Contacts of the helix formed by residues 12 - 29 (chain D) in PDB entry 1EQB
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 12 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C ARG* 2.5 36.0 + - - -
274C VAL* 4.2 7.6 - - + +
277C LYS* 3.8 13.0 - - + +
8D ILE* 2.6 27.6 + - + +
11D TYR* 1.3 87.5 - - + +
13D ALA* 1.3 60.8 + - - +
14D GLU* 3.5 10.6 + - - +
15D LEU* 3.2 28.7 + - - +
16D TRP* 3.1 15.2 + - - +
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Residues in contact with ALA 13 (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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9D ALA 4.1 13.0 + - - +
10D ASP 5.4 0.2 - - - -
11D TYR 4.0 0.8 - - - -
12D ASP* 1.3 70.6 - - - +
14D GLU* 1.3 59.7 + - - +
16D TRP* 3.6 10.2 - - + +
17D GLN* 2.8 37.4 + - - +
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Residues in contact with GLU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 5.0 4.3 - - - +
77C LEU* 4.0 30.3 - - + +
81C ARG* 4.5 5.8 + - - +
12D ASP* 3.2 10.9 - - - +
13D ALA* 1.3 81.9 - - + +
15D LEU* 1.3 60.6 + - - +
17D GLN* 3.9 7.6 + - - +
18D ALA* 3.5 18.4 + - - +
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Residues in contact with LEU 15 (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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74C VAL* 4.0 32.3 - - + -
77C LEU* 3.7 21.7 - - + +
270C ALA* 3.6 24.7 - - + +
273C ALA* 4.3 9.6 - - + -
274C VAL* 3.9 16.2 - - + +
8D ILE* 4.1 14.8 - - + -
12D ASP* 3.2 29.1 + - - +
14D GLU* 1.3 77.2 - - - +
16D TRP* 1.3 67.6 + - - +
18D ALA* 3.4 2.3 + - - +
19D MET* 3.0 41.6 + - + +
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Residues in contact with TRP 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLN* 3.2 29.8 - - + -
8D ILE* 4.0 19.4 - - + +
9D ALA* 3.6 36.3 - - + +
12D ASP 3.1 17.0 + - - +
13D ALA* 3.2 7.6 + - + +
15D LEU* 1.3 76.5 - - - +
17D GLN* 1.3 58.6 + - - +
19D MET* 3.1 22.6 + - + +
20D GLU* 2.8 67.3 + - + +
23D LYS* 6.2 0.2 - - - -
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Residues in contact with GLN 17 (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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13D ALA* 2.8 20.1 + - - +
14D GLU* 3.9 7.4 + - - +
15D LEU 3.3 0.2 - - - -
16D TRP* 1.3 79.7 - - - +
18D ALA* 1.3 63.4 - - - +
20D GLU* 3.3 5.8 + - - +
21D GLN* 3.0 44.8 + - + +
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Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C TYR* 3.6 24.9 - - - +
73C ILE* 3.6 33.7 - - + -
74C VAL* 4.1 9.6 - - + -
77C LEU* 5.5 0.2 - - + -
14D GLU 3.5 6.9 + - - +
15D LEU* 3.4 8.9 + - - +
16D TRP 3.3 0.4 - - - -
17D GLN* 1.3 78.5 - - - +
19D MET* 1.3 62.6 + - - +
21D GLN* 3.3 11.6 + - - +
22D GLU* 3.1 18.7 + - - +
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Residues in contact with MET 19 (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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45C GLN* 4.8 1.3 - - + +
46C ALA* 4.0 16.4 - - + -
49C SER* 3.4 37.5 - - - +
51C LEU* 4.2 24.1 - - + +
74C VAL* 4.9 1.8 - - + -
270C ALA* 4.7 2.9 - - + -
8D ILE* 4.1 17.9 - - + -
15D LEU* 3.0 39.8 + - + +
16D TRP* 3.4 25.4 - - + +
18D ALA* 1.3 76.5 - - - +
20D GLU* 1.3 66.6 + - - +
22D GLU* 3.0 19.3 + - - +
23D LYS* 3.0 11.5 + - - +
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Residues in contact with GLU 20 (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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16D TRP* 2.8 66.6 + - + +
17D GLN* 3.7 5.6 - - - +
19D MET* 1.3 73.4 - - - +
21D GLN* 1.3 62.6 + - + +
23D LYS* 3.0 50.8 + - - +
24D VAL* 3.1 14.5 + - + +
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Residues in contact with GLN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C TYR* 3.4 44.9 + - + -
73C ILE* 4.4 7.3 - - - +
17D GLN* 3.0 38.5 + - + +
18D ALA* 3.6 8.8 + - - +
19D MET 3.1 0.4 - - - -
20D GLU* 1.3 73.9 - - + +
22D GLU* 1.3 55.7 + - - +
24D VAL* 3.1 8.6 + - - +
25D ARG* 2.8 34.5 + - - +
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Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLN* 5.3 0.9 - - + -
51C LEU* 3.3 31.2 - - + +
54C LYS* 3.8 10.6 - - - +
67C GLY 4.2 2.6 - - - +
70C TYR* 3.9 20.2 - - + +
71C VAL* 4.2 9.6 + - + +
18D ALA 3.1 10.9 + - - +
19D MET 3.0 10.2 + - - +
21D GLN* 1.3 77.2 - - - +
23D LYS* 1.3 63.1 + - - +
25D ARG* 2.4 41.0 + - - -
26D GLN* 2.7 52.9 + - - +
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 3.6 35.1 - - - +
50C GLN* 3.7 30.7 + - + +
16D TRP* 6.2 0.2 - - - -
19D MET 3.0 11.1 + - - +
20D GLU* 3.0 43.7 + - - +
22D GLU* 1.3 78.4 - - - +
24D VAL* 1.3 59.8 + - + +
26D GLN* 3.7 4.5 + - - +
27D GLU* 3.7 21.0 + - - +
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU* 3.1 12.9 + - + +
21D GLN* 3.1 9.5 + - - +
23D LYS* 1.3 76.4 - - + +
25D ARG* 1.3 53.9 + - - +
26D GLN 3.2 1.8 - - - -
27D GLU* 2.8 10.1 + - + +
28D GLU* 2.8 63.1 + - + +
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Residues in contact with ARG 25 (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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54C LYS* 3.6 14.8 - - - +
67C GLY* 3.2 27.6 + - - -
69C GLU* 3.8 12.8 - - - +
70C TYR* 3.8 20.4 - - + -
21D GLN 2.8 15.9 + - - +
22D GLU* 2.4 52.0 + - - +
24D VAL* 1.3 76.6 - - - +
26D GLN* 1.3 71.1 + - - +
28D GLU* 4.4 3.6 - - - +
29D HIS* 2.9 71.3 + - + +
31D GLU* 2.7 38.3 + - - +
36D GLU* 4.8 0.8 + - - -
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Residues in contact with GLN 26 (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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50C GLN* 2.8 52.5 + - - +
51C LEU* 4.7 1.0 - - - +
53C ASN* 3.1 28.2 + - - +
54C LYS* 4.7 3.0 - - - +
22D GLU* 2.7 48.0 + - - +
23D LYS 3.9 6.3 - - - +
24D VAL 3.2 0.2 - - - -
25D ARG* 1.3 90.8 - - - +
27D GLU* 1.3 60.3 + - + +
29D HIS* 4.0 2.8 - - - +
31D GLU* 5.6 1.1 - - - -
38D TYR* 3.8 22.6 + - + -
372D ARG* 3.9 3.8 + - - -
415D VAL* 3.3 21.3 - - + +
416D TYR* 4.2 2.4 - - - -
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Residues in contact with GLU 27 (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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4C ARG* 5.5 0.6 + - - +
50C GLN* 6.1 0.7 - - - +
23D LYS 3.7 13.0 - - - +
24D VAL* 2.8 12.3 + - + +
26D GLN* 1.3 81.3 - - + +
28D GLU* 1.3 63.8 + - + +
29D HIS 3.3 0.8 + - - -
372D ARG* 2.4 28.1 + - - +
410D CYS* 3.4 11.4 - - - +
414D PRO* 3.3 16.6 - - - +
415D VAL* 2.9 25.6 + - - +
416D TYR* 2.9 39.7 + - - +
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Residues in contact with GLU 28 (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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24D VAL* 2.8 43.5 + - + +
25D ARG* 4.4 1.9 - - - +
27D GLU* 1.3 76.3 - - + +
29D HIS* 1.3 64.1 + - + +
341D ASN* 2.8 29.8 + - - +
406D VAL* 4.1 0.5 - - - +
407D LEU* 3.8 26.0 - - + +
410D CYS* 3.8 15.5 - - - -
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Residues in contact with HIS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLY* 5.2 2.2 - - - -
69C GLU* 4.4 9.4 - - - -
25D ARG* 2.9 47.4 + - + +
26D GLN* 4.0 5.4 - - - +
27D GLU 3.3 0.4 - - - -
28D GLU* 1.3 83.7 - - + +
30D ILE* 1.3 61.7 + - - +
31D GLU* 3.4 17.6 + - + +
38D TYR* 4.2 1.4 + - - -
338D GLY* 4.8 6.5 - - - -
341D ASN* 3.2 45.6 + - - +
343D THR* 3.2 21.6 + - - +
372D ARG* 2.8 23.5 + - - -
410D CYS* 4.0 2.2 - - - -
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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
------------------------------------------------------------
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