 4.5 - - - +
21A SER* 1.3 78.4 - - - +
23A TYR* 1.3 57.3 + - - +
25A ILE* 3.5 4.9 + - - +
26A GLN* 3.0 64.2 + - - +
637C VAL* 4.3 24.1 - - + +
638C LYS 2.9 27.7 + - - +
639C PHE* 4.2 6.8 + - - +
640C THR* 5.5 2.0 - - - -
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG 3.3 3.0 + - - +
20A TYR* 3.0 4.0 + + - +
22A LYS* 1.3 81.1 - - - +
24A ILE* 1.3 61.3 + - + +
26A GLN* 5.1 1.3 - - - -
27A ASP* 2.7 73.9 + - + +
28A ARG* 3.7 30.9 - - - -
43A ARG* 5.1 6.6 + - - -
74A HIS* 5.7 0.5 - - - -
75A PRO* 5.5 1.9 - - - +
76A HIS* 3.3 24.7 + + - -
509C THR* 3.1 49.8 - - + -
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 2.9 51.6 + - + +
21A SER* 3.3 20.2 - - - +
23A TYR* 1.3 75.0 - - + +
25A ILE* 1.3 57.0 + - - +
28A ARG* 3.8 33.9 - - + +
29A ALA* 3.2 29.8 + - + +
170A ILE 4.7 4.0 - - - +
171A SER* 3.6 25.7 + - - +
172A ALA* 4.0 16.4 - - + -
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER 2.9 25.8 + - - +
22A LYS 3.8 2.7 - - - +
24A ILE* 1.3 80.5 - - + +
26A GLN* 1.3 64.7 + - - +
27A ASP 3.3 0.6 + - - -
30A LEU* 3.7 31.2 + - + +
171A SER* 3.3 19.1 - - - +
172A ALA 3.5 20.2 - - - +
174A TYR* 4.3 8.3 - - + -
332A ILE* 3.6 14.3 - - + +
337A PRO* 3.8 28.9 - - + -
633C ILE* 4.2 23.6 - - + -
639C PHE* 4.1 14.1 - - + -
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.0 42.7 + - - +
23A TYR* 5.3 0.5 - - - -
25A ILE* 1.3 78.4 - - + +
27A ASP* 1.3 76.9 + - - +
28A ARG 3.9 0.7 - - - -
30A LEU 5.0 3.4 - - - +
39A PRO* 4.7 2.9 - - - +
332A ILE* 4.3 16.5 - - + +
335A PHE* 3.0 39.3 + - + +
639C PHE* 3.4 44.4 + - + +
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Residues in contact with ASP 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 2.7 54.3 + - + +
26A GLN* 1.3 91.4 - - - +
28A ARG* 1.3 61.9 + - - +
39A PRO* 3.0 29.2 - - + +
43A ARG* 5.6 1.4 + - - -
74A HIS* 5.8 2.8 - - - -
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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
------------------------------------------------------------
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