Contacts of the helix formed by residues 16 - 32 (chain A) in PDB entry 3P3W
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 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.7 17.4 - - - +
13A MET* 2.7 40.1 + - + +
14A ARG 3.7 9.0 - - - +
15A ASN* 1.3 81.9 - - + +
17A VAL* 1.3 62.9 + - - +
18A GLN 3.5 1.8 - - - -
19A GLU* 3.5 23.1 - - - +
20A HIS* 3.1 23.0 + - - +
76A PHE* 4.4 26.5 - - + -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 3.4 14.3 + - - +
16A THR* 1.3 82.8 - - - +
18A GLN* 1.3 61.1 + - - +
20A HIS* 3.3 16.7 + - + +
21A SER* 3.3 14.7 + - - -
268A PRO* 3.8 29.4 - - + +
269A GLU* 4.1 16.4 - - + -
276A LYS* 5.6 2.6 - - - +
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 1.3 75.8 - - - +
19A GLU* 1.3 64.8 + - - +
21A SER* 3.1 6.5 + - - -
22A ALA* 2.9 27.7 + - - +
259A TRP* 4.2 18.3 - - + +
268A PRO 4.6 0.7 - - - +
269A GLU* 3.2 44.1 + - + +
273A ALA* 3.2 10.2 + - - +
274A PRO 2.8 27.2 + - - -
275A LEU* 3.8 3.5 - - - +
276A LYS* 3.0 36.5 + - + +
279A SER* 2.8 24.3 + - - +
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.6 13.9 - - + -
15A ASN 4.1 6.9 - - - +
16A THR* 3.5 34.0 - - - +
17A VAL 4.0 0.2 + - - -
18A GLN* 1.3 81.4 + - - +
20A HIS* 1.3 57.2 + - - +
22A ALA* 3.4 3.7 + - - -
23A PHE* 2.9 27.5 + - - +
76A PHE* 3.9 15.3 - - + -
276A LYS* 4.2 11.2 + - - +
278A THR* 2.7 28.8 + - - +
279A SER* 3.5 22.4 + - - +
282A THR* 3.4 19.2 - - - +
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Residues in contact with HIS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.6 23.3 - - + -
16A THR 3.1 13.8 + - - +
17A VAL* 3.4 12.8 - - - +
18A GLN 3.2 0.2 - - - -
19A GLU* 1.3 75.4 - - - +
21A SER* 1.3 63.0 + - - +
23A PHE* 3.2 7.5 + + - +
24A ARG* 2.9 35.1 + - + +
45A TYR* 5.0 12.5 + + - -
47A VAL* 3.8 28.5 - - + +
49A HIS* 3.9 29.2 + + + -
266A GLU 5.9 1.1 - - - -
268A PRO* 5.3 9.9 - - + -
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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 VAL 3.3 3.2 + - - -
18A GLN* 3.1 8.6 + - - -
20A HIS* 1.3 77.6 - - - +
22A ALA* 1.3 63.1 + - - +
24A ARG* 3.5 2.2 + - - +
25A PHE* 3.1 26.3 + - - +
259A TRP* 3.9 12.4 - - - -
266A GLU 5.7 0.4 - - - -
267A PHE* 3.8 24.3 - - - +
268A PRO* 2.6 49.6 + - - +
270A ALA* 5.0 0.7 - - - -
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Residues in contact with ALA 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 GLN 2.9 16.5 + - - +
19A GLU 3.5 5.8 - - - +
21A SER* 1.3 75.8 - - - +
23A PHE* 1.3 60.4 + - - +
25A PHE* 4.2 1.5 - - - +
26A ALA* 3.3 23.6 + - - +
255A PHE* 6.0 2.4 - - + -
259A TRP* 3.7 19.0 - - + -
275A LEU* 5.9 0.4 - - + -
279A SER* 3.3 37.0 - - - +
282A THR* 4.1 5.3 - - - +
283A HIS* 4.4 6.7 - - + +
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Residues in contact with PHE 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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8A ILE* 4.0 21.5 - - + -
9A GLY 5.0 0.4 - - - -
10A GLY* 4.7 11.9 - - - -
12A PHE* 3.6 22.2 - + + -
19A GLU 2.9 14.2 + - - +
20A HIS* 3.3 14.4 - + - +
22A ALA* 1.3 75.8 - - - +
24A ARG* 1.3 64.7 + - + +
26A ALA* 3.4 10.4 + - - +
27A VAL* 3.3 22.9 + - + +
45A TYR* 3.5 47.1 - + + -
47A VAL* 5.2 1.1 - - + -
74A PHE* 3.6 41.3 - + + -
282A THR* 3.8 5.6 - - + -
286A ILE* 3.7 23.3 - - + -
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Residues in contact with ARG 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 HIS* 2.9 27.3 + - + +
21A SER* 4.1 2.0 - - - +
23A PHE* 1.3 77.6 - - - +
25A PHE* 1.3 61.1 + - - +
27A VAL* 3.4 8.5 + - - +
28A GLN* 3.4 41.4 + - + +
45A TYR* 3.4 27.3 + - + +
266A GLU* 2.9 46.2 + - - +
267A PHE* 3.9 18.2 - - + -
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Residues in contact with PHE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER 3.1 17.8 + - - +
22A ALA 4.4 2.0 - - - +
24A ARG* 1.3 72.4 - - - +
26A ALA* 1.3 65.9 + - - +
27A VAL 3.1 2.0 - - - -
28A GLN* 3.1 22.8 + - + +
29A LEU* 3.2 41.3 + - + +
255A PHE* 3.7 30.1 - + - -
258A ARG* 4.0 33.0 - - + -
259A TRP* 4.2 12.3 - + + -
262A LEU* 3.7 41.3 - - + -
267A PHE* 3.9 12.7 - + + -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 3.3 19.2 + - - +
23A PHE 3.7 5.4 - - - +
24A ARG 3.3 0.4 - - - -
25A PHE* 1.3 78.3 - - - +
27A VAL* 1.3 61.4 - - - +
29A LEU* 3.9 22.8 - - - +
30A TYR* 4.2 4.5 + - - +
283A HIS* 4.1 19.5 - - + -
286A ILE* 3.4 43.6 - - + +
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Residues in contact with VAL 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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8A ILE* 5.6 1.8 - - + -
23A PHE* 3.3 24.2 - - + +
24A ARG 3.4 7.1 + - - +
25A PHE 3.1 0.4 - - - -
26A ALA* 1.3 79.7 - - - +
28A GLN* 1.3 60.7 + - + +
30A TYR* 3.4 3.6 + - - +
31A ASN* 3.1 35.6 + - - +
43A LEU* 3.4 46.4 - - + +
45A TYR* 4.0 33.0 - - + -
286A ILE* 4.9 6.7 - - + -
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Residues in contact with GLN 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 ARG* 3.4 30.2 + - + +
25A PHE* 3.1 17.7 + - + +
27A VAL* 1.3 81.8 - - + +
29A LEU* 1.3 57.0 + - - +
31A ASN* 3.9 6.4 - - - +
32A THR* 3.0 34.3 + - - +
262A LEU* 5.7 1.2 - - - +
267A PHE* 3.5 31.7 - - - -
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Residues in contact with LEU 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 PHE* 3.2 49.5 + - + +
26A ALA* 3.9 10.3 - - - +
28A GLN* 1.3 75.6 - - - +
30A TYR* 1.3 66.5 + - + +
32A THR* 3.3 21.7 - - + +
33A ASN* 4.4 5.7 - - - +
255A PHE* 4.6 4.9 - - + -
258A ARG* 6.5 1.6 - - - -
283A HIS* 4.2 26.9 - - + +
286A ILE* 5.9 2.5 - - + -
287A LEU* 5.4 9.0 - - + -
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Residues in contact with TYR 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 ALA 4.3 8.7 - - - +
27A VAL* 3.4 6.5 + - - +
28A GLN 3.2 0.4 - - - -
29A LEU* 1.3 85.3 - - + +
31A ASN* 1.3 75.7 + - - +
32A THR 3.2 2.5 + - - -
33A ASN* 3.8 17.8 - - - +
38A GLU* 3.4 12.8 - - + -
39A LYS* 3.7 14.5 - - + +
40A PRO* 3.4 8.7 - - - +
41A PHE* 3.0 67.9 + + - -
43A LEU* 4.1 21.5 - - + -
286A ILE* 5.6 4.3 - - + -
290A ALA* 4.7 11.2 - - + -
294A ARG* 3.3 28.8 + - - -
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Residues in contact with ASN 31 (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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27A VAL* 3.1 26.1 + - - +
28A GLN* 3.9 6.0 - - - +
30A TYR* 1.3 80.0 - - - +
32A THR* 1.3 58.0 + - - +
33A ASN* 2.9 12.3 + - - +
42A HIS* 3.3 40.9 + - + +
43A LEU* 3.0 46.5 + - - +
44A ASN* 4.6 0.6 + - - -
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN 3.0 21.6 + - - +
29A LEU* 3.3 19.7 - - + +
30A TYR 4.2 0.4 - - - -
31A ASN* 1.3 72.7 - - - +
33A ASN* 1.3 66.8 + - - +
34A GLN* 3.5 5.5 - - - +
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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