Contacts of the helix formed by residues 14 - 26 (chain A) in PDB entry 1YF9
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 ASN 14 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER* 1.3 81.0 + - - +
15A ARG* 1.3 58.7 + - - +
16A ARG* 3.1 8.3 + - - +
17A ARG* 2.9 44.0 + - + +
18A GLU* 3.2 25.3 + - - +
37A VAL* 5.8 0.5 - - - +
64A PRO 4.1 0.6 + - - -
65A SER 2.8 31.2 + - - +
66A ASP* 4.2 0.4 - - - +
67A TYR 2.8 27.9 + - - +
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 3.3 13.2 + - - +
14A ASN* 1.3 71.6 + - - +
16A ARG* 1.3 68.9 + - - +
18A GLU* 3.7 16.0 - - - +
19A MET* 3.0 28.6 + - - +
124C PRO* 3.4 53.5 + - + +
125C SER* 5.9 0.2 - - - +
126C ASP* 5.7 2.4 + - - -
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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
----------------------------------------------------------
14A ASN* 3.1 8.8 + - - +
15A ARG* 1.3 83.6 - - - +
17A ARG* 1.3 65.8 + - - +
19A MET* 3.3 24.5 + - + +
20A ASP* 3.0 29.2 + - - +
67A TYR* 4.2 4.0 - - + -
68A PRO* 4.1 27.8 - - + -
69A PHE* 6.1 3.4 - - - -
104A MET* 6.3 0.8 - - - +
99C GLN* 3.8 33.7 + - - +
123C ASN* 4.3 0.6 + - - -
124C PRO* 3.5 29.4 - - - +
125C SER* 5.2 1.2 - - - +
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 4.1 17.8 + - - -
14A ASN* 2.9 31.0 + - - +
16A ARG* 1.3 76.2 - - - +
18A GLU* 1.3 64.0 + - - +
20A ASP* 3.4 1.0 + - - +
21A TYR* 3.0 24.6 + - - +
36A THR* 5.7 0.6 + - - -
37A VAL* 4.0 22.5 - - + +
38A ALA* 3.7 18.1 - - - +
63A LEU* 2.8 51.5 + - + +
64A PRO 3.3 20.8 + - - -
65A SER* 3.5 15.8 - - - +
67A TYR* 3.6 17.3 - - + -
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Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN 3.2 15.3 + - - +
15A ARG* 3.7 16.8 - - - +
17A ARG* 1.3 80.2 - - - +
19A MET* 1.3 63.7 + - - +
21A TYR* 3.4 5.0 + - - +
22A MET* 3.0 42.0 + - + +
37A VAL* 4.6 15.9 - - + +
121C TYR* 4.0 19.5 + - + +
137C HIS* 4.0 22.3 + - - -
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Residues in contact with MET 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG 3.0 17.1 + - - +
16A ARG* 3.7 38.1 - - + +
17A ARG 3.3 0.2 - - - -
18A GLU* 1.3 75.9 + - - +
20A ASP* 1.3 73.5 + - - +
22A MET* 3.3 2.6 + - - +
23A ARG* 3.0 73.6 + - - +
600A CL 4.6 0.2 - - - -
121C TYR* 3.9 12.9 - - + +
122C PRO 3.7 12.1 - - - +
123C ASN* 3.8 10.1 - - - +
124C PRO* 3.8 21.1 - - + -
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Residues in contact with ASP 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 18.6 + - - +
17A ARG 4.1 0.9 - - - +
19A MET* 1.3 93.7 - - - +
21A TYR* 1.3 64.8 - - - +
23A ARG* 3.5 13.9 + - - +
24A LEU* 3.1 23.7 + - - +
63A LEU* 5.2 0.4 - - + -
67A TYR* 2.6 37.4 + - + +
68A PRO* 5.5 0.9 - - - +
105A TYR 5.1 2.8 - - - +
106A GLN* 5.5 7.1 + - - -
107A LEU* 4.0 23.8 + - + +
108A GLU* 4.8 3.2 - - - +
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Residues in contact with TYR 21 (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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17A ARG 3.0 18.4 + - - +
18A GLU 3.7 2.0 - - - +
20A ASP* 1.3 77.6 - - - +
22A MET* 1.3 87.8 + - + +
24A LEU* 3.2 7.4 + - + +
25A CYS* 3.0 49.0 + - - -
31A VAL* 4.9 0.4 - - + -
33A PRO* 3.3 28.8 - - - +
36A THR 4.6 1.9 + - - -
37A VAL* 3.5 41.1 - - + +
39A GLU 5.0 0.2 - - - -
40A PHE* 3.5 45.5 - + + -
63A LEU* 4.5 7.6 - - + +
107A LEU* 5.2 0.9 - - - -
401A CL 3.8 13.9 - - + +
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Residues in contact with MET 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 GLU* 3.0 28.4 + - + +
19A MET 3.8 0.4 - - - +
21A TYR* 1.3 101.8 - - + +
23A ARG* 1.3 58.3 + - - +
25A CYS* 3.3 7.1 + - - +
26A ASN* 2.9 32.7 + - - +
37A VAL* 4.3 11.9 - - + -
121C TYR* 3.4 45.3 - - + +
140C ARG* 3.5 25.2 + - - +
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET* 3.0 46.6 + - - +
20A ASP* 3.8 14.3 + - - +
21A TYR 3.3 0.2 - - - -
22A MET* 1.3 76.9 - - - +
24A LEU* 1.3 62.4 + - - +
26A ASN 3.6 5.4 + - - +
27A SER* 4.0 1.9 - - - -
106A GLN* 5.4 7.7 - - - +
108A GLU* 3.9 5.2 - - - +
600A CL 3.2 32.3 - - - +
117C GLN* 3.0 56.4 + - - +
118C LEU* 3.7 15.0 - - - +
120C ARG* 3.2 29.8 - - + -
121C TYR* 2.8 36.7 + - + +
123C ASN 3.7 2.2 - - - +
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Residues in contact with LEU 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 ASP 3.1 11.8 + - - +
21A TYR* 3.2 10.5 + - + +
23A ARG* 1.3 77.4 - - - +
25A CYS* 1.3 56.9 + - - +
27A SER* 2.7 24.4 + - - -
29A ARG* 3.8 19.8 - - - +
31A VAL* 3.9 16.6 - - + +
40A PHE* 3.6 32.1 - - + -
42A VAL* 4.2 7.6 - - + -
107A LEU* 4.2 11.0 - - + -
108A GLU* 3.6 35.6 + - + +
111A PHE* 3.6 33.9 - - + -
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Residues in contact with CYS 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 TYR* 3.0 58.3 + - + +
22A MET* 3.3 9.2 + - - +
24A LEU* 1.3 77.7 - - - +
26A ASN* 1.3 55.7 + - - +
27A SER 3.0 13.7 + - - +
29A ARG 5.2 2.8 - - - +
31A VAL* 3.8 25.1 - - - -
33A PRO* 5.8 1.1 - - - -
49C GLY 5.0 0.2 - - - +
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Residues in contact with ASN 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 MET 2.9 17.8 + - - +
23A ARG 3.6 1.1 + - - -
24A LEU 3.4 0.6 - - - -
25A CYS* 1.3 73.3 - - - +
27A SER* 1.3 57.8 + - - +
49C GLY 3.3 20.9 - - - +
50C THR* 3.4 21.0 - - - +
51C PRO* 4.1 12.1 - - - +
119C LEU 4.4 1.4 + - - -
120C ARG* 2.7 58.3 + - + +
140C ARG* 3.5 21.8 + - - +
144C ASP* 5.1 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
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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