Contacts of the helix formed by residues 14 - 30 (chain A) in PDB entry 2FVY
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 ASP 14 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TYR* 2.6 39.8 + - + +
11A LYS* 3.2 23.2 + - + +
12A TYR 3.7 0.2 - - - +
13A ASP* 1.3 78.8 + - - +
15A ASN* 1.3 67.7 + - - +
16A PHE 3.2 5.9 + - - -
17A MET* 2.8 27.9 + - + +
18A SER* 2.8 22.4 + - - -
183A TRP* 4.5 4.6 - - - +
310A BGC 2.7 30.6 + - - -
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Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP 3.9 8.8 - - - +
14A ASP* 1.3 74.7 + - - +
16A PHE* 1.3 63.1 + - - +
18A SER* 3.3 13.9 + - - -
19A VAL* 3.3 17.8 + - - +
183A TRP 4.9 2.0 + - - +
184A ASP* 5.8 0.5 - - - -
185A THR* 4.4 7.1 + - - -
211A ASN* 6.1 0.4 - - - +
213A ALA* 3.5 26.0 - - + +
216A MET* 3.9 23.0 - - - +
236A ASP* 6.0 0.2 - - - +
238A LEU* 3.6 20.6 - - + +
240A GLU* 4.9 5.3 + - - -
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Residues in contact with PHE 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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14A ASP* 3.2 3.9 + - - +
15A ASN* 1.3 79.1 - - - +
17A MET* 1.3 74.6 - - - +
19A VAL* 3.0 16.3 + - + +
20A VAL* 3.0 34.1 + - + +
91A ASN* 3.7 24.0 - - + -
236A ASP* 3.5 23.3 + - + +
238A LEU* 3.8 10.7 - - + +
256A ASN* 3.4 48.2 - - + -
258A ALA* 3.8 14.4 - - + -
261A GLN* 4.1 14.8 - - - -
310A BGC 3.5 32.5 + - - +
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Residues in contact with MET 17 (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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9A ILE* 4.0 20.6 - - + -
10A TYR* 3.9 14.6 - - + -
11A LYS 4.1 1.3 - - - +
12A TYR 4.6 0.4 - - - -
14A ASP* 2.8 29.8 + - + +
16A PHE* 1.3 85.4 - - + +
18A SER* 1.3 55.8 + - - +
20A VAL* 3.7 14.0 - - + +
21A ARG* 2.8 35.6 + - - +
66A ASN* 3.4 31.2 - - - +
90A PHE* 3.7 26.0 - - + -
91A ASN* 3.5 31.0 - - - +
310A BGC 4.6 1.1 - - - -
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Residues in contact with SER 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR 3.6 10.5 + - - -
13A ASP* 5.2 1.8 - - - -
14A ASP 2.8 13.8 + - - -
15A ASN* 3.3 13.9 - - - -
16A PHE 3.1 0.2 - - - -
17A MET* 1.3 73.7 - - - +
19A VAL* 1.3 65.8 + - - +
21A ARG* 3.4 18.1 + - - +
22A LYS* 3.1 53.2 + - - +
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Residues in contact with VAL 19 (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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15A ASN 3.3 14.6 + - - +
16A PHE* 3.0 8.6 + - + +
18A SER* 1.3 78.5 - - - +
20A VAL* 1.3 61.9 + - - +
22A LYS* 3.4 5.7 + - - +
23A ALA* 3.1 21.7 + - - +
238A LEU* 4.0 13.5 - - + -
239A PRO* 3.9 33.7 - - + -
258A ALA* 3.5 22.4 - - + -
259A ASN* 5.3 6.3 - - - +
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Residues in contact with VAL 20 (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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16A PHE* 3.0 46.0 + - + +
17A MET* 3.7 27.6 - - + +
19A VAL* 1.3 76.4 - - - +
21A ARG* 1.4 58.5 + - - +
23A ALA* 3.1 5.8 + - - +
24A ILE* 2.9 36.0 + - + +
90A PHE* 3.9 19.1 - - + -
91A ASN* 6.1 0.4 - - + -
258A ALA* 3.6 17.3 - - + +
261A GLN* 5.3 6.1 - - + +
262A ALA* 4.4 12.3 - - + +
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.8 24.4 - - + +
12A TYR* 2.9 81.2 + - - +
13A ASP* 5.0 2.0 - - - +
17A MET 2.8 22.0 + - - +
18A SER* 3.4 23.4 + - - +
20A VAL* 1.4 73.9 - - - +
22A LYS* 1.3 79.0 + - - +
24A ILE* 3.3 5.8 + - - +
25A GLU* 3.0 38.1 + - - +
38A MET* 3.6 16.6 - - + +
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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 SER* 3.1 38.4 + - - +
19A VAL* 3.9 5.8 - - - +
21A ARG* 1.3 95.2 - - - +
23A ALA* 1.3 60.9 + - - +
25A GLU* 3.3 22.0 + - - +
26A GLN* 3.2 26.1 + - - +
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Residues in contact with ALA 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 VAL 3.1 14.5 + - - +
20A VAL 3.1 8.0 + - - +
22A LYS* 1.3 74.7 - - - +
24A ILE* 1.3 64.3 + - - +
26A GLN* 3.1 9.5 + - - +
27A ASP* 3.0 27.0 + - - +
258A ALA 4.3 4.7 - - - +
259A ASN* 3.8 24.9 - - - +
262A ALA* 3.5 15.7 - - + -
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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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7A VAL* 4.4 13.2 - - + -
9A ILE* 4.7 0.4 - - + -
20A VAL* 2.9 22.9 + - + +
21A ARG* 3.3 10.5 + - - +
23A ALA* 1.3 74.9 - - - +
25A GLU* 1.4 64.3 + - - +
27A ASP* 3.1 9.2 + - - +
28A ALA* 2.9 21.5 + - - +
36A LEU* 4.4 22.9 - - + -
38A MET* 4.5 6.7 - - - -
90A PHE* 3.7 37.5 - - + -
262A ALA* 3.6 23.6 - - + +
265A THR* 4.6 9.0 - - + -
266A PHE* 4.9 13.5 - - + -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.0 21.7 + - - +
22A LYS* 3.5 28.2 + - - +
23A ALA 3.2 0.2 - - - -
24A ILE* 1.4 77.4 - - - +
26A GLN* 1.4 61.2 + - - +
28A ALA* 3.4 1.6 + - - +
29A LYS* 2.9 50.3 + - + +
36A LEU* 3.9 16.7 - - + +
38A MET* 3.5 22.1 - - + +
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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 3.2 12.5 + - - +
23A ALA* 3.1 10.7 + - - +
25A GLU* 1.4 74.0 - - - +
27A ASP* 1.3 67.1 + - - +
29A LYS* 3.2 36.7 + - - +
30A ALA* 3.1 22.5 + - - +
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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
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23A ALA* 3.0 19.6 + - - +
24A ILE* 3.6 6.4 - - - +
26A GLN* 1.3 76.4 - - - +
28A ALA* 1.3 62.4 + - - +
30A ALA* 3.3 15.8 + - - +
31A ALA* 3.6 6.8 + - - +
259A ASN 4.6 0.9 - - - +
262A ALA* 3.6 7.8 - - - +
263A LYS* 3.0 60.1 + - - +
266A PHE* 3.8 32.3 - - + -
267A ASP* 5.5 0.5 - - - +
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Residues in contact with ALA 28 (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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24A ILE 2.9 15.4 + - - +
25A GLU 3.8 3.8 - - - +
27A ASP* 1.3 77.6 - - - +
29A LYS* 1.3 63.4 + - + +
31A ALA* 3.0 24.3 + - - +
34A VAL* 4.4 11.8 - - + +
36A LEU* 4.0 31.6 - - + -
266A PHE* 3.6 25.5 - - + -
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Residues in contact with LYS 29 (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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25A GLU* 2.9 37.7 + - + +
26A GLN* 3.2 37.3 + - - +
28A ALA* 1.3 74.7 - - - +
30A ALA* 1.3 61.4 + - - +
31A ALA 3.4 4.5 + - - +
32A PRO* 4.7 2.4 - - - +
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Residues in contact with ALA 30 (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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26A GLN 3.1 10.9 + - - +
27A ASP* 3.6 11.9 - - - +
28A ALA 3.1 1.2 - - - -
29A LYS* 1.3 78.2 - - - +
31A ALA* 1.3 54.8 + - - +
32A PRO* 3.4 11.1 - - - +
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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