Contacts of the helix formed by residues 14 - 30 (chain D) in PDB entry 3REO
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 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A LYS* 3.5 32.3 - - + -
352A VAL* 3.2 30.6 + - - +
353A ALA* 4.8 3.8 - - - +
12D ILE 3.3 10.0 + - - +
13D PRO* 1.3 78.6 - - - +
15D HIS* 1.3 66.9 + - - +
16D SER* 3.3 2.6 + - - -
17D SER* 2.7 25.8 + - - -
18D ASP* 2.9 27.3 + - - +
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Residues in contact with HIS 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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193B LYS* 3.9 31.5 + - + +
196B GLU* 5.6 6.3 - - - -
14D THR* 1.3 75.2 - - - +
16D SER* 1.3 62.3 + - - +
18D ASP* 3.6 8.4 + - - +
19D GLU* 3.0 24.8 + - - +
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Residues in contact with SER 16 (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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335A GLU* 5.0 4.2 + - - -
352A VAL* 3.8 35.5 + - - +
353A ALA 6.1 0.7 - - - -
354A SER* 6.5 0.2 - - - -
360A TYR* 5.6 3.9 - - - -
14D THR* 3.1 9.5 + - - -
15D HIS* 1.3 80.1 - - - +
17D SER* 1.3 61.8 + - - +
19D GLU* 3.4 7.1 + - - +
20D GLU* 3.2 20.4 + - - +
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Residues in contact with SER 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 5.4 5.3 - - - +
11D ILE* 4.8 13.5 - - - -
12D ILE 4.6 3.4 - - - -
13D PRO* 3.4 10.8 - - - +
14D THR* 2.7 36.7 + - - -
16D SER* 1.3 79.6 - - - +
18D ASP* 1.3 61.2 + - - +
20D GLU* 3.2 8.9 + - - +
21D ALA* 3.0 27.3 + - - +
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Residues in contact with ASP 18 (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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116B LYS* 3.8 29.6 + - - +
117B PHE* 3.3 26.7 - - + -
193B LYS* 5.6 1.1 - - - +
357B PHE* 4.2 7.7 - - + -
13D PRO* 4.8 7.8 - - - +
14D THR 2.9 22.1 + - - +
15D HIS* 3.6 10.6 + - - +
17D SER* 1.3 79.6 + - - +
19D GLU* 1.3 60.9 + - - +
21D ALA* 4.3 2.2 - - - +
22D ASN* 2.9 27.5 + - - +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 2.9 27.0 + - - +
355B CYS* 4.7 8.2 - - - +
356B ALA* 3.9 1.7 - - - -
357B PHE* 2.9 44.6 + - + -
358B ASN* 3.5 10.7 + - - +
15D HIS 3.0 17.6 + - - +
16D SER* 3.7 7.6 - - - +
18D ASP* 1.3 75.8 - - - +
20D GLU* 1.3 64.0 + - - +
22D ASN* 3.2 1.6 + - - +
23D LEU* 3.0 43.4 + - + +
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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
----------------------------------------------------------
311B ILE* 2.5 47.9 - - - +
16D SER 3.2 12.8 + - - +
17D SER* 3.2 9.8 + - - +
19D GLU* 1.3 77.6 - - - +
21D ALA* 1.3 58.3 + - - +
23D LEU* 3.4 4.4 + - - +
24D PHE* 2.9 21.9 + - - +
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Residues in contact with ALA 21 (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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113B PRO* 3.7 33.2 - - + +
114B VAL* 3.5 16.6 - - - +
116B LYS* 5.9 0.4 - - + -
117B PHE* 3.7 16.3 - - + -
17D SER 3.0 15.3 + - - +
18D ASP* 3.6 6.5 - - - +
20D GLU* 1.3 77.8 - - - +
22D ASN* 1.3 64.9 + - - +
24D PHE* 3.4 5.1 + - - -
25D ALA* 3.0 18.7 + - - +
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Residues in contact with ASN 22 (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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117B PHE* 3.7 22.8 - - + -
127B LEU* 3.7 12.2 - - - +
186B ASN* 5.4 1.4 + - - +
189B ILE* 3.5 29.9 - - - +
190B THR* 5.2 1.2 + - - -
357B PHE* 3.5 39.8 - - + +
18D ASP 2.9 18.7 + - - +
19D GLU 3.8 0.4 - - - +
21D ALA* 1.3 77.8 - - - +
23D LEU* 1.3 64.6 + - - +
25D ALA* 3.2 5.7 + - - +
26D MET* 3.0 32.4 + - - +
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Residues in contact with LEU 23 (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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301B TYR* 5.5 0.7 - - - +
311B ILE* 3.6 14.8 - - + -
312B ALA* 4.0 26.7 - - + +
315B VAL* 3.2 23.0 - - + +
357B PHE* 3.7 24.9 - - - +
358B ASN* 3.9 21.3 - - + +
19D GLU* 3.0 38.7 + - + +
20D GLU* 4.0 4.5 - - - +
22D ASN* 1.3 80.4 - - - +
24D PHE* 1.3 60.3 + - - +
26D MET* 3.2 4.7 + - + -
27D GLN* 2.8 26.0 + - - +
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Residues in contact with PHE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 5.9 0.7 - - + -
90B TYR* 3.2 31.2 - + + -
91B SER* 3.9 16.8 - - - -
92B VAL* 4.1 2.7 - - + -
114B VAL* 3.6 26.7 - - + -
311B ILE* 3.6 17.8 - - + +
20D GLU* 2.9 26.4 + - + +
21D ALA* 3.7 5.4 - - - +
22D ASN 3.3 0.2 - - - -
23D LEU* 1.3 77.0 - - - +
25D ALA* 1.3 56.2 + - - +
27D GLN* 3.1 22.3 + - - -
28D LEU* 2.9 60.0 + - + +
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 3.5 21.0 - - + +
117B PHE* 4.3 5.2 - - + -
118B LEU* 4.0 22.3 - - + +
127B LEU* 3.9 18.6 - - + -
131B LEU* 4.8 2.4 - - - +
21D ALA 3.0 9.6 + - - +
22D ASN 3.5 7.9 - - - +
24D PHE* 1.3 73.4 - - - +
26D MET* 1.3 64.8 + - - +
28D LEU* 3.3 8.6 + - - +
29D ALA* 3.0 23.8 + - - +
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Residues in contact with MET 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.8 14.6 - - + -
130B PHE* 3.3 43.8 - - + -
186B ASN* 3.5 25.1 - - - +
269B TRP* 4.1 6.1 - - + -
301B TYR* 3.7 20.4 - - - +
315B VAL* 3.9 18.6 - - + -
22D ASN* 3.0 30.6 + - - +
23D LEU* 3.6 12.1 - - + +
25D ALA* 1.3 77.7 - - - +
27D GLN* 1.3 62.4 + - - +
29D ALA* 3.2 12.4 + - - +
30D SER* 3.2 17.2 + - - -
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Residues in contact with GLN 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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311B ILE* 3.8 20.3 - - + +
314B LYS* 3.4 26.6 - - + +
315B VAL* 3.7 12.7 - - + +
318B HIS* 3.4 26.6 - - + -
23D LEU 2.8 13.5 + - - +
24D PHE* 3.1 31.3 + - - +
26D MET* 1.3 76.1 - - - +
28D LEU* 1.3 62.0 + - - +
30D SER 3.5 0.3 + - - -
31D ALA* 3.1 21.4 + - + +
90D TYR* 3.1 22.3 + - - +
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Residues in contact with LEU 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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34B LEU* 3.5 31.9 - - + -
35B PRO* 3.7 14.2 - - - +
38B LEU* 3.9 25.1 - - + -
92B VAL* 3.8 28.0 - - + -
114B VAL* 4.1 21.8 - - + -
118B LEU* 4.7 2.5 - - + -
131B LEU* 4.5 3.0 - - + +
24D PHE* 2.9 41.2 + - + +
25D ALA* 3.6 6.5 - - - +
26D MET 3.3 0.2 - - - -
27D GLN* 1.3 73.8 - - + +
29D ALA* 1.3 67.2 + - - +
31D ALA* 3.1 19.8 + - + +
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Residues in contact with ALA 29 (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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35B PRO* 4.7 0.9 - - - +
130B PHE* 3.9 31.0 - - + -
131B LEU* 3.8 29.8 - - + -
134B ALA* 3.2 18.0 - - + +
135B THR* 3.6 15.6 - - - +
25D ALA 3.0 13.1 + - - +
26D MET* 3.4 11.4 - - - +
28D LEU* 1.3 76.6 - - - +
30D SER* 1.3 57.9 + - - +
31D ALA 3.8 0.3 + - - -
32D ALA* 5.2 0.5 + - - +
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Residues in contact with SER 30 (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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130B PHE* 5.8 2.9 - - - -
134B ALA* 4.6 6.5 - - - -
315B VAL* 5.8 0.5 - - - -
318B HIS* 2.9 36.2 + - - +
319B THR* 5.5 2.1 - - - +
322B LEU* 4.1 27.8 - - - -
26D MET 3.2 12.1 + - - -
27D GLN* 3.7 1.1 - - - -
28D LEU 3.1 0.2 - - - -
29D ALA* 1.3 80.2 - - - +
31D ALA* 1.3 62.4 + - - +
32D ALA* 3.2 3.6 - - - -
33D VAL* 3.1 25.2 + - - +
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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