Contacts of the helix formed by residues 16 - 32 (chain E) in PDB entry 3IYD
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 ARG 16 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1281C TYR 5.0 0.6 + - - -
482D ALA* 4.0 17.9 + - + +
483D LEU* 3.2 43.0 - - - +
488D ASN* 6.4 0.7 - - - -
614D LEU* 6.4 1.1 - - - -
902D ASP* 5.0 2.2 + - - -
904D ALA* 6.3 1.2 - - - +
905D ARG* 3.6 38.9 - - - +
907D HIS* 5.6 3.8 + - + -
910D ASN* 3.0 9.1 + - + +
913D GLU* 3.0 27.7 + - - -
10E VAL* 4.4 16.2 - - + -
15E ASN* 1.3 72.8 - - - +
17E PHE* 1.3 88.5 + - + +
18E ASP 3.1 2.3 + - - -
19E LEU* 3.3 16.7 + - - +
20E VAL* 3.6 12.7 + - + +
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Residues in contact with PHE 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281C TYR 3.3 27.4 - - - -
1282C GLY* 3.7 13.5 - - - -
483D LEU* 4.6 6.1 - - + -
910D ASN* 3.1 24.3 + - + +
911D LYS 3.7 17.0 - - - +
912D GLY 3.8 15.9 - - - -
913D GLU* 3.1 41.7 - - + -
1360D GLY 3.9 19.3 - - - +
1361D THR* 4.3 13.9 - - - +
1366D HIS* 3.8 13.8 + - + -
16E ARG* 1.3 100.5 - - + +
18E ASP* 1.3 60.9 + - - +
20E VAL* 3.4 24.0 - - + +
21E LEU 4.2 0.2 + - - -
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Residues in contact with ASP 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910D ASN* 4.2 2.2 + - - +
1366D HIS* 3.2 26.3 + - + +
1369D ARG* 3.0 44.5 + - - +
1370D MET* 5.6 1.0 - - - +
13E ILE* 3.3 14.9 - - - +
15E ASN* 3.3 26.2 + - + +
16E ARG 3.1 0.4 - - - -
17E PHE* 1.3 75.4 - - - +
19E LEU* 1.3 64.0 + - - +
20E VAL 3.0 5.9 + - - -
21E LEU* 3.3 5.9 + - - +
22E VAL* 3.1 27.3 + - - +
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Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D LEU* 5.0 7.6 - - + -
482D ALA* 6.0 4.3 - - + -
6E VAL 6.0 0.4 - - - +
9E ALA* 4.0 39.9 - - + +
10E VAL* 5.0 9.6 - - + -
13E ILE* 5.3 4.9 - - + +
15E ASN* 4.6 7.6 + - - +
16E ARG* 3.3 13.4 + - - +
18E ASP* 1.3 79.0 - - - +
20E VAL* 1.3 68.1 + - + +
22E VAL* 3.3 22.6 + - + -
23E ALA* 3.3 15.0 + - + +
60E ASN* 5.0 15.9 - - - +
63E ILE* 4.2 18.2 - - + -
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Residues in contact with VAL 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D GLU* 3.8 18.2 - - - +
478D LEU* 3.6 14.6 - - + +
479D GLU* 4.0 17.7 - - + +
482D ALA* 4.6 18.2 - - + -
483D LEU* 5.8 5.6 - - + -
1361D THR* 3.7 26.2 - - + +
16E ARG* 3.6 14.4 - - + +
17E PHE* 3.4 23.3 - - + +
18E ASP 3.0 0.8 + - - -
19E LEU* 1.3 82.7 - - + +
21E LEU* 1.3 62.8 + - - +
23E ALA 3.0 9.9 + - - -
24E ALA* 3.1 13.6 + - + +
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285C TYR* 4.8 14.1 - - + +
475D GLU* 4.5 4.9 - - - +
1361D THR* 3.6 28.5 - - + +
1362D GLY* 4.9 5.8 - - - -
1366D HIS* 3.4 37.5 - - + +
1367D GLN* 5.2 5.2 - - + -
1369D ARG 5.5 3.6 - - - +
1370D MET* 6.1 2.7 - - - -
1371D ARG* 5.0 2.1 - - - +
17E PHE 4.2 0.2 + - - -
18E ASP* 3.3 3.3 + - - +
20E VAL* 1.3 75.8 - - - +
22E VAL* 1.3 65.2 + - - +
23E ALA 3.1 0.4 - - - -
24E ALA* 3.2 23.1 + - + -
25E ARG* 3.3 53.0 + - + +
26E ARG* 4.2 1.6 + - - +
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1369D ARG* 5.5 1.6 - - - +
1370D MET 5.0 4.7 - - - +
1371D ARG* 3.7 41.2 - - + +
18E ASP* 3.1 36.7 + - - +
19E LEU* 3.3 17.3 - - + +
20E VAL 3.1 0.4 - - - -
21E LEU* 1.3 78.4 - - - +
23E ALA* 1.3 58.0 + - + +
26E ARG* 3.9 12.8 - - - +
59E ILE* 4.7 2.4 - - - +
63E ILE* 3.7 34.8 - - + +
66E VAL* 5.0 7.4 - - + -
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D LEU* 4.5 0.7 - - - +
478D LEU* 3.5 17.6 - - + +
19E LEU* 3.3 11.4 + - + +
20E VAL 3.0 7.9 + - - +
22E VAL* 1.3 81.8 - - + +
24E ALA* 1.3 54.4 + - - +
27E ALA* 3.4 20.1 - - - +
59E ILE* 3.7 23.2 - - + +
60E ASN* 3.3 31.9 - - - +
63E ILE* 6.3 1.3 - - + -
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Residues in contact with ALA 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D LEU* 5.1 0.9 - - - +
475D GLU* 3.7 40.1 - - + +
478D LEU* 5.0 2.2 - - + -
20E VAL* 3.1 18.1 + - + +
21E LEU* 3.2 13.5 + - + -
22E VAL 3.5 0.4 + - - -
23E ALA* 1.3 78.0 - - - +
25E ARG* 1.3 61.0 + - - +
26E ARG 2.9 9.3 + - - +
27E ALA* 3.2 1.0 + - - +
28E ARG* 3.1 31.6 + - - +
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Residues in contact with ARG 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285C TYR* 5.4 3.1 - - + +
475D GLU* 5.1 0.4 - - - +
1367D GLN* 4.3 10.7 + - - +
1369D ARG 4.6 2.0 + - - -
1370D MET* 3.2 51.0 - - + +
1371D ARG 5.6 2.5 - - - +
1372D ARG* 6.0 6.4 - - + +
21E LEU* 3.3 49.5 - - + +
24E ALA* 1.3 77.2 - - - +
26E ARG* 1.3 58.5 + - + +
28E ARG* 3.6 27.2 + - - +
29E GLN* 3.2 26.2 + - - +
73E GLN* 3.4 29.9 + - - +
76E GLU* 2.8 41.3 + - - +
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Residues in contact with ARG 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371D ARG* 3.2 28.2 + - + +
1372D ARG* 4.3 13.1 + - + +
1374D ALA* 4.2 6.3 - - - +
1375D ALA* 3.5 36.2 - - - +
21E LEU 4.8 1.3 - - - +
22E VAL 3.9 16.2 - - - +
24E ALA 2.9 0.8 - - - +
25E ARG* 1.3 83.3 - - + +
27E ALA* 1.3 67.7 + - - +
28E ARG 3.4 0.4 - - - -
29E GLN* 3.2 16.8 + - - +
30E MET* 3.0 39.5 + - - +
37E PRO* 4.0 20.8 + - - +
38E LEU* 4.1 20.6 - - - +
59E ILE* 4.9 9.0 - - - -
62E GLN* 5.0 13.1 - - - +
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Residues in contact with ALA 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D LEU* 3.5 29.7 - - + +
23E ALA 3.4 23.6 - - - +
24E ALA 3.2 3.5 + - - +
26E ARG* 1.3 79.6 - - - +
28E ARG* 1.3 61.1 + - - +
30E MET* 3.0 24.0 + - - +
31E GLN* 3.7 5.0 + - - +
59E ILE* 3.6 25.9 - - + +
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Residues in contact with ARG 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285C TYR* 3.5 27.7 + - - -
1313C HIS* 3.4 39.7 + - + +
1315C MET* 6.2 1.2 - - - +
1316C GLU* 3.2 29.4 + - - +
473D THR* 5.1 1.3 - - - -
474D LEU* 4.3 13.1 - - + +
475D GLU* 4.5 18.5 - - - +
24E ALA 3.1 14.2 + - - +
25E ARG* 3.6 21.2 + - - +
27E ALA* 1.3 78.4 - - - +
29E GLN* 1.3 64.0 + - - +
30E MET 3.3 0.2 - - - -
31E GLN* 3.7 1.9 + - - +
32E VAL* 3.4 28.8 + - - +
76E GLU* 3.9 27.1 + - - -
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Residues in contact with GLN 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372D ARG* 3.0 45.9 - - - +
1374D ALA* 5.6 4.8 - - - +
25E ARG 3.2 23.5 - - - +
26E ARG* 3.4 16.1 - - - +
27E ALA 3.0 0.6 - - - -
28E ARG* 1.3 83.9 - - + +
30E MET* 1.3 63.3 + - - +
31E GLN 3.2 0.7 - - - -
32E VAL* 3.3 8.6 - - + +
33E GLY* 3.1 20.6 + - - -
37E PRO* 5.7 1.0 - - - +
76E GLU* 3.4 20.9 + - - +
80E LEU* 3.4 30.9 - - + +
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Residues in contact with MET 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ARG* 3.0 27.5 + - - +
27E ALA* 3.0 14.5 + - - +
29E GLN* 1.3 79.3 - - - +
31E GLN* 1.3 55.6 + - + +
33E GLY* 3.8 1.5 - - - -
34E GLY 2.8 37.7 + - - +
35E LYS* 3.9 30.2 + - + -
37E PRO* 5.3 6.1 - - + +
38E LEU* 3.7 42.2 - - + +
45E LYS* 6.5 0.9 - - - -
57E GLY* 6.6 0.2 - - - -
58E LEU 5.3 9.0 - - - +
59E ILE* 6.5 2.0 - - - -
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Residues in contact with GLN 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1311C GLY 5.4 4.5 - - - +
1312C ASN* 3.5 26.6 - - - +
1313C HIS* 3.2 38.9 + - + +
474D LEU* 3.3 28.2 - - + +
27E ALA 3.7 9.1 + - - +
28E ARG 4.1 1.3 - - - +
29E GLN 3.2 0.4 - - - -
30E MET* 1.3 77.7 - - + +
32E VAL* 1.3 59.3 + - - +
33E GLY 3.1 5.5 + - - -
34E GLY* 3.3 15.2 + - - +
56E GLU* 4.9 14.5 + - - -
86E ILE* 4.8 2.4 - - - +
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Residues in contact with VAL 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313C HIS* 3.6 38.4 - - + +
1315C MET* 4.7 13.9 - - + -
28E ARG* 3.4 19.0 + - - +
29E GLN* 3.3 22.2 - - + +
31E GLN* 1.3 75.2 - - - +
33E GLY* 1.3 57.3 + - - +
34E GLY 3.5 0.4 - - - -
80E LEU* 3.7 21.5 - - + +
81E GLN* 5.4 10.8 - - + +
84E THR 4.9 2.1 - - - +
86E ILE* 3.2 36.2 - - + +
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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