Contacts of the helix formed by residues 32 - 52 (chain D) in PDB entry 2I62
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 HIS 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D GLU* 3.7 20.8 + - + -
24D LYS* 3.5 42.6 + - + +
25D TYR 6.2 0.2 - - - -
27D SER* 4.4 7.0 + - - +
31D ARG* 1.3 108.7 + - + +
33D CYS* 1.3 66.0 + - - +
34D ALA 3.3 3.4 - - - -
35D GLU* 3.1 23.3 + - + +
36D ASN* 3.0 24.2 + - - +
244D SER* 5.0 2.0 - - - -
247D THR* 5.7 2.9 - - - -
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Residues in contact with CYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLY 5.5 0.2 - - - -
30D SER* 3.3 26.0 - - - -
31D ARG* 4.4 1.6 - - - -
32D HIS* 1.3 76.6 - - - +
34D ALA* 1.3 56.8 + - - +
36D ASN* 3.2 12.9 + - - +
37D GLU* 3.0 29.1 + - - +
40D ARG* 4.8 1.4 + - - -
244D SER* 5.3 0.2 + - - -
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D HIS 3.3 0.8 - - - -
33D CYS* 1.3 77.2 - - - +
35D GLU* 1.3 64.0 + - - +
37D GLU* 3.4 7.0 + - - +
38D ILE* 3.1 28.0 + - - +
241D GLN* 5.5 0.3 - - - +
242D ASN 3.5 14.6 - - - +
243D TYR 3.8 0.7 - - - -
244D SER* 3.4 37.8 + - - +
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Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LYS 3.7 24.0 - - - +
25D TYR* 4.1 25.9 - - + +
32D HIS* 3.1 25.7 + - + +
34D ALA* 1.3 76.9 - - - +
36D ASN* 1.3 57.8 + - - +
38D ILE* 3.5 3.7 + - - +
39D LEU* 3.0 28.3 + - - +
243D TYR* 3.4 27.7 - - + -
244D SER* 2.7 48.0 + - - -
247D THR* 3.4 15.7 + - + +
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Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D TYR 5.1 3.5 - - - +
28D PHE* 3.4 38.6 + - + -
29D GLY 2.9 28.6 + - - -
31D ARG 3.3 14.0 + - - +
32D HIS* 3.0 18.5 + - - +
33D CYS* 3.2 15.4 + - - +
35D GLU* 1.3 74.4 - - - +
37D GLU* 1.3 60.3 + - - +
39D LEU* 3.2 5.7 + - - +
40D ARG* 3.0 52.8 + - - +
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Residues in contact with GLU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D CYS 3.0 16.2 + - - +
34D ALA* 3.8 7.0 - - - +
36D ASN* 1.3 73.6 - - - +
38D ILE* 1.3 65.1 + - - +
40D ARG* 3.0 33.9 + - - +
41D HIS* 2.8 57.3 + - - -
241D GLN* 3.3 29.6 - - + +
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ALA 3.1 12.5 + - - +
35D GLU 3.8 4.0 - - - +
37D GLU* 1.3 75.7 - - - +
39D LEU* 1.3 59.6 + - - +
41D HIS* 3.1 7.1 + - - +
42D LEU* 2.9 46.6 + - + +
239D ILE* 5.1 2.0 - - + +
241D GLN* 3.7 21.5 - - + +
242D ASN 3.5 6.5 - - - +
243D TYR* 3.3 66.9 - - + +
253D LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D TYR 4.3 4.3 - - - +
26D TYR* 3.8 42.2 - - + -
28D PHE* 3.8 19.7 - - + -
35D GLU 3.0 15.2 + - - +
36D ASN* 3.2 8.9 + - - +
38D ILE* 1.3 76.1 - - - +
40D ARG* 1.3 63.1 + - - +
42D LEU* 3.3 7.1 + - + +
43D LEU* 2.9 43.3 + - + +
70D TYR* 3.8 28.3 - - + -
111D VAL* 3.7 26.0 - - + -
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Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D PHE* 3.5 33.0 + - + -
29D GLY 5.7 0.8 + - - -
33D CYS 4.8 1.0 + - - -
36D ASN* 3.0 25.3 + - - +
37D GLU* 3.0 56.7 + - - +
39D LEU* 1.3 75.4 - - - +
41D HIS* 1.3 59.8 + - + +
43D LEU* 3.4 4.2 + - - +
44D LYS* 3.0 34.8 + - - +
114D TYR* 3.5 35.8 - - + +
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Residues in contact with HIS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C GLU* 6.1 1.1 - - - -
37D GLU* 2.8 47.0 + - - +
38D ILE 3.1 7.9 + - - +
40D ARG* 1.3 77.2 - - + +
42D LEU* 1.3 60.4 + - - +
44D LYS* 3.2 16.4 + - + +
45D ASN* 2.9 36.6 + - - +
239D ILE* 3.8 26.8 - - + +
240D SER* 5.7 1.7 + - - -
241D GLN* 3.7 30.1 + - + +
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 4.9 3.6 - - + +
38D ILE* 2.9 33.9 + - + +
39D LEU* 3.6 13.7 - - + +
41D HIS* 1.3 75.9 - - - +
43D LEU* 1.3 57.0 + - - +
45D ASN* 3.4 2.7 + - - +
46D LEU* 2.9 38.1 + - + +
70D TYR* 3.9 37.0 - - + +
165D LEU* 4.7 11.0 - - + -
197D VAL* 3.5 34.3 - - + -
239D ILE* 3.5 22.4 - - + -
243D TYR* 5.1 0.4 - - - +
253D LEU* 4.7 8.1 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D PHE* 5.3 2.2 - - + -
39D LEU* 2.9 35.1 + - + +
40D ARG* 3.7 5.2 - - - +
42D LEU* 1.3 73.5 - - - +
44D LYS* 1.3 58.6 - - - +
46D LEU* 3.3 6.2 + - + +
47D PHE* 2.8 31.7 + - - +
70D TYR* 3.6 37.9 - - + +
74D SER* 4.7 1.6 + - - -
111D VAL* 3.7 24.5 - - + +
114D TYR* 3.9 20.6 - - + -
115D VAL* 3.6 22.7 - - + +
118D LEU* 3.6 16.2 - - + +
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Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 3.0 21.6 + - - +
41D HIS* 3.2 18.8 + - + +
43D LEU* 1.3 74.3 - - - +
45D ASN* 1.3 62.6 + - - +
47D PHE* 3.3 6.3 + - + +
48D LYS* 2.9 35.8 + - + +
114D TYR* 3.1 24.1 + - - +
118D LEU* 3.8 29.2 - - + +
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Residues in contact with ASN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D HIS* 2.9 23.7 + - - +
42D LEU* 3.8 6.1 - - + +
44D LYS* 1.3 79.9 - - - +
46D LEU* 1.3 58.9 + - + +
48D LYS* 3.3 8.6 + - - +
49D ILE* 3.0 34.5 + - - +
197D VAL* 6.1 0.4 - - + -
237D GLU* 3.6 21.3 - - - +
238D VAL 5.3 0.6 + - - -
239D ILE* 3.6 24.2 - - + +
255D SER* 2.9 31.9 + - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 2.9 24.9 + - + +
43D LEU* 3.9 6.7 - - + +
45D ASN* 1.3 74.3 - - + +
47D PHE* 1.3 66.7 + - - +
49D ILE* 4.4 6.1 - - + -
50D PHE* 2.9 55.9 + - + +
70D TYR* 4.0 21.8 - - + +
71D GLN* 3.8 32.5 - - + +
74D SER* 3.8 7.6 - - - -
162D LEU* 4.6 11.2 - - + -
164D THR* 4.9 3.1 - - + -
195D VAL* 4.6 6.1 - - + -
197D VAL* 4.3 24.0 - - + -
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Residues in contact with PHE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU 2.8 19.4 + - - +
44D LYS* 3.4 8.1 - - + +
46D LEU* 1.3 76.2 - - - +
48D LYS* 1.3 71.1 - - + +
51D CYS* 2.8 57.5 + - + +
52D LEU* 3.6 29.8 + - + -
74D SER* 3.4 14.5 + - - +
118D LEU* 3.4 42.6 - - + -
119D GLU* 3.5 34.5 - - + -
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Residues in contact with LYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LYS* 4.8 20.1 - - - +
44D LYS* 2.9 21.3 + - + +
45D ASN* 3.7 9.6 - - - +
46D LEU 3.3 0.2 - - - -
47D PHE* 1.3 88.0 - - + +
49D ILE* 1.3 65.0 + - + +
52D LEU* 3.4 57.5 + - + +
235D GLN* 4.7 6.8 + - - +
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASN 3.0 22.8 + - - +
46D LEU* 3.8 11.0 - - + +
47D PHE 3.3 0.2 - - - -
48D LYS* 1.3 80.4 - - + +
50D PHE* 1.3 71.2 + - + +
51D CYS 3.8 0.2 + - - -
52D LEU 4.5 1.9 + - - -
53D GLY* 4.8 4.3 + - - -
55D VAL* 3.6 23.8 + - + +
195D VAL* 4.0 34.8 - - + -
235D GLN* 3.7 19.5 + - + +
255D SER* 4.0 28.7 - - - +
256D LEU* 4.5 3.4 - - - +
257D VAL* 3.5 31.6 - - + -
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 2.9 47.4 + - + +
49D ILE* 1.3 83.1 - - + +
51D CYS* 1.3 59.8 + - - +
52D LEU 3.8 0.2 - - - -
53D GLY 5.5 1.6 - - - +
55D VAL* 3.7 33.6 - - + +
56D LYS* 5.0 1.6 - - - +
60D LEU* 3.8 31.6 - - + -
71D GLN 4.5 4.3 - - - -
74D SER* 3.8 19.1 - - - +
75D ALA* 3.6 24.5 - - + -
78D SER* 2.5 31.3 + - - +
79D PHE* 3.8 12.3 - + - -
160D CYS* 4.1 2.2 - - - -
162D LEU* 4.1 13.7 - - + -
195D VAL* 4.0 17.3 - - + -
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Residues in contact with CYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D PHE* 2.8 47.6 + - + +
50D PHE* 1.3 82.0 - - - +
52D LEU* 1.3 66.2 + - + +
53D GLY 3.8 3.1 + - - -
56D LYS* 5.6 6.2 - - - +
74D SER* 4.0 14.8 - - - -
77D GLU* 4.3 10.8 - - - -
78D SER* 4.6 0.9 - - - -
119D GLU* 3.7 22.9 - - - -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PHE* 3.6 29.8 - - + +
48D LYS* 3.4 59.9 + - + +
49D ILE 4.5 0.2 + - - -
50D PHE 3.8 0.4 - - - -
51D CYS* 1.3 93.8 - - + +
53D GLY* 1.3 55.1 + - - +
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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
------------------------------------------------------------
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