Contacts of the helix formed by residues 12 - 29 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C ILE* 2.7 21.5 + - + +
11C TYR* 1.3 84.1 - - + +
13C ALA* 1.3 62.6 + - - +
14C GLU* 3.0 10.4 + - - +
15C LEU* 2.9 35.6 + - - +
16C TRP* 3.1 11.1 + - - +
81D ARG* 2.4 37.2 + - - -
274D VAL* 4.4 5.1 - - + +
277D LYS* 3.7 18.6 - - + +
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Residues in contact with ALA 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE 4.2 0.4 + - - -
9C ALA 4.2 13.1 + - - +
10C ASP 5.3 0.6 - - - -
11C TYR 4.0 1.0 - - - -
12C ASP* 1.3 71.9 - - - +
14C GLU* 1.3 57.2 + - - +
16C TRP* 3.7 11.2 - - + +
17C GLN* 2.9 34.0 + - - +
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP* 3.0 9.2 + - - +
13C ALA* 1.3 75.9 - - - +
15C LEU* 1.3 66.4 + - - +
17C GLN* 3.4 6.4 + - - +
18C ALA* 3.4 21.1 + - - +
73D ILE* 5.0 3.5 - - + +
77D LEU* 3.7 30.8 - - + +
81D ARG* 3.9 8.0 + - - -
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.9 20.0 - - + -
12C ASP* 2.9 30.5 + - - +
14C GLU* 1.3 79.7 - - - +
16C TRP* 1.3 59.4 + - - +
18C ALA* 3.5 1.7 + - - +
19C MET* 3.0 42.7 + - + +
74D VAL* 4.1 28.0 - - + -
77D LEU* 3.7 21.7 - - + +
81D ARG* 4.3 0.4 - - - +
270D ALA* 3.6 23.6 - - + +
273D ALA* 4.5 3.8 - - + -
274D VAL* 3.8 19.5 - - + +
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Residues in contact with TRP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.8 20.8 - - + +
9C ALA* 3.6 38.6 - - + +
12C ASP 3.1 14.9 + - - +
13C ALA* 3.9 7.4 - - - +
14C GLU 3.2 0.2 - - - -
15C LEU* 1.3 77.0 - - - +
17C GLN* 1.3 61.9 + - - +
19C MET* 4.4 17.5 - - + -
20C GLU* 3.0 64.9 + - + +
23C LYS* 6.2 0.2 - - - -
45D GLN* 3.3 27.6 - - + -
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Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 2.9 20.1 + - - +
14C GLU* 3.8 6.5 - - - +
15C LEU 3.3 0.4 - - - -
16C TRP* 1.3 80.7 - - - +
18C ALA* 1.3 57.1 + - - +
20C GLU* 3.6 4.4 + - - +
21C GLN* 3.0 56.7 + - + +
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU 3.4 7.7 + - - +
15C LEU* 3.9 7.6 - - - +
16C TRP 3.4 0.2 - - - -
17C GLN* 1.3 77.0 - - - +
19C MET* 1.3 66.3 + - - +
21C GLN* 3.3 10.3 + - - -
22C GLU* 3.1 18.4 + - - +
70D TYR* 3.6 19.7 - - - +
73D ILE* 3.5 38.6 - - + -
74D VAL* 4.1 11.2 - - + +
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Residues in contact with MET 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.8 24.2 - - + -
15C LEU* 3.0 37.9 + - + +
16C TRP* 3.8 21.5 - - + +
18C ALA* 1.3 76.4 - - - +
20C GLU* 1.3 64.8 + - - +
22C GLU* 3.0 19.5 + - - +
23C LYS* 3.0 11.9 + - - +
45D GLN* 4.8 1.8 - - + +
46D ALA* 4.0 17.3 - - + +
49D SER* 3.4 37.2 - - - +
51D LEU* 4.2 22.6 - - + +
74D VAL* 4.9 2.0 - - + -
270D ALA* 4.7 3.1 - - + -
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 3.0 65.7 + - + +
17C GLN* 3.9 5.4 - - - +
19C MET* 1.3 76.9 - - - +
21C GLN* 1.3 62.3 + - + +
23C LYS* 3.0 50.6 + - - +
24C VAL* 3.1 14.6 + - + +
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Residues in contact with GLN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLN* 3.0 43.9 + - + +
18C ALA* 3.6 8.1 - - - +
19C MET 3.2 0.2 - - - -
20C GLU* 1.3 74.9 - - + +
22C GLU* 1.3 55.7 + - - +
24C VAL* 3.1 8.8 + - - +
25C ARG* 2.8 34.0 + - - +
70D TYR* 3.5 45.5 + - + -
73D ILE* 4.3 7.8 - - - +
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Residues in contact with GLU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ALA 3.1 12.0 + - - +
19C MET 3.0 10.7 + - - +
21C GLN* 1.3 76.0 - - - +
23C LYS* 1.3 57.1 + - - +
25C ARG* 2.4 41.0 + - - -
26C GLN* 2.7 57.2 + - - +
50D GLN* 5.3 0.9 - - + -
51D LEU* 3.3 29.8 - - + -
54D LYS* 3.8 5.0 - - - +
67D GLY 4.2 2.6 - - - +
70D TYR* 3.9 20.7 - - + +
71D VAL* 4.2 14.4 - - + +
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 6.2 0.6 - - - -
19C MET 3.0 10.7 + - - +
20C GLU* 3.0 45.0 + - - +
22C GLU* 1.3 81.1 - - - +
24C VAL* 1.3 59.4 - - + +
26C GLN* 3.7 4.2 + - - +
27C GLU* 3.7 21.6 + - + +
50D GLN* 3.8 38.3 + - + +
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLU* 3.1 13.9 + - + +
21C GLN* 3.1 8.7 + - - +
23C LYS* 1.3 77.1 - - + +
25C ARG* 1.3 59.5 + - - +
26C GLN 3.2 1.6 - - - -
27C GLU* 2.8 9.3 + - + +
28C GLU* 2.8 57.9 + - + +
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Residues in contact with ARG 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLN 2.8 20.1 + - - +
22C GLU* 2.4 53.6 + - - +
24C VAL* 1.3 73.2 - - - +
26C GLN* 1.3 72.5 + - - +
28C GLU* 4.4 3.1 - - - +
29C HIS* 2.9 71.0 + - + +
31C GLU* 2.6 39.4 + - - +
36C GLU* 4.7 0.4 + - - -
54D LYS* 3.6 13.8 - - - +
67D GLY* 3.1 28.3 + - - -
69D GLU* 3.7 13.2 - - - +
70D TYR* 3.7 21.1 - - + -
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Residues in contact with GLN 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLU* 2.7 47.7 + - - +
23C LYS 3.8 6.3 - - - +
24C VAL 3.2 0.2 - - - -
25C ARG* 1.3 90.1 - - - +
27C GLU* 1.3 60.8 + - + +
29C HIS* 3.9 3.5 - - - +
31C GLU* 5.6 1.3 - - - -
38C TYR* 3.7 22.7 + - + -
372C ARG* 3.8 3.6 + - - -
415C VAL* 3.4 20.1 - - + +
416C TYR* 4.2 2.5 - - + -
50D GLN* 2.9 49.1 + - - +
51D LEU* 4.6 1.2 - - - +
53D ASN* 3.1 28.6 + - - +
54D LYS* 4.7 3.2 - - - +
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Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LYS* 3.7 13.5 - - + +
24C VAL* 2.8 12.4 + - + +
26C GLN* 1.3 80.4 - - + +
28C GLU* 1.3 64.4 + - + +
29C HIS 3.3 0.4 - - - -
372C ARG* 2.4 27.8 + - - +
410C CYS* 3.4 8.5 - - - +
414C PRO* 3.4 15.6 - - - +
415C VAL* 3.0 26.2 + - - +
416C TYR* 2.9 37.2 + - - +
50D GLN* 5.7 1.0 + - - +
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 2.8 43.7 + - + +
25C ARG* 4.4 3.3 - - - +
27C GLU* 1.3 76.2 - - + +
29C HIS* 1.3 61.9 + - + +
341C ASN* 2.8 29.9 + - - +
406C VAL* 4.2 0.2 - - - +
407C LEU* 3.5 32.1 - - + +
410C CYS* 3.8 12.2 - - - -
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Residues in contact with HIS 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG* 2.9 46.6 + - + +
26C GLN 3.9 4.9 - - - +
27C GLU 3.3 0.4 - - - -
28C GLU* 1.3 83.2 - - + +
30C ILE* 1.3 63.1 + - - +
31C GLU* 3.4 17.1 + - + +
38C TYR* 4.2 1.7 + - - -
338C GLY* 4.8 6.5 - - - -
341C ASN* 3.2 46.8 + - - +
343C THR* 3.2 21.2 + - - +
372C ARG* 2.8 24.7 + - - -
410C CYS* 4.1 0.7 - - - -
67D GLY* 5.0 2.4 - - - -
69D GLU* 4.3 10.3 - - - -
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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